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    Seed Germination and Pre-Harvest Sprouting
    DONG HuiXue, WANG JiRui
    Scientia Agricultura Sinica    2024, 57 (7): 1215-1219.   DOI: 10.3864/j.issn.0578-1752.2024.07.001
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    Physiological and Molecular Effects of Salicylic Acid on Rice Seed Germination at Low Temperature
    CHEN BingXian, ZHANG Qi, DAI ZhangYan, ZHOU Xu, LIU Jun
    Scientia Agricultura Sinica    2024, 57 (7): 1220-1236.   DOI: 10.3864/j.issn.0578-1752.2024.07.002
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    【Objective】The study investigated the impact of salicylic acid (SA) priming on the germination vigor and physiological response of rice seeds under low temperatures. It aimed to reveal the expression patterns of genes related to abscisic acid (ABA) and gibberellin (GA) metabolic pathways as well as cell wall relaxation genes by SA priming. This research provided a theoretical basis for the study of rice seed germination at low temperatures.【Method】Using indica three-line hybrid rice Taifengyou 208 seeds as materials, the effects of SA on seed germination vigor and physiology responses under low temperature were analyzed through seed priming treatment, and the expression patterns of genes related to ABA, GA and expansin in response to SA were analyzed by qRT-PCR.【Result】Low temperature (15 ℃) significantly delayed the germination process of rice seeds. In seeds germinated at low temperatures for one day, the endogenous SA concentration was 1.7 times higher than that at normal temperatures (28 ℃). However, for five-day-old seedlings, the SA concentration under low temperature was only 0.6% of that at normal temperatures. SA could effectively enhanced germination vigor of seeds at low temperature, with the most significant effects observed at 2 000 μmol·L-1 SA. This concentration significantly increased the germination index, vigor index, shoot length, root length, fresh weight, and dry weight of seeds under low temperature conditions. Notably, the vigor index was three times that of non-primed seeds (CK1) and two times that of water-primed seeds (CK2). In terms of physiological indexes, SA priming increased the contents of soluble sugar, proline and active oxygen, enhanced the activities of total amylase, β-amylase, superoxide dismutase (SOD) and catalase (CAT), and decreased the content of malondialdehyde (MDA). Compared with CK1, 2 000 μmol·L-1 SA decreased the ABA content by 79%, and increased the IAA and GA1 contents by 32.2% and 2.66 times, respectively. In terms of gene expression, the expression levels of ABA synthesizing genes OsNCED2 and OsNCED3 were decreased by 94.26% and 90.24% compared with CK1 in seeds primed by 2 000 μmol·L-1 SA, respectively, whereas the expression levels of ABA decomposing genes OsABA8’ox2 and OsABA8’ox3 were 5.9 and 3.9 times higher than that of CK1, respectively. Compared with CK1, SA priming significantly upregulated the expression of GA synthesizing genes OsCPS1, OsKAO and OsGA20ox1, while it significantly downregulated the expression of GA decomposing genes OsGA2ox2 and OsGA2ox6. In several candidate genes encoding cell wall relaxation protein, e.t. expansin, all but OsEXPB11 were significantly upregulated to some extent by priming. Compared with CK1, 2 000 μmol·L-1 SA increased the expression levels of OsEXPA2, OsEXPB4 and OsEXPB6 to 12.2, 5.9 and 6.1 times, respectively.【Conclusion】SA priming can significantly alleviate the impact of low temperatures on rice seed germination and seedling growth, which is likely due to SA enhancing the activity of antioxidant enzymes such as SOD and CAT, reducing the production of MDA, and increasing the content of soluble sugars and proline, thereby strengthening the tolerance of seeds and seedlings to low temperatures. On the other hand, SA priming decreases endogenous ABA content, increases GA1 content, enhances the activities of total amylase and β-amylase, and promotes the expression of genes related to cell wall relaxation, thus facilitating seed germination and seedling growth at low temperature.

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    Effect of Flour and Cooking/Baking Qualities by Sprouted Wheat
    LIANG WangZhuang, TANG YaNan, LIU JiaHui, GUO XiaoJiang, DONG HuiXue, QI PengFei, WANG JiRui
    Scientia Agricultura Sinica    2024, 57 (7): 1267-1280.   DOI: 10.3864/j.issn.0578-1752.2024.07.005
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    【Objective】Continuous rainy weather during the wheat harvest season can cause wheat pre-harvest sprouting (PHS) and even germination, thus impacting wheat yield and quality. Evaluating the effect of flour made by blending different proportions of sprouted wheat with regular wheat on the baking/steaming quality of flour processing products can explore the possibility of using a slight degree of sprouted wheat to examine the possibility of reducing food waste. 【Method】In this study, blends of Zhengmai 583 (Zheng 583) and Kechengmai 6 (Ke 6) wheat with 30%, 50%, and 100% sprouted wheat were prepared, respectively. The degradation of wheat flour from blended wheat was evaluated by the falling number, sedimentation value, wet/dry gluten content, dough development time, and dough stability time. The baking/steaming characteristics of bread, dumpling wrapper, Chinese steamed bread (CSB), sponge cake, noodle, and cookie made from blended wheat were evaluated by sensory scores and quality parameters. 【Result】As the proportion of sprouted wheat increased (30%, 50%, and 100%), the dough development time of Zheng 583 flour first increased and then decreased, while the dough stability time gradually reduced. However, the changes in the two parameters of Ke 6 both showed a trend of first decreasing, then increasing, and finally decreasing. The falling number, sedimentation value, wet/dry gluten content, and farinogram parameters of mixed wheat decreased in both cultivars. The specific volume of Zheng 583 CSB increased and then decreased, while the particular volume of Ke 6 CSB gradually reduced. The exact volume of the Zheng 583 sponge cake gradually increased, while the specific volume of the Ke 6 sponge cake remained unchanged. The particular volume of the bread, area of the cookies, cooking loss of the noodles, and turbidity index (A*) of the dumpling soup changed the same trend in both cultivars. Compared to the control (without sprouted wheat), the specific volume of bread decreased by 11.33% and 17.44%, the cookies area increased by 24.10% and 7.49%, the noodles cooking loss increased by 22.99% and 9.69%, and the A* value of the dumpling soup increased by 8.93% and 13.32% in Z583 and Ke 6 of 100% SW, respectively. The bread, Chinese steamed bread, the dumpling wrapper of two cultivars, and the noodles of Zheng 583 showed significant deterioration in the 30% SW gradient. The sponge cake and cookie of the two cultivars showed significant deterioration in the 50% SW gradient. The noodles of Ke 6 showed significant deterioration in the 100% SW gradient. 【Conclusion】The baking/steaming quality of bread, dumpling wrappers, Chinese steamed bread, sponge cake, noodle, and the cookie was seriously affected by PHS. The influence of PHS is different in various wheat cultivars but has the same trend. When the degree of PHS is slight, it has little effect on the baking quality of cookies and sponge cakes.

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    Chemical Composition and Bioactivity of Dissolvable Organic Matter in Biochars
    BIAN RongJun,LIU XiaoYu,ZHENG JuFeng,CHENG Kun,ZHANG XuHui,LI LianQing,PAN GenXing
    Scientia Agricultura Sinica    2022, 55 (11): 2174-2186.   DOI: 10.3864/j.issn.0578-1752.2022.11.008
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    Volatile organic components escape from the solid feedstock when biomass pyrolyze, which is re-absorbed onto the surface of biochar in the form of dissolvable organic matter (DOM) following cooling. The condense Biochar DOM has a complex chemical composition, mainly containing small molecular weight organics, polycyclic hydrocarbons rich in functional groups. With high activity of chemical reaction and biological stimulation, the biochar DOM may alter the form and availability of nutrients and pollutants, mediating microbial abundance and community structure, and regulating plant growth and metabolism. These activities and chemical compositions vary with types of biomass feedstock and pyrolysis conditions. The role of biochar DOM in biological regulation is generally recognized as bio-promotion though a few DOM molecules is known of potential toxicity to plants, animals and microbes. In order to reach a differential and valorized utilization, the biochar DOM could be extracted for producing commercial liquid fertilizer. The identification of potential bio-toxic molecules in biochar DOM in relation to feedstock and pyrolysis condition deserve further studies, which is fundamental for optimizing production of biochar and biochar-derived products, and minimizing environmental risks following land allocation.

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    Commercialization Status and Existing Problems of RNA Biopesticides
    GUAN RuoBing,LI HaiChao,MIAO XueXia
    Scientia Agricultura Sinica    2022, 55 (15): 2949-2960.   DOI: 10.3864/j.issn.0578-1752.2022.15.007
    Abstract1012)   HTML77)    PDF (482KB)(319)       Save

    RNA biopesticides use the principle of RNA interference (RNAi) to inhibit the expression of important genes in target organisms, causing the developmental retardation or death of harmful organisms, thereby achieving the purpose of pest control. The technology does not alter the genome of pests and cause adverse effects on the ecosystem. RNA biopesticides are called “the third revolution in the history of pesticides” because they have the advantages of precision, high efficiency, green and pollution-free, etc. In recent years, with the approval of Bayer’s insect-resistant transgenic maize MON87411 which expressing insect dsRNA, major traditional agrochemical companies have invested a lot of manpower and material resources in layout and product development. In addition, it has also attracted the attention of the capital market, and large numbers of companies based on RNAi technology for pest control have emerged, which has greatly accelerated the industrialization of RNA biopesticides. With the rapid development of RNA biopesticides, it will be bound to change the global pesticide market pattern, which is undoubtedly a new challenge. Although the R&D program in this field started early and the starting point is relatively high in our country, most of the research mainly focuses on basic theories, and the application development is relatively weak, which has lagged far behind the international counterparts. Compared with traditional pesticides, RNA biopesticides have their own unique features in both mechanism and application development. It is urgent to improve the corresponding laws and regulations to supervise and guide production, promote the rapid development of RNA biopesticides in our country, and reduce the risk of international pesticide giants forming a technological monopoly in this field. Based on this, this paper systematically summarized the current domestic and foreign R&D status, commercialization, and future development trends of RNA biopesticides, as well as the regulations and policies related to RNA biopesticides in Europe, the United States and other countries. In addition, the paper also pointed out some urgent problems in the progress of R&D and industrialization of RNA biopesticides, hoping to provide a useful reference for the development and supervision of RNA biopesticides in China.

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    Research on the Mechanisms of Pre-Harvest Sprouting and Resistant Breeding in Wheat
    DONG HuiXue, CHEN Qian, GUO XiaoJiang, WANG JiRui
    Scientia Agricultura Sinica    2024, 57 (7): 1237-1254.   DOI: 10.3864/j.issn.0578-1752.2024.07.003
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    Pre-harvest sprouting (PHS) refers to the germination of cereal crops on the spike in high humidity conditions before grain harvest. Wheat PHS is a significant problem that affects both the yield and quality of wheat. Seed dormancy level is a major factor influencing the resistance of wheat PHS, and domesticated crops often exhibit reduced seed dormancy levels, making cultivated wheat more prone to PHS compared to its wild ancestors. Wheat PHS is mainly regulated by external environmental factors such as temperature and humidity, as well as internal plant hormones (GAs, ABA, IAA, MeJA, ET, BR). Researchers have identified a range of materials resistant to PHS, cloned key genes regulating PHS resistance, such as PM19, MFT, MKK3, Myb10-3D, Vp1. New wheat materials resistant to PHS have been successfully developed through molecular marker-assisted selection, artificial synthesis of wheat, and CRISPR/Cas9 gene editing technology. This article reviews the genetic mechanism of PHS resistance in wheat and the latest progress in PHS resistance breeding research. In the future, it is necessary to continue exploring key genes related to PHS resistance, and employ biotechnological breeding methods to cultivate new PHS-resistant wheat varieties.

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    Utilization Efficiency of Improving the Resistance for Pre-Harvest Sprouting by Synthetic Hexaploid Wheat and Chinese Wheat Landrace
    LIU ZeHou, WANG Qin, YE MeiJin, WAN HongShen, YANG Ning, YANG ManYu, YANG WuYun, LI Jun
    Scientia Agricultura Sinica    2024, 57 (7): 1255-1266.   DOI: 10.3864/j.issn.0578-1752.2024.07.004
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    【Objective】Pre-harvest sprouting (PHS) is a serious limiting factor for wheat (Triticum aestivum L.) grain yield and end-use quality. Synthetic hexaploid wheats (SHW) and wheat landraces (WL) are important germplasm resources for improving PHS resistance in wheat. The objective of this study is to utilize PHS-resistant loci from SHW and WL for breeding PHS-resistant elite materials, which will provide a theoretical basis for improving PHS resistance of wheat cultivars.【Method】In this study, SYN792 (a synthetic hexaploid wheat from CIMMYT) and Fulingxuxumai (a Chinese wheat landrace) were used as female parents to cross and backcross with Chuanmai 45 (a sensitive variety to PHS), respectively. Two BC1F7 populations including 1 796 lines were established. Seed germination index (GI) and seed germination rate of each spike (SGR) in different environments were used to evaluate PHS resistance. Two germination temperature of 25 ℃ (18GI) and 32 ℃ (19GI) were set to examine seed germinability in 2018 and 2019. 1 796 BC1F7 lines were evaluated preliminarily by SGR phenotype and molecular markers detection in 2017, and the introgression lines with PHS-3D and PHS-A1 resistant loci and SGR less than 35% were screened. Introgression lines with PHS-3D and PHS-A1 resistant loci were used to analyze utilization efficiency of SHW and WL in PHS-resistance breeding by identifying PHS-resistance and yield related traits in 2018 and 2019.【Result】PHS resistance of 1 796 lines was evaluated preliminarily, and 537 lines with SGR value less than 35% were screened for further molecular marker detection. A total of 332 lines with PHS-3D and PHS-A1 were selected by SSR marker, and the frequency of WL introgression lines was significantly higher than that of SHW introgression lines. 332 introgression lines were used to analyze PHS-resistance and yield related traits in 2018 and 2019. There was a significant positive correlation between different PHS indexes in different years, but there was no significant difference in the values of 18GI, 18SGR and 19SGR between SHW and WL introgression lines. The average values of 18SGR, 19SGR and 18GI in SHW and WL introgression lines were lower than 23%. As far as GI value was concerned, there was obvious difference between different germination temperatures. At the germination temperature of 32 ℃, the mean 19GI value of SHW PHS-3D introgression lines was significantly lower than that of WL PHS-A1 introgression lines. Grain color was associated with PHS resistance in SHW introgression lines, and the red-grained SHW introgression lines had lower the mean GI and SGR values than the white-grained lines. Among 73 SHW introgression lines, 11 white-grained lines showed medium or higher resistance to PHS,and the GI values of 14 red-grained lines at different germination temperatures were lower than 35%. According to the data of agronomic traits in 2018 and 2019, thousand grain weight of SHW introgression lines was significantly higher than that of WL introgression lines, but the number of grains per spike was significantly lower than that of WL introgression lines. 23 elite introgression lines including seven SHW introgression lines and 16 WL introgression lines were selected. Two SHW white-grained introgression lines had better resistance to PHS, and the GI values of two red-grained introgression lines at different germination temperatures were lower than 25%.【Conclusion】It is feasible to transfer PHS-3D and PHS-A1 resistance loci to PHS from SHW and WL for improving PHS-resistance of modern wheat cultivars. In this study, the breeding efficiency of WL for PHS-resistance was better than that of SHW. However, the stability of PHS-resistance of SHW introgression lines was better than that of WL introgression lines. 23 SHW and WL elite introgression lines could be used as parents to improve the PHS-resistance and yield traits in wheat. In particular, the white-grained SHW introgression line No.5201 and the red-grained SHW introgression lines No.5497 and No.5505 were very valuable parents for wheat breeding of PHS resistance.

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    PSORA: A Strategy Based on High-Throughput Sequence for Analysis of T-DNA Insertion Sites
    MA XueMeng,YU ChengMin,SAI XiaoLing,LIU Zhen,SANG HaiYang,CUI BaiMing
    Scientia Agricultura Sinica    2022, 55 (15): 2875-2882.   DOI: 10.3864/j.issn.0578-1752.2022.15.001
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    【Objective】The purpose of this study was to establish a simple and efficient approach for identifying all T-DNA insertion sites. 【Method】A T-DNA insertion sites analysis approach based on high-throughput sequence technologies was developed, called PSORA: Parallel sequencing of one round amplicons. The process involves high-throughput amplicon sequencing of a round of thermal asymmetric PCR (TAIL-PCR) and bioinformatics analysis of T-DNA insertion sites, which reduces concerns about the specificity of TAIL-PCR. In PSORA, only two primers are required, a degenerate primer and a T-DNA specific primer. A 6-nt Barcode was designed at the 5’ end of the specific primers for labeling different transgenic events. All five transgenic events (L1, L6, L9, L15 and L19) of tobacco used in this study were produced via Agrobacterium mediated transformation with plasmids pBI121. In addition, the results of PSORA are confirmed by standard PCR. 【Result】The T-DNA insertion sites of five transgenic events were analyzed by PSORA. The results showed that L6 contained two insertion sites (36 316 bp on NW_015801367 and 42 202 bp on NW_015950898), the lines of L9, L15 and L19 each contained one insertion site (The insertion site of L9 was located at 235 969 bp on NW_015943682. The insertion site of L15 was located at 60 529 bp on NW_015802951 and the insertion site of L19 was located at 12 188 bp on NW_015863435), but the insertion site of L1 could not be detected. PCR was performed to validate the results from bioinformatics analysis, transgenic events with different insertion sites were used as negative controls for each other, and the wild type (WT) was used as a blank control. The results showed that specific amplification consistent with expectations was obtained in each transgenic event. The effectiveness of PSORA was successfully confirmed. 【Conclusion】PSORA is an effective strategy to analyze T-DNA insertion sites. PSORA can parse the comprehensive molecular characteristics of all T-DNA insertion events simultaneously, making it simpler and faster than the traditional methods of genome walking.

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    Expression Pattern of the Rice α-Amylase Genes Related with the Process of Floret Opening
    ZHANG Ji, ZHOU ShangLing, HE Fa, LIU LiSha, ZHANG YuJuan, HE JinYu, DU XiaoQiu
    Scientia Agricultura Sinica    2023, 56 (7): 1275-1282.   DOI: 10.3864/j.issn.0578-1752.2023.07.006
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    【Objective】 Starch degradation is involved in lodicule absorbing abundant water and swelling during rice floret opening, but the amylase genes associated with this process have not been identified yet. 【Method】 To identify the swelling of tissues during floret opening, the in vitro rice panicles absorbed diluted Fuchsin basic and the dye remains were observed after florets were closing again. The starch grain distribution in rice florets before and during anthesis from stage 11 to stage 14 (according to 14 stages of rice anther development) was detected using iodide staining. The spatial-temporal expression patterns of 10 α-amylase genes were detected by RT-PCR, RT-qPCR and GUS staining. 【Result】 Before floret opening, the stamens, pistils and lodicules are enclosed by the lemma and palea through marginal tissues of palea (mtp). Rapid swelling of the lodicules causes floret opening by separating the lemma from the palea. After the in vitro panicles absorbed diluted Fuchsin basic during floret opening, the dye remains were observed located in the joint between mtp and lodicules and filaments. Iodide staining showed that the starch grains were mainly located in the stamens and mtp and a small amount of starch grains in the lodicules at stage 12 (before floret opening), whereas the starch grains in the mtp and lodicules were almost completely degraded at stage 13-14 (during floret opening). RT-PCR showed that OsRAmy2A and OsRAmy3D began to express from stage 12 and were expressed with high levels at stage 13-14. The expression levels of the two genes decreased at DAP1 (1 day after pollination). OsRAmy3E and OsRAmy3F kept expressed during this process. The expression level of OsRAmy3E was higher than that of OsRAmy3F. The RT-qPCR analysis showed that the expression level of OsRAmy2A increased most dramatically at stage 13-14, followed by OsRAMy3A and OsRAMy3E. Further, the transgenic plants expressing the GUS reporter gene driven by the OsRAmy2A promoter were generated. The GUS signaling was located only in the lemma, palea and mtp at stage 12 and the expression of the GUS gene driven by the RAmy2A promoter was induced in the mtp, lodicules and filaments at stage 13-14. 【Conclusion】 These data indicated that starch grain degradation in the mtp and lodicules at stage 13-14 might be related with high expression levels of some α-amylase genes such as OsRAmy2A and OsRAmy3D, probably involved in controlling lodicules swelling and floret opening in rice.

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    Understanding and Thinking About Some Problems of Fruit Tree Germplasm Resources and Genetic Breeding
    CHEN XueSen,WANG Nan,ZHANG ZongYing,MAO ZhiQuan,YIN ChengMiao
    Scientia Agricultura Sinica    2022, 55 (17): 3395-3410.   DOI: 10.3864/j.issn.0578-1752.2022.17.011
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    This review summarized the research progress of fruit tree germplasm resources and genetic breeding as well as the understanding and thinking of several issues. The main results were as follows: 1. Although China was the world’s largest fruit tree resource country and the origin and evolution center (one of) of many fruit trees, such as citrus, apple, pear, peach, longan, loquat, banana, kiwi, plum, apricot, jujube and persimmon, the discovery, innovation and utilization of wild germplasm and famous local varieties needed to be further strengthened. 2. According to the source of genetic variation, the fruit tree breeding mainly had two approaches: hybrid breeding and bud sports selection; the first generation of fruit tree hybrids was widely separated, and the genotype with the strongest heterosis was selected for each breeding. It became a new variety through asexual reproduction, and was used for a long time in production. The three hypotheses of dominant, superdominant and epistasis were the main genetic basis of heterosis; the analysis of the main characters of the new varieties of Fuji and Luli apples, Muscat Hamburg grape, and Shannongsu pear and their parents showed that selecting varieties with complementary traits as hybrid parents and selecting varieties with complex genetic background as female parents were important guidelines for the efficient utilization of fruit tree heterosis. Hybrid breeding was to determine the breeding goals according to the variety needs of the industry, to carry out parental selection and matching, and to breed new varieties with complementary parental traits and obvious heterosis. Bud mutation selection was the use of somatic natural mutations and epigenetics to repair and improve the individual traits of the main plant varieties in production; therefore, the organic combination of hybrid breeding and bud sports selection was an important technical approach to solve the variety problem of fruit tree industry. 3. In the face of rural revitalization and the country’s reform of the talent evaluation mechanism of “Persist in evaluating talents based on ability, actual performance and contribution, and overcome the tendency of only education, qualifications, and papers”, this review explained the scientific research ideas and classic cases that agricultural scientists must adhere to “Equal emphasis on technological innovation and the combination of good varieties and methods”.

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    Research Progress on the Application of Non-Saccharomyces During Wine Fermentation
    WANG ChunXiao, YU JunZhu, ZHOU WenYa, XU YinHu
    Scientia Agricultura Sinica    2023, 56 (3): 529-548.   DOI: 10.3864/j.issn.0578-1752.2023.03.011
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    Non-Saccharomyces yeast are naturally present on grape skin, which mainly play their roles in the maceration and initial stage of fermentation during winemaking process. More and more concerns have been recently focused on the application of non-Saccharomyces yeast in wine fermentation. Non-Saccharomyces yeast often have weaker fermentation ability than Saccharomyces cerevisiae and can convert the reducing sugar into ethanol and other fermentation by-products. Therefore, non-Saccharomyces are the potential excellent yeast for producing wine with complex flavor traits and lower ethanol degree. Different non-Saccharomyces yeast species have different metabolic characteristics in wine fermentation applications. The selection of non-Saccharomyces yeasts with certain characteristics for application in fermentation can improve the specialized quality of wine. This review was based on the initial summary on the species, winemaking traits, and application ways of commercial non-Saccharomyces yeast, and emphasized on the positive role of non-Saccharomyces in wine color, aroma, taste, safety and health, their metabolic mechanisms and corresponding research hotspot. The positive role of non-Saccharomyces in wine color included the promotion of high acid production, high polysaccharide production, high extracellular pyruvate production and low sorption properties. Different non-Saccharomyces yeast could promote the fruity aroma enhancement in wine by low production of ethanol, acetaldehyde, and volatile phenols, and high production of ethyl acetate, acetic acid ester, ethyl ester, higher alcohols, and enzymes related with the release of terpene and mercaptan, and therefore improve the aroma complexity of wine. Non-Saccharomyces yeast could regulate wine mouthfeel traits by high production of glycerol, polysaccharide, and lactic acid, and degradation of malic acid. In addition, non-Saccharomyces yeast could improve the safety quality of wine by decreasing the SO2 dosage as biological control agent, and reducing the content of toxic compounds through metabolic degradation during alcoholic fermentation. This review further analyzed the current research status on genome and microsatellite loci analysis. The main inoculation strategies were discussed on application of non-Saccharomyces yeast during wine fermentation, and six aspects were posed for further research concern. This review provided theoretical references for the research on application of the non-Saccharomyces yeasts in wine alcoholic fermentation.

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    Genome-Wide Association Study of Ear Related Traits in Maize Hybrids
    LI Ting,DONG Yuan,ZHANG Jun,FENG ZhiQian,WANG YaPeng,HAO YinChuan,ZHANG XingHua,XUE JiQuan,XU ShuTu
    Scientia Agricultura Sinica    2022, 55 (13): 2485-2499.   DOI: 10.3864/j.issn.0578-1752.2022.13.001
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    【Objective】Ear traits are important components of grain yield in maize. Dissecting their genetic basis and mining significant SNPs using genome-wide association study (GWAS) can provide references for cloning functional genes and breeding high-yield maize varieties. 【Method】A total of 115 superior inbred lines from Shaan A group and Shaan B group, as well as four domestic backbone lines were selected as parents. Based on NCⅡ genetic design, an association population consisting of 442 hybrids was constructed, which was planted in two different environments to collect phenotype data of ear traits. Meanwhile, all parental lines were sequenced by the tunable genotyping by sequencing (tGBS) protocols. According to the genotype of inbred lines, altogether 19 461 high-quality SNPs were inferred in the association population. Then, GWAS was performed using 19 461 SNPs and phenotype data by three models including additive, dominance and epistasis, respectively. Combining with the transcriptome data of maize ear related tissues in the public database and the annotation information of genes, candidate genes were predicted. 【Result】Phenotypic data analysis showed that eight ear traits followed a continuous distribution, and there were 3.78%-45.25% of phenotypic variation. Analysis of variance indicated that environment and genotype effects reached an extremely significant level (P<0.001), and the range of broad-sense heritability was from 54.15% to 68.89%. And there were significantly positive or negative correlations among ear traits of hybrids. In total, 16, 3, 79 significant SNPs/pairs were identified under additive, dominant, and epistatic models, respectively. The significant loci detected by the three models cumulatively explained 38.21%-60.69% of the phenotypic variation of each trait. The cumulative phenotypic variation of significant SNP detected by additive model and epistatic model was 0.00-41.26% and 15.18%-45.36%, respectively. Effect analysis of significant SNPs identified by additive and dominant models showed most SNPs with additive or partial dominance effects, and only two with over-dominance effects. Further, only seven single-SNPs and five interaction pairs explained more than 5% of the phenotypic variation, and 17 candidate genes were predicted based on the SNP locations and gene expression information. 【Conclusion】Ear traits of maize hybrids were mainly affected by additive and epistasis effects, but less by dominance effects. Multiple SNPs identified by additive and dominant models showed additive and partially dominance effects, and aggregating favorable alleles of these SNPs could improve the target traits.

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    Construction of High Density Genetic Map for RIL Population and QTL Analysis of Heat Tolerance at Seedling Stage in Rice (Oryza sativa L.)
    LIU Jin,HU JiaXiao,MA XiaoDing,CHEN Wu,LE Si,JO Sumin,CUI Di,ZHOU HuiYing,ZHANG LiNa,SHIN Dongjin,LI MaoMao,HAN LongZhi,YU LiQin
    Scientia Agricultura Sinica    2022, 55 (22): 4327-4341.   DOI: 10.3864/j.issn.0578-1752.2022.22.001
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    【Objective】 With global warming, high temperature has an increasing impact on food crop safe. Excavation of heat tolerance gene resources is the most direct green ecological method to cultivate new varieties of heat resistance and eliminate the harm of high temperature, which also the basis for clarifying the physiological, biochemical and molecular genetic mechanism of heat tolerance.【Method】Establishing the identification and evaluation method of heat tolerance at seedling stage, a set of RIL populations was structured from the extreme heat-tolerance Ganzaoxian58(GZX58) and heat-sensitive Junambyeo (JNB), and then the high density genetic map was constructed using genotyping by resequencing technology. To converting SNP information into Bin genotype of the RIL population using sliding window method, which predicting the recombination breakpoints on the chromosomes, finally a high density BinMap genetic map was constructed. Based on the genotype and phenotype data of the 171 lines, QTL mapping of the high temperature seedling survival rate (HTSR) and heat tolerance class (HTC) was performed by ICIM method of the QTL IciMapping software.【Result】A high-density genetic map containing 3 321 Bin markers was constructed, the number of Bin markers for each chromosome between 159 and 400, the average physical distance two markers was about to 106 kb; heat tolerance of the parents and RIL populations was identified by stepwise heat stress at seedlings stage, there have a significant negative correlation between HTSR and HTC, in addition, there has a significant positive correlation between HTSR and indica gene frequency (Fi), which the higher of the Fi, the heat tolerance is better; the bi-modal continuous distribution of phenotype traits from the RIL population showed that the heat tolerance is regulated by few major QTL. A total of 12 QTL controlling with heat tolerance at seedling stage, there have 8 and 4 QTL regulating for HTSR and HTC, respectively. There has a significant genetic overlap from HTSR and HTC, qHTS2, qHTS7 and qHTS8, three major QTL cluster play an important role in regulating the heat tolerance at seedling stage. Among these QTL, qHTS7 was a novel major QTL cluster, which has a strong effect on enhancing the heat resistance at seedling stage. 【Conclusion】 We constructed a high density genetic linkage map containing 3 321 Bin markers, which be used to analyzed the heat tolerance gene from the GZX58 at seedling stage, there have three key QTL cluster identified associated with the heat tolerance, a novel QTL cluster qHTS7 was discovered, efficient acquisition of target segments and candidate genes based on high-density genetic mapping, eight key candidate genes were selected by bioinformatics for regulation of the heat tolerance.

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    Screening and Functional Analysis in Heat-Tolerance of the Upstream Transcription Factors of Pepper CaHsfA2
    LIU RuiYao,HUANG GuoHong,LI HaiYan,LIANG MinMin,LU MingHui
    Scientia Agricultura Sinica    2022, 55 (16): 3200-3209.   DOI: 10.3864/j.issn.0578-1752.2022.16.011
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    【Background】 Pepper is widely cultivated as a vegetable around the world. With the increasing frequency of extreme high temperature weather in recent years, the heat stress has become one of the main environmental factors affecting pepper productivity, due to its feature of warm-prone but heat-sensitive. Therefore, it is very important for pepper production to clarify its mechanisms supporting heat-tolerance and then to develop pepper varieties with heat tolerance. 【Objective】 Since the heat shock transcription factor HsfA2 plays important roles in plant heat tolerance, the upstream transcription factors of pepper CaHsfA2 were screened and functionally analyzed in heat-tolerance in this study, in order to provide the theoretical basis for further understanding the mechanisms of heat tolerance of pepper. 【Method】 The 955 bp promoter sequence upstream of start codon of CaHsfA2 was used as the bait, the yeast one-hybrid (Y1H) technology was applied to screen the upstream transcription factors of CaHsfA2, and their interactions were checked by Y1H point-to-point hybridization, dual-luciferase reporter system (Dual-Luciferase), and LUC assay (LCA). For the candidate upstream transcription factors of CaHsfA2, their dynamic expression under heat stress in pepper heat-tolerant line R9 were analyzed by qRT-PCR technology; the subcellular localization were fulfilled through the transient gene expression technology, and its functional analysis in heat tolerance were performed by using the virus-induced gene silencing technology (VIGS). 【Result】 CaBES1 was identified as the candidate upstream transcription factor of CaHsfA2, and their interactions were confirmed. By the analysis of Dual-Luciferase system and CaHsfA2 expression in CaBES1-silenced pepper plants, it was suggested that CaBES1 negatively regulated the transcription of CaHsfA2. The result of subcellular localization showed that CaBES1 was expressed in both cell membrane and nucleus. After heat stress treatment, the fluorescence signal in the nucleus was enhanced, which was consistent with the property of CaBES1 transferring from cytoplasm to nucleus when it performed its biological functions. By dynamic expression pattern analysis, under heat stress, the expression level of CaBES1 decreased firstly and then increased, which also indicated that CaBES1 could respond to heat signal and laid a foundation for the further functional study in heat tolerance. After CaBES1 was silenced in pepper, by comparing the phenotype, relative electrical conductivity and chlorophyll content of silenced plants and control plants, it was inferred that silencing of CaBES1 increased the expression of CaHsfA2 and enhanced the heat tolerance of pepper. 【Conclusion】 CaBES1 inhibited pepper heat tolerance by negatively regulating the expression of CaHsfA2.

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    Preparation and Identification of Monoclonal Antibodies to P30 Protein and Establishment of Blocking ELISA to Detecting Antibodies Against African Swine Fever Virus
    ZHANG FengXi,XIAO Qi,ZHU JiaPing,YIN LiHong,ZHAO XiaLing,YAN MingShuai,XU JinHua,WEN LiBin,NIU JiaQiang,HE KongWang
    Scientia Agricultura Sinica    2022, 55 (16): 3256-3266.   DOI: 10.3864/j.issn.0578-1752.2022.16.015
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    【Background】 African swine fever (ASF) first appeared in China in August 2018, causing great harm to the pig industry and heavy losses. At present, there is no safe and effective vaccine to prevent ASF, so the establishment of rapid and specific detection method provides an effective means for the prevention and control of ASF. 【Objective】To prepare specific monoclonal antibodies against African swine fever virus (ASFV) and establish a rapid and specific detection method for ASF. Provide technical means for the detection and prevention and control of ASF. 【Method】The expression vector pET-28a-P30 was constructed and the rP30 protein was obtained by prokaryotic expression system. The purified rP30 protein was used as antigen to immunize BALB/c mice. The specific hybridoma cell line of ASFV P30 protein was prepared by cell fusion and cell subcloning. The truncated expression of P30 protein was performed, and Western Blot and indirect enzyme-linked immunosorbent assay (iELISA) were used to identify the antigen epitope corresponding to the monoclonal antibody. The prepared monoclonal antibody was used to establish the detection method of blocking ELISA antibody for ASF. 【Result】 The results of double digestion and PCR showed that the recombinant vector pET-28a-P30 was constructed, and the sequence was not mutated by sequencing. After IPTG induction, the recombinant P30 protein was mainly expressed in the inclusion body with a molecular weight of about 33 kD. The purified P30 protein was mixed with 1﹕1 Freund's adjuvant to immunize mice. After three immunizations, the serum titer of mice reached 1﹕102 400, indicating that the expressed protein had good immunogenicity. Eight P30 protein-specific hybridoma cells were obtained by cell fusion and subcloning. The eight monoclonal antibodies obtained by Western Blot and indirect immunofluorescence assay (IFA) showed good reactivity. The superposition test showed that all the 8 monoclonal antibodies had the same antigenic sites. Different fragments of P30 protein were truncated, and the prepared 2-12B monoclonal antibodies were selected to react with different truncated P30 proteins, showing that the antigenic epitope region of the monoclonal antibodies was 187-194aa. The ASF blocking ELISA antibody detection method was successfully established by using 2-12B monoclonal antibody and optimizing the conditions. 190 clinical samples were detected and compared with commercial African swine fever ELISA antibody detection kit. The positive coincidence rate of the two methods was 90.91 %, and the total coincidence rate was 96.32 %. 【Conclusion】 In this study, ASFV P30 protein was successfully obtained. Eight specific monoclonal antibodies with good reactivity were screened by iELISA, Western Blot and IFA, and the antigen recognition epitopes were 187-194 aa. The monoclonal antibody was used to establish a high specificity and sensitivity ASFV blocking ELISA antibody detection method, which provided a means and support for the detection and prevention of ASF.

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    Yield of Wheat and Maize and Utilization Efficiency of Nitrogen, Phosphorus and Potassium in Xinjiang
    TANG MingYao,SHEN ChongYang,CHEN ShuHuang,TANG GuangMu,LI QingJun,YAN CuiXia,GENG QingLong,FU GuoHai
    Scientia Agricultura Sinica    2022, 55 (14): 2762-2774.   DOI: 10.3864/j.issn.0578-1752.2022.14.007
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    【Objective】The objectives of the present paper were to understand current status of fertilizer utilization efficiency of wheat and maize in Xinjiang, to optimize their nutrient management, and to improve fertilizer utilization efficiency, so as to provide basic data and technique support for the food security of Xinjiang and as well as all the country. 【Method】72 field trials (40 for wheat and 32 for maize) were carried out in main grain growing areas of Xinjiang from 2018 to 2020. Four different treatments of fertilizer application were designed, including nitrogen, phosphorus and potassium (NPK), no nitrogen (PK), no phosphorus (NK), and no potassium (NP). Each experiment was conducted in triplicate. Then, the nutrient uptake of main grain crops, the response of nitrogen, phosphorus, and potassium fertilizers, the agronomic efficiency, the utilization rate and other parameters were examined under the current conditions of fertilization for agricultural production in Xinjiang. 【Result】(1) The average application amounts of N, P and K fertilizers for wheat in Xinjiang were 233.1 kg N·hm-2, 128.0 kg P2O5·hm-2 and 75.5 kg K2O·hm-2, respectively; the average application amounts of N, P and K fertilizers for maize were 254.9 kg N·hm-2, 148.0 kg P2O5·hm-2 and 67.8 kg K2O·hm-2, respectively. (2) The wheat yield of per unit area was 7 505 kg·hm-2 under NPK treatment, and the yield responses of N, P and K fertilizers were 2 206 kg·hm-2 (500-3 795 kg·hm-2), 2016 kg·hm-2 (288-4 230 kg·hm-2), and 1 362 kg·hm-2 (105-2 910 kg·hm-2), respectively. The average rates of yield increase for N, P and K fertilizers were 45.0%, 39.7% and 23.0%, respectively. The yield per unit area of maize under NPK treatment was 13 715 kg·hm-2, and the yield responses of N, P and K fertilizers were 4 657 kg·hm-2 (1 559-6 900 kg·hm-2), 1 942 kg·hm-2 (473-4 699 kg·hm-2), and 1 297 kg·hm-2 (113-5 440 kg·hm-2), respectively. The average rates of yield increase for N, P and K fertilizers were 52.2%, 21.2%, and 15.5%, respectively. (3) The uptakes of N and K by wheat and maize were relatively large, whereas the uptake of phosphorus was relatively small. The application of chemical fertilizers could significantly promote the uptake of nitrogen, phosphorus and potassium by plants, and increase the accumulation of nitrogen, phosphorus and potassium in soil. For NPK treatment, it required 2.7 kg (1.7-4.0 kg) of nitrogen (N), 0.8 kg (0.4-1.3 kg) of phosphorus (P2O5), and 2.1 kg (1.2-3.9 kg) of potassium (K2O) to form 100 kg of grains for wheat; for maize using the NPK treatment, it required 2.1 kg (1.5-2.9 kg) of nitrogen (N), 0.8 kg (0.4-1.2 kg) phosphorus (P2O5), and 2.1 kg (0.7-3.4 kg) of potassium (K2O) to form 100 kg of grains. (4) The agronomic efficiency of nitrogen fertilizer for maize was higher than that of wheat. There were no significant differences in the agronomic efficiencies of phosphorus and potassium fertilizers. The agronomic efficiencies of N, P and K fertilizers for wheat were 9.6, 15.9 and 18.7 kg·kg-1, respectively. Therefore, the agronomic efficiencies of P and K fertilizers were significantly higher than that of nitrogen fertilizer. The agronomic efficiencies of nitrogen, phosphorus, and potassium fertilizers for maize were 18.7, 13.4 and 18.1 kg·kg-1, respectively, N and K fertilizers were significantly higher than P fertilizer. (5) The utilization rates of N, P and K fertilizers for wheat were 41.4%, 21.8% and 45.2%, respectively. The utilization rates of N, P and K fertilizers for maize were 46.9%, 20.5% and 49.6%, respectively. The N and K utilization efficiency for wheat and maize were significantly higher than that of P. 【Conclusion】To date, the yield of wheat and maize in Xinjiang was high, the utilization efficiency of nitrogen, phosphorus and potassium was at a high level, and the utilization efficiency of nitrogen and potassium was significantly higher than that of phosphorus. In Xinjiang, wheat and maize yield was most sensitive to nitrogen deficiency. The phosphorus deficiency had lower influence on the wheat and maize yield, and the potassium deficiency had the lowest reduction. The amount of nitrogen application applied to wheat and maize in Xinjiang was reasonable. In contrast, the amount of potassium application was seriously insufficient. The excessive application of phosphate in wheat existed. In the future, it was necessary to increase the input of potassium fertilizer for wheat and maize and to reduce the input of phosphorus fertilizer for wheat.

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    Research Progress on Machine Learning for Genomic Selection in Animals
    LI MianYan, WANG LiXian, ZHAO FuPing
    Scientia Agricultura Sinica    2023, 56 (18): 3682-3692.   DOI: 10.3864/j.issn.0578-1752.2023.18.015
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    Genomic selection is defined as using the molecular marker information that covered the whole genome to estimate individual’s breeding values. Using genome information can avoid many problems caused by pedigree errors so as to improve selection accuracy and shorten breeding generation intervals. According to different statistical models, methods of estimated genomic breeding value (GEBV) can be divided into based on BLUP (best linear unbiased prediction) theory, based on Bayesian theory and others. At present, GBLUP and its improved method ssGBLUP have been widely employed. Accuracy is the most used evaluation metric for genomic selection models, which is to evaluate the similarity between the true value and the estimated value. The factors that affect the accuracy can be reflected from the model, which can be divided into controllable factors and uncontrollable factors. Traditional genomic selection methods have promoted the rapid development of animal breeding, but these methods are currently facing many challenges such as multi-population, multi-omics, and computing. What’s more, they cannot capture the nonlinear relationship between high-dimensional genomic data. As a branch of artificial intelligence, machine learning is very close to biological mastery of natural language processing. Machine learning extracts features from data and automatically summarizes the rules and use to make predictions for new data. For genomic information, machine learning does not require distribution assumptions, and all marker information can be considered in the model. Compared with traditional genomic selection methods, machine learning can more easily capture complex relationships between genotypes, phenotypes, and the environment. Therefore, machine learning has certain advantages in animal genomic selection. According to the amount and type of supervision received during training, machine learning can be classified into supervised learning, unsupervised learning, semi-supervised learning, and reinforcement learning. The main difference is whether the input data is labeled. The machine learning methods currently applied in animal genomic selection are all supervised learning. Supervised learning can handle both classification and regression problems, requiring the algorithm to be provided with labeled data and the desired output. In recent years, the application of machine learning in animal genomic selection has been increasing, especially in dairy and beef cattle. In this review, machine learning algorithms are divided into three categories: single algorithm, ensemble algorithm and deep learning, and their research progress in animal genomic selection were summarized. The most used single algorithms are KRR and SVR, both of which use kernel tricks to learn nonlinear functions and map data to higher-dimensional kernel spaces in the original space. Currently commonly used kernel functions are linear kernel, cosine kernel, Gaussian kernel, and polynomial kernel. Deep learning, also known as a deep neural network, consists of multiple layers of connected neurons. An ensemble learning algorithm refers to fusing different learners together to obtain a stronger supervised model. In the past decade, the related literature on machine learning and deep learning has shown exponential growth. And its application in genomic selection is also gradually increasing. Although machine learning has obvious advantages in some aspects, it still faces many challenges in estimating the genetic breeding value of complex traits in animals. The interpretability of some models is low, which is not conducive to the adjustment of data, parameters, and features. Data heterogeneity, sparsity, and outliers can also cause data noise for machine learning. There are also problems such as overfitting, large marks and small samples, and parameter adjustment. Therefore, each step needs to be handled carefully while training the model. This paper introduced the traditional methods of genomic selection and the problems they face, the concept and classification of machine learning. We discussed the research progress and current challenges of machine learning in animal genomic selection. A Case and some application suggestions were given to provide a certain reference for the application of machine learning in animal genomic selection.

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    Principle, Optimization and Application of Mixed Models in Genome- Wide Association Study
    TAN LiZhi, ZHAO YiQiang
    Scientia Agricultura Sinica    2023, 56 (9): 1617-1632.   DOI: 10.3864/j.issn.0578-1752.2023.09.001
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    Genome-wide association study (GWAS) is an effective method to locate genomic loci that are significantly associated with traits. With the accumulated phenotypic data, the continuous development of high-throughput genotyping technology, and the improved statistical methods, it promotes the wide application of GWAS in area of human disease and animal and plant genetics. False positives are one of the important concerns that impair the reliability of genome-wide association results. To control the false positives, in addition to correcting the P-values, GWAS models have been continuously improved from the naive methods like ANOVA (for quantitative trait) or Chi-square test (for quality trait), to general linear model (GLM), which incorporates fixed-effect covariates, to the mixed linear model (MLM), which incorporates random effects. Fitting individual genetic effects into random effects defined by the genomic relationships matrix (GRM) is commonly adapted currently. Since the parameter estimation of MLM consumes a lot of computational resources, researchers have tried to optimize solving models and constructing GRM (which also improves computing efficiency), and the time complexity gradually decreased from O(MN3) to O(MN) for MLM-based methods, achieving a great leap in computational speed and statistical efficacy. For inflations caused by unbalanced case-control data, researchers further correct the generalized mixed linear model (GLMM). This paper comprehensively introduces the basic principles and development of GWAS, with specific emphasis on the model improvement and optimization details. We also list the applications of MLM in GWAS in agriculture, including progress on animals, plants and microbes, as well as the application of haplotype in GWAS. Finally, we give prospects on the future developments of GWAS from the viewpoints of further model optimization and experimental design.

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    Crop Classification with Time Series Remote Sensing Based on Bi-LSTM Model
    HUANG Chong,HOU XiangJun
    Scientia Agricultura Sinica    2022, 55 (21): 4144-4157.   DOI: 10.3864/j.issn.0578-1752.2022.21.005
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    【Objective】Timely and accurate crop classification mapping is an important basis for agricultural situation monitoring. This study explores the potential of deep learning in time series remote sensing crop classification and early identification based on a bidirectional long short-term memory network model.【Method】In this paper, Yellow River Delta region was chosen as an example and a time-series NDVI dataset were constructed by using Sentinel-2 year-round available satellite images as the data source. A recurrent neural network architecture is used to build a bidirectional long short-term memory (Bi-LSTM) model for structured time-series remote sensing data to carry out crop classification, then the generalization ability of the model is evaluated. Through adjusting the length of time series, we explore the earliest identifiable time of different crops under the condition of satisfying certain mapping accuracy. 【Result】 Growth characteristics represented by time series remote sensing images have great potential to discriminate different crops. The overall accuracy of the Bi-LSTM model reached 90.9% with a Kappa coefficient of 0.892. By testing the effects of different time series lengths on crop classification, the earliest identifiable time of typical crops was obtained. The accuracy of crops such as winter-wheat and rice could improve significantly after the emergence of unique characteristics. Crops such as cotton and spring maize required complete growth sequences to ensure classification accuracy.【Conclusion】The structured feature information embedded in satellite image time series could effectively reduce crop spectral confusion at specific time periods. The Bi-LSTM model was able to consider both forward and backward temporal state information and could learn the spectral change characteristics of crops, which was excellent in the identification of confusing crops such as rice, cotton and spring maize. In addition, the deep learning model could effectively capture the variation trend on the sample in general, and showed better generalization ability and robustness in the crop multi-classification task. This study provided a feasible idea for regional crop mapping with high accuracy by integrating deep learning and remote sensing time series.

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    Environmental Safety Risks in Agricultural Application of Effluents from Sugar Molasses-Based Fermentation Industries
    WANG XiaoBin, YAN Xiang, LI XiuYing, TU Cheng, SUN ZhaoKai
    Scientia Agricultura Sinica    2023, 56 (3): 490-507.   DOI: 10.3864/j.issn.0578-1752.2023.03.008
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    Sugar molasses is a by-product from sugar industries. The sugar molasses-based fermentation industries mainly refer to the fermentation industries using molasses from sugar mills as raw materials for alcohol or yeast fermentation. A large volume of effluents can be produced in the process of sugar molasses-based alcohol or yeast fermentation. Considering the possibility of resource utilization with such effluents, many sugar-producing countries (such as Brazil, India, and China) use the effluents for crop irrigation and fertilization or soil remediation directly into the farmlands by waste disposal methods. Because the effluents from sugar molasses-based fermentation industries are both high concentration organic wastewater, and heavy metal-polluted wastewater, which are difficult to be treated. With the long-term disposal of such effluents into the farmlands in some sugar-producing countries, the problems about ecological environment pollution in soil-crop-water systems are increasingly exposed. At present, some fertilizer production enterprises in China use such effluents as raw materials to produce organic water-soluble fertilizers (accounting for 32%), but the long-term research and monitoring data about environmental safety risks for agricultural application of the effluents from sugar molasses-based fermentation industries are still lack. This paper collected the relevant scientific research literatures since 1980 on the pollution characteristics of the effluents from sugar molasses-based fermentation industries, and their environmental impacts on agricultural application. Through the investigation and review on the relevant research data, this paper evaluated the environmental safety risks for agricultural application of the effluents from sugar molasses-based fermentation industries: (1) Such effluents were at a risk of seriously exceeding the limits for water quality standards, and a risk of ecotoxicity to plants. For example, such effluents had strong acidity, and high salinity, and contained not only high load organic pollutants, but also several heavy metals including 5 heavy metals (As, Hg, Cd, Pb and Cr), as well as other pollutants (such as Mn, Cu, Zn, Ni and Se, etc.). The concentrations of these pollutants mostly exceeded the limits of the Standards for Irrigation Water Quality (GB 5084—2021). (2) Such effluents for agricultural application were at a risk of farmland pollution. The concentrations of pollutants (such as Cu, Cd, Cr, Zn, Ni, Mn, Pb and Cl) detected from the soil samples irrigated with such effluents were about 10-641 times higher than those in the control soil. (3) Such effluents for agricultural application were at a safety risk of agricultural products. The concentrations of pollutants (such as Cu, Cd, Cr, Zn, Ni, Mn and Pb) detected in the grains of crops (wheat and mustard) irrigated with such effluents were about 3-12 times higher than those in the control crops, in which all the pollutants detected in the crops irrigated with such effluents exceeded both the allowable limits specified by FAO/WHO, but also the Maximum Levels of Contaminants in Food (GB 2762—2017) specified by China. In view of the issue of environmental safety risks for agricultural application of such effluents, therefore, it is necessary to strengthen the quality detection and risk control on the organic water-soluble fertilizer products with such effluents as raw material, to enable the safety of effluent utilization in agriculture.

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    Function of FCS-Like Zinc-Finger Protein OsFLZ18 in Regulating Rice Flowering Time
    MA YaMei,ZHANG ShaoHong,ZHAO JunLiang,LIU Bin
    Scientia Agricultura Sinica    2022, 55 (20): 3875-3884.   DOI: 10.3864/j.issn.0578-1752.2022.20.001
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    【Objective】Flowering time is an important agronomic trait which determines the yield and regional adaptability of rice, but the underlining molecular regulatory mechanism need further study. FCS-like Zinc finger proteins (FLZs) are a class of plant specific regulatory proteins which play essential roles in plant growth and stress response, but their functions in regulating flowering time have not been reported. This study aims to investigate the potential function of FLZ proteins in rice flowering time control. The finding will broaden our understanding on the molecular regulatory mechanism of rice flowering time.and provide new theoretical basis and gene resource for rice breeding. 【Method】Based on the target sequences published in RGAP database, OsFLZ18 overexpression vector and CRISPR-Cas9 vector were generated and introduced into Japonica variety Nipponbare by Agrobacterium tumefaciens-mediated genetic transformation assay. Homozygous CRISPR knockout mutants were screened by PCR and sequencing analyses. The quantitative real-time PCR (qRT-PCR) assay was used to examine the spatial-temporal expression and diurnal rhythmic expression of OsFLZ18, as well as the effects of OsFLZ18 on the transcription of several known flowering time-related genes. Yeast two-hybrid assay (Y2H) was used to test the interaction between OsFLZ18 and the flowering time-related regulatory proteins.【Result】OsFLZ18 was ubiquitously expressed in various rice tissues, with the highest expression level in 14 day-old seedling, followed by leaf sheaths and leaf blades at the tillering stage, and stem and young panicles at reproductive stages. The OsFLZ18-CRISPR vector was constructed and transformed into Nipponbare. Two independent homozygous OE lines (OE-2, OE-3) with higher OsFLZ18 expression level and two homozygous mutants (CRISPR-21, CRISPR-25) were selected for further study. Phenotypic observation showed that the OE lines flowered later than the wild-type plants under both natural long-day and short-day conditions in Guangzhou, while the CRISPR lines had no obvious differences in heading date when compared to the wild-type plants. The expression levels of Ehd1, Hd3a and RFT1 were significantly decreased in OE-2 plants compared with those in the wild-type plants under artificial short-day conditions, but no significant difference in the expression level of Hd1 was observed between them. The results of Y2H experiment showed that OsFLZ18 interacted with OsMADS51, a positive regulator of rice flowering time. Furthermore, OsFLZ18 exhibits a diurnal rhythmic expression profile, showing lower expression levels in the daytime and higher expression levels at night with a peak at midnight. 【Conclusion】Overexpression of OsFLZ18 delays rice flowering time.

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    Function of Maize ZCN7 in Regulating Drought Resistance at Flowering Stage
    LI Yan, TAO KeYu, HU Yue, LI YongXiang, ZHANG DengFeng, LI ChunHui, HE GuanHua, SONG YanChun, SHI YunSu, LI Yu, WANG TianYu, ZOU HuaWen, LIU XuYang
    Scientia Agricultura Sinica    2023, 56 (16): 3051-3061.   DOI: 10.3864/j.issn.0578-1752.2023.16.001
    Abstract715)   HTML157)    PDF (1718KB)(1886)       Save

    【Objective】The main producing areas of maize is mostly located on the arid or semi-arid region that relying on the rainfed farming in China. The maize production losses caused by drought is a great threaten to food security. As a cross-pollinating crop, maize is mostly sensitive to water stress during flowering time. Drought at flowering stage will lead to asynchronous development between the male and female flower and cause massive grain yield loss. Thus, mining drought resistance related genes at flowering stage is important for maize drought resistance improvement and breeding. 【Method】In the present study, the phylogenic tree of 24 ZCN genes in maize genome, which is homologs of Arabidopsis FT gene, was build. The gene expression patterns of ZCN7 were analysis using qRT-PCR and in vivo GFP fluorescence imaging. A maize natural population consisting of 118 diverse inbred lines were planted in three environments, Beijing in 2021 and 2022 and Urumqi in 2022, to identify the flowering time related traits under different water treatments. The genomic variants around ZCN7 were detected by PCR and Sanger sequencing. The candidate gene association analysis was performed based on mixed linear model and the significant associated variants with drought induced anthesis-silking interval was obtained. The gene expression level of ZCN7 in natural population at flowering time was also measured by qRT-PCR. The differences of drought resistance traits and ZCN7 expression were compared between different haplotypes of significant associated variant. The Ubi1:ZCN7 overexpression transgenic maize were obtained, and the phenotypic performance was identified under different water treatments. 【Result】The 24 ZCN genes in maize genome included 15 FT like genes, 6 TFL1 like genes and 3 MFT like genes. The protein sequence of ZCN genes varied from 111 nn to 193 nn. The ZCN7 showed close relationship with ZCN8 and the protein sequence identity was 83.3% between the two genes. ZCN7 showed highest gene expression in the leaf blade at V12 stage. And the ZCN7-promoter:GFP vector was transformed to Arabidopsis and the GFP showed enriched signal at the blade edge of mature leaf. The candidate gene association analysis revealed a SNP variant at 1001 bp upstream of ZCN7 start codon had highest association signal with drought induced anthesis-silking interval under drought. The A/A and G/G haplotypes of SNP-1001 included 78 and 27 inbred lines, respectively. The anthesis-silking interval of A/A haplotype lines were significantly lower than G/G lines. And the ZCN7 gene expression of A/A haplotype lines were significantly higher than G/G lines. In addition, the ZCN7 overexpression transgenic lines showed significantly decreased anthesis-silking interval than wild type lines. Under drought, the anthesis-silking intervals of OE1 and OE2 were 2.3 and 2.6 days shorter than wild type lines. And the grain yield per plant and kernel number per plant of transgenic lines were significantly higher than wild type lines under drought, while the hundred kernel weight, kernel length and kernel width showed no significant difference. 【Conclusion】The maize ZCN7 played positive role in drought resistance and its overexpression improved grain yield by reducing anthesis-silking interval under drought.

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    Colistin Promotes mcr-1-positive IncI2 Plasmid Conjugation Between Escherichia coli
    WANG XueYang,JIANG JunYao,YANG Lu,SHAO DongYan,WU CongMing,SHEN JianZhong,SHEN YingBo,WANG Yang
    Scientia Agricultura Sinica    2022, 55 (14): 2862-2874.   DOI: 10.3864/j.issn.0578-1752.2022.14.015
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    【Background】 Colistin is a last line antibiotic for the treatment of clinical infections caused by multi-drug resistant Gram-negative bacteria, and it has also been extensively used in animal industry as a feed additive and therapeutic drug. In 2015, Chinese researchers discovered the plasmid-mediated colistin resistance gene mcr-1, indicating that this last defense line is at risk of being breached. However, the effects of bactericidal concentration and sub-inhibitory concentration of colistin on the transmission of mcr-1-positive plasmid is still unknown. 【Objective】 This study used the most prevalent mcr-1-positive plasmid IncI2 as an object to explore the influence on the conjugative transfer frequency under different colistin concentrations. 【Method】 The conjugation experiment under different colistin concentrations (0.02-4 μg·mL-1) was carried out by the broth method. Real time quantitative PCR and the constructed formula were used to calculate the conjugative transfer frequency at different timepoints (1-24 h) and also different colistin concentrations. The cell membrane permeability and ROS production of donor and recipient bacteria under different colistin concentrations were detected by using PI dye and reactive oxygen species (ROS) detection kit, respectively. Colistin negative group and the three treatment groups (0.02, 1, and 4 μg·mL-1) were subjected to RNA sequencing as control, low, medium and high concentration groups, respectively, and the gene differential expression was analyzed by Deseq2 software. All statistical analysis were conducted by Prism v8.2.0 software. 【Result】 A formula was established to calculate the conjugative frequency in this study, and it was found that the bactericidal concentration (4 μg·mL-1) of colistin significantly increased the conjugative transfer frequency of mcr-1-positive IncI2 plasmid by 3-10 times at different timepoints, whilst no significant difference on other concentrations. Transcriptome results showed that when compared with control group, the expression of genes related to type IV secretion system (T4SS) in IncI2 plasmid, including virB1, virB2, virB5 and traC, were significantly increased in all colistin concentrations groups. In addition, the expressional level of type I fimbrium biosynthesis genes were significantly increased in all colistin groups. PI staining results showed that 2 and 4μg·mL-1 colistin could elevate the cell membrane permeability in donor and recipient bacteria, and the coincidently transcriptome results showed that the expressional levels of membrane-related genes, including ompAX, bamDE, lolB, yiaD, csgEF, were significantly up-regulated. However, ROS production and expressional level of related genes were not significantly increased after colistin treatment. 【Conclusion】 This study revealed that colistin promoted the conjugative transfer frequency of mcr-1-positive IncI2 plasmid between E. coli by increasing the activity of bacterial T4SS, cell membrane permeability and pilus formation, suggesting the bactericidal concentration of colistin could increase the plasmid transmission in all survived mcr-1-positive E. coli. Therefore, the therapeutic use of colistin in animals might maintain the existence and transmission of mcr-1-positive plasmids. In addition, since colistin has been approved for clinical use in human medicine, this phenomenon could lead to the failure on colistin treatment for mcr-1-positive pathogens.

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    Influence of Plastic Film on Agricultural Production and Its Pollution Control
    ZHANG JinRui,REN SiYang,DAI JiZhao,DING Fan,XIAO MouLiang,LIU XueJun,YAN ChangRong,GE TiDa,WANG JingKuan,LIU Qin,WANG Kai,ZHANG FuSuo
    Scientia Agricultura Sinica    2022, 55 (20): 3983-3996.   DOI: 10.3864/j.issn.0578-1752.2022.20.010
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    Plastic film has been widely used in the farmland all over the world especially in arid and semi-arid areas because of its remarkable agricultural benefits, such as increasing soil temperature and moisture, reducing weed and pest damage, extending crop-growing areas, and consequently improving crop yield and quality. However, the degradation rate of plastic film is extremely slow, and the recovery of plastic film is also relatively backward in China, which lead to a large number of plastic debris in the farmland, causing plastic residues and microplastics pollution in the soil environment. Based on literature, investigation and statistical data, this research reviewed and prospects the impact of plastic film on agricultural production and pollution control in China. Plastic residues and microplastics have been reported to change the physical and chemical properties of soil, restrict soil water and nutrient transport, do harm to the growth, development and reproduction of soil animals and plants, change the abundance and community structure of soil microorganisms, and damage the soil health. In the long-term, plastic residues and microplastics pollution will cause a decline in crop yield and quality. Microplastics had the potential to be absorbed by plants, enter the human body through the food chain and pose a threat to human health. In addition, the large specific surface area of microplastics enabled them to become carriers of other pollutants (e.g. heavy metals, pesticides and antibiotics), causing combined pollution to the soil ecological environment. The standard of plastic film production and use in China was gradually being improved, however, there was still a certain gap compared with developed countries and regions. In addition, a sustainable recycling system of plastic film and the policy of preventing plastic residue and microplastics pollution have not been well formed in China, and the study of microplastics pollution in Chinese farmland soil was still very limited. Therefore, it is critical to solve the problem of plastic residues and microplastics pollution in the soil by evaluating the present situation of plastic residues and microplastics pollution in soils, quantifying the effects of microplastics on the soil environment, and evaluating risks of microplastics to the soil ecosystems, as well as exploring the measures of controlling soil plastic residues and microplastics pollution, and formulating relevant policies and regulations of preventing these pollution.

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    Accurate Identification and Comprehensive Evaluation of Panicle Phenotypic Traits of Landraces and Cultivars of Sorghum bicolor (L.) Moench in China
    XU Xiao,REN GenZeng,ZHAO XinRui,CHANG JinHua,CUI JiangHui
    Scientia Agricultura Sinica    2022, 55 (11): 2092-2108.   DOI: 10.3864/j.issn.0578-1752.2022.11.002
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    【Objective】 Through the research on the phenotypic diversity and genetic variation of the sorghum germplasm resources in the panicle, we will screen for superior sorghum germplasm, enrich the genetic information of sorghum panicle-related traits, and provide a reference for the conservation and efficient use of existing germplasm resources and the selection and breeding of new varieties.【Method】 Using 320 sorghum accessions from different parts of China as test materials, we accurately identified 12 panicle traits (grain length, grain width, thousand-grain weight, grain hardness, grain density, corneous endosperm rate, kernel weight per panicle, main panicle length, panicle neck length, panicle neck diameter, primary branches length, primary branches number) in two different ecological environments. A comprehensive evaluation of sorghum germplasm resources using correlation analysis, principal component analysis, cluster analysis, and other methods. We screened elite sorghum germplasms with different outstanding characteristics according to the comprehensive evaluation value F and target traits. 【Result】 The frequency distribution of each quantitative trait showed a trend of high in the middle and low on both sides. The two-year frequency distribution and curve trend of grain hardness, kernel weight per panicle and grain density, and corneous endosperm rate were similar at the Baoding and Jinzhong test sites. Most of the traits only showed normal distribution in one year or a single location. Except for the main panicle length and number of primary branches, the other traits differed between the two test sites in the same year. The mean diversity index (H') distribution of the 12 panicle traits ranged from 1.72 to 2.11, among which the average diversity index of grain hardness was the highest, and the average diversity index of primary branches length was the lowest. The coefficients of variation of grain hardness, corneous endosperm rate, kernel weight per panicle, primary branches length, and the number of primary branches were all higher than 30.00%. The cumulative contribution rate of the extracted four principal components was 65.39%. Cluster analysis classified the 320 accessions into three groups, class I can be used as the germplasm for screening process (broom) sorghum; class II is suitable for selecting excellent germplasm for grain (brewing) sorghum; class III was the germplasm with poor panicle traits. We screen 29 superior germplasm with outstanding characteristics according to the comprehensive score value F and target traits. 【Conclusion】 The variability of sorghum germplasm resources in panicle traits was rich and diverse; the coefficient of variation of corneous endosperm rate and primary branches length was high; grain length, grain width, grain hardness, grain density, and kernel weight per panicle were significantly affected by environmental conditions. We screened 29 superior germplasm.

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    Genome-Wide Identification and Expression Analysis of DIR Gene Family in Cucumber
    ZHANG KaiJing, HE ShuaiShuai, JIA Li, HU YuChao, YANG DeKun, LU XiaoMin, ZHANG QiAn, YAN CongSheng
    Scientia Agricultura Sinica    2023, 56 (4): 711-728.   DOI: 10.3864/j.issn.0578-1752.2023.04.010
    Abstract689)   HTML129)    PDF (9399KB)(331)       Save

    【Objective】 Based on the cucumber (Cucumis sativus L.) genome information and transcriptome sequencing big-data, the DIR gene family in cucumber was identified with bioinformatics methods, and the expression pattern analysis of DIR family genes in different tissues and stresses response were analyzed. It would lay an important foundation for further study on the biological function of cucumber DIR genes. 【Method】 With the reported HMM model file of DIR gene, the probable DIR genes ID from the cucumber protein database was firstly identified using HMMSearch program in the HMMER software package. The cucumber DIR genes were ultimately verified using online tools Pfam and SMART. The tools of ExPASy, TBtools, GSDS, MEME, MEGA, MCScanX and Circos were used to analyze the physicochemical characteristics, chromosomal distributions, gene structure, phylogenetic tree and synteny of cucumber DIR genes. Based on cucumber transcriptome sequencing big-data of different tissues and under different stresses, transcriptome sequencing analysis was re-analyzed using cucumber V3 version genome information. The data of cucumber DIR genes in different transcriptome sequencing analysis were retrieved. The expression heatmaps of DIR gene family were drawn using TBtools software, and the expression patterns of cucumber DIR genes in different tissues and stresses response were analyzed. 【Result】 Total of 23 DIR genes were identified from cucumber genome, which distributed to 7 chromosomes. The number of amino acids of these DIR genes ranged from 78 to 684, and the molecular weight ranged from 8.70 to 73.82 kD. Phylogenetic analysis divided the cucumber DIR genes into 3 subgroups, the structure and motif of the genes in each subgroup were similar. Synteny analysis showed that the 12 cucumber DIR genes were collinearity with 19 Arabidopsis DIR genes and with 27 kinds of linear relationships, and 12 cucumber DIR genes were collinearity and with 11 rice DIR genes with 19 kinds of linear relationships. While only 8 cucumber DIR genes were conservative, which were not collinearity with any DIR gene in Arabidopsis and rice. Tissue-specific expression analysis revealed that some cucumber DIR genes had low or no expression levels in all tissues including root, stem, flower, fruit, leaf and so on, some cucumber DIR genes had high expression levels in all tissues, and some DIR genes had specific expression levels in some tissues, but no or low expression levels in other tissues. This suggested that different cucumber DIR genes had tissue specific expression patterns. The expression profiles analysis of cucumber DIR genes under biotic and abiotic stresses conditions revealed that cucumber DIR gene, CsaV3_4G023490, were up-regulated expression in response to all stresses, which meant this gene played an important role in the process of cucumber growth and development. 【Conclusion】 Total of 23 DIR genes were identified in cucumber, which were divided into 3 subgroups. The gene members in each subgroup were highly conserved, and the gene structure and protein conserved domain were different among 3 subgroups. The expression patterns of cucumber DIR genes in different tissues and stresses response were different, which coordinately regulated the growth and development of cucumber.

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    Research Progress on Root System Architecture and Drought Resistance in Wheat
    ZHANG YuZhou, WANG YiZhao, GAO RuXi, LIU YiFan
    Scientia Agricultura Sinica    2024, 57 (9): 1633-1645.   DOI: 10.3864/j.issn.0578-1752.2024.09.002
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    Wheat is the most important cereal crop, and drought is the most significant abiotic stress factor that severely affects wheat growth and development. Plant root system, as a primary organ for crops to acquire water and nutrients, directly determines the efficiency of soil water utilization. In recent years, increasing evidence has shown that plant root system architecture (RSA) plays an important role in plant tolerance to drought stress. This review summarizes the current research progress on the regulation of wheat drought tolerance determined by RSA. First, we present how root tropism especially root gravitropism shapes the RSA, summarize the relevant genes and molecular regulatory mechanism involved in root gravitropic growth, and explain how the root tropism-regulated RSA is implicated in wheat adaptation to drought stress. In addition to root tropic growth, the root development also participates in the RSA formation and the plant adaptability to drought stress. Therefore, this review further summarizes how wheat regulates root development to alter its root system morphology (including increasing root length, modifying lateral root number and root hair density, etc.), thereby enhancing its water acqusition from the soil and its adaption to drought environment. The identified genes involved in wheat root development under drought stress conditions are also systematically summarized. Furthermore, as the underground part of plants, the revelation of RSA has always been a challenging task, which hinders our understanding of the relationship between RSA and plant drought tolerance. Therefore, this review also summarized the available techniques used to analyze the RSA at two- and three-dimension levels. These techniques can measure and analyze wheat root length, density, growth direction, and morphology parameters, laying technical support for an insightful understanding of the relationship between wheat RSA and drought resistance. Finally, we discuss the prospect of the improvement of RSA in breeding wheat drought-resistant varieties, as well as provide an outlook for how to identify genes regulating wheat RSA and pinpoint their regulatory mechanism. In summary, the relationship between wheat RSA and drought resistant is closely associated. The continuous development of sequencing techniques, along with the deepening research on the regulatory mechanism of wheat RSA, will provide new means and strategies for the further breeding of drought-tolerance wheat varieties.

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    Effects of Long-Term Straw Return and Nitrogen Application Rate on Organic Carbon Storage, Components and Aggregates in Cultivated Layers
    GUO RongBo, LI GuoDong, PAN MengYu, ZHENG XianFeng, WANG ZhaoHui, HE Gang
    Scientia Agricultura Sinica    2023, 56 (20): 4035-4048.   DOI: 10.3864/j.issn.0578-1752.2023.20.009
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    【Objective】The results of carbon sequestration studies on combining straw returning with nitrogen fertilizer are controversial. Aimed at such problem, this experiment was carried out to reveal the effects of combining straw returning with nitrogen fertilizer on Carbon sequestration capacity and mechanism of farmland, so as to provide a reference for the future research. 【Method】Based on 11 years of long-term positioning experiments, this paper adopted split-zone design, the main treatment included straw returning to soil and removal straw from field, and the subplots included three N application rate, which were no nitrogen (N0), 168 kg·hm-2 (N168, nitrogen), and 336 kg·hm-2 (N336, excessive nitrogen application). 【Result】Compared with wheat without nitrogen fertilizer, wheat yield increased by 14.4%-19.5% with nitrogen fertilizer. The effect of straw returning to the field on yield was not significant. Straw returning significantly increased the cumulative input of soil carbon by 70.8% (P<0.05), but had no significant effect on soil organic carbon storage. Compared N0, the nitrogen application significantly increased soil carbon accumulation input and soil organic carbon storage by 7.7%-8.5% (P<0.05) and 4.7%-8.1% (P<0.05), respectively. The application of nitrogen fertilizer significantly increased the carbon fixation rate by 32.7%-56.1% (P<0.05), and N336 significantly increased the soil carbon fixation efficiency by 51.8% (P<0.05); straw returning to the field did not significantly improve the soil carbon fixation rate, but significantly reduced the carbon fixation efficiency by 30.9% (P<0.05). Both nitrogen application and straw returning could improve soil carbon pool capacity, and N0 and N168 have reached carbon saturation. The content of soluble organic carbon (DOC), microbial biomass carbon (MBC) and easily oxidized organic carbon (EO) in the soil increased by 4.6%, 11.2% and 4.5% respectively after returning straw to the field. Compared N0, DOC under N168 and N336 increased by 14.12% and 29.54% respectively; MBC decreased by 14.0% and 28.0% on average, respectively; EO increased by 8.2% and 11.5%, respectively. Straw returning to the field was beneficial to the improvement of soil DOC/SOC and microbial entropy. Applying nitrogen fertilizer was beneficial to the increase of DOC/SOC, but reduced the microbial entropy. Both straw returning and nitrogen fertilizer application had no effect on soil EO/SOC. Both straw returning and nitrogen application were beneficial to the improvement of macroaggregates (>0.25 mm), and straw returning significantly increased the organic carbon content of macroaggregates by 5.2%. The average weight diameter (MWD) and geometric average diameter (GMD) of aggregates under non-return showed a trend of first increasing and then decreasing with the increase of nitrogen level, while under straw returning, it showed an increase with the increase of nitrogen level. Straw returning increased the MWD and GMD of aggregates by 8.8% and 7.5% respectively, and the application of nitrogen fertilizer increased the MWD and GMD by 14.1%-22.7% and 16.8%-23.4% respectively, compared with CK. Both straw returning and nitrogen application could improve the distribution of organic carbon in large aggregates. 【Conclusion】Straw returning with nitrogen fertilizer could increase carbon input, increase activated organic carbon content, reduce microbial activity, and improve the protection of organic carbon by aggregates.

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    QTL Mapping and Molecular Marker Development of Traits Related to Grain Weight in Wheat
    ZHANG ZeYuan, LI Yue, ZHAO WenSha, GU JingJing, ZHANG AoYan, ZHANG HaiLong, SONG PengBo, WU JianHui, ZHANG ChuanLiang, SONG QuanHao, JIAN JunTao, SUN DaoJie, WANG XingRong
    Scientia Agricultura Sinica    2023, 56 (21): 4137-4149.   DOI: 10.3864/j.issn.0578-1752.2023.21.001
    Abstract671)   HTML59)    PDF (4065KB)(682)       Save

    【Objective】The yield of wheat, the second-highest-yielding food product in the world, has a major impact by grain weight. This research used materials from a recombinant inbred line (RIL) population derived from Heshangtou (HST) and Longchun 23 (LC23). Based on 55K SNP genotype data, QTL mapping was performed for traits related to grain weight of wheat, and co-segregation markers of major grain length QTL were developed and verified to provide reference for molecular marker assisted selection breeding.【Method】The wheat 55K SNP microarray was used to genotype parents and RIL populations, and a high density genetic linkage map was constructed, and its correlation with Chinese spring reference genome IWGSC RefSeq v1.0 was analyzed. QTL mapping of traits related to grain weight in multiple environments based on inclusive composite interval mapping method. The analysis of variance of major effect QTLs were performed to judge the additive interaction effect among different QTLs, and to analyse its effect on traits related to grain weight. At the same time, the corresponding kompetitive allele specific PCR marker was developed according to the closely linked SNP loci of major QTL for grain length, and verified in 242 wheat accessions worldwide.【Result】In this study, a high density genetic map of Heshangtou/Longchun 23 RIL population was constructed, with full length 4 543 cM, including 22 linkage groups, covering 21 chromosomes of wheat, and the average genetic distance was 1.7 cM. There was a significant correlation between genetic map and physical map, and the Pearson correlation coefficient were 0.77-0.99 (P<0.001). A total of 51 QTLs related to grain weight were detected, among them, 4 stable major QTLs were found in multi-environments (three or more environments) and distributed on 2D, 5A, 6B and 7D chromosomes. According to the physical interval and functional markers, it is inferred that stable major QTLs Qtkw.nwafu-2D.1 and Qtkw.nwafu-7D are photoperiod gene Ppd-D1 and flowering gene FT-D1, respectively. The analysis of variance shows that there is a significant interaction between them. The favorite alleles polymerization of Qtkw.nwafu-2D.1 and Qtkw.nwafu-7D can significantly increase thousand grain weight and grain width of wheat. In addition, the corresponding KASP molecular detection marker AX-111067709 was developed based on the co-segregated SNP of the major locus Qgl.nwafu-5A for grain length, which was significantly correlated with grain length and grain weight traits in a diversity panel comprising of 242 wheat accessions, and could increase grain length by 3.33% to 4.59% and grain weight 5.70% to 10.35% in different environments (P<0.001).【Conclusion】There are several genetic loci that affect traits linked to grain weight in Heshangtou (HST) and Longchun 23 (LC23), and Qtkw.nwafu-2D.1 and Qtkw.nwafu-7D dramatically increased thousand grain weight and grain width through additive interaction effects. Qgl.nwafu-5A is significantly correlated with grain weight and grain length, and its co-segregated molecular marker AX-11106770 can be used in molecular marker assisted selection breeding.

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    Candidate Gene Localization of ZmDLE1 Gene Regulating Plant Height and Ear Height in Maize
    ZHOU WenQi, ZHANG HeTong, HE HaiJun, GONG DianMing, YANG YanZhong, LIU ZhongXiang, LI YongSheng, WANG XiaoJuan, LIAN XiaoRong, ZHOU YuQian, QIU FaZhan
    Scientia Agricultura Sinica    2023, 56 (5): 821-837.   DOI: 10.3864/j.issn.0578-1752.2023.05.002
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    【Objective】 Plant height is one of the important target traits in maize plant type breeding, which is closely related not only to mechanized grain harvesting and lodging resistance, but also to maize yield. Therefore, it is of great theoretical and breeding value to isolate QTL/gene of maize plant height and analyze its function. This study aims to locate a novel maize dwarf gene ZmDLE1, clarify its biological function, and provide important theoretical basis and gene resources for accelerating the improvement of maize plant type. 【Method】 A single recessive mutant was derived in maize inbred line LY8405, from Crop Research Institute of Gansu Academy of Agricultural Sciences, by chemical mutagenic agent Ethyl Methyl Sulfonate (EMS). A maize dwarf and low ear mutant was isolated from the M2 progeny, and the M3 and M4 progeny could stably inherit, which was named dwarf and low ear mutant1 (Zmdle1). The F2 population was constructed by hybridization with Mo17 and was identified by bulked segregate analysis-sequencing (BSA-seq) and target segment recombination exchange. Based on the Mo17 reference genome, the genes in the target region were obtained and functionally annotated to locate candidate genes.【Result】Phenotypic identification of Zmdle1 was carried out, and the phenotype of Zmdle1 at seedling stage was not significantly different from that of the control LY8405. The plant height and ear height of Zmdle1 at mature stage were reduced by 87.2 cm and 55.4 cm, respectively, accounting for about 35.0% and 62.9%, difference is extremely significant. Morphological observation showed that the decrease of internode number and the shortening of internode cell length were the main reasons for the significant decrease of plant height and ear height of Zmdle1. The genetic analysis of the mutant gene was conducted by using the F2:3 genetic populations. The Zmdle1 mutant is inherited in a 3﹕1 (χ2=2.854) ratio and is a single recessive gene. Therefore, according to the results of BSA-seq, the candidate gene ZmDLE1 was initially located in the 15 Mb region of Bin1.09-1.10 on chromosome 1 of maize. The polymorphism molecular markers were further developed using the re-sequencing results of Mo17 and Zmdle1, and the target gene was accurately cloned by map-based cloning. Finally, the candidate genes were mapped to the size range of 600 kb, and there were 16 candidate genes in this range. By comparing the re-sequencing data, it was found that Zm00001d033231 gene changed into A at the 2062 position G, which resulted in amino acid changing from glycine to serine, and the transcription level expression was significantly reduced compared with LY8405. Zm00001d033234 changed from T to C at the 223rd position leading to the 75th amino acid changed from serine to proline, and there was no significant difference in transcription level. Through association analysis of natural populations and the predicted genes for functional annotation, it was found that Zm00001d033231 and Zm00001d033234 were related to the growth and development of maize. 【Conclusion】 The candidate gene ZmDLE1 in the Bin1.09 region at the end of chromosome 1, was identified to effectively regulate maize plant height and ear height, and the target region was reduced to 600 kb by fine localization. Association analysis showed that Zm00001d033231 was genetic locus significantly associated with plant height within the target region.

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    Effects of Reducing Nitrogen Application Rate on the Yields of Three Major Cereals in China
    DU WenTing,LEI XiaoXiao,LU HuiYu,WANG YunFeng,XU JiaXing,LUO CaiXia,ZHANG ShuLan
    Scientia Agricultura Sinica    2022, 55 (24): 4863-4878.   DOI: 10.3864/j.issn.0578-1752.2022.24.007
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    【Objective】 The present study investigated the effects of reducing nitrogen application rate on the yields of three major cereals in China and its relationship with soil and other factors, so as to clarify the feasibility of reducing nitrogen application. 【Method】 90 published papers from 2010 to 2021 were collected and analyzed the effects of different nitrogen fertilizer reduction ratios on yield, and its relationship with planting systems and different conditions (fertilizer type, soil organic matter content, total nitrogen, soil pH, and water management). 【Result】 Compared with conventional fertilization rate, 0-40% nitrogen reduction did not significantly reduce the yield of rice, 0-30% nitrogen reduction did not significantly affect the yields of wheat and maize, when the nitrogen reduction was 30%-40%, the yield of wheat and maize significantly reduced by 6.1% and 5.4%, respectively. The yield level without nitrogen input area did not significantly affect crop yield of the three cereals following reduction of nitrogen rate. When soil total nitrogen was more than 2 g·kg-1, rice yield with reduced nitrogen application (6.5 t·hm-2) was significantly higher than that with conventional nitrogen application (6.3 t·hm-2); when total nitrogen was more than 1 g·kg-1, wheat yield with reduced nitrogen application (6.9 t·hm-2) was significantly lower than that with conventional nitrogen application (7.4 t·hm-2); when total nitrogen was more than 1.5 g·kg-1, maize yield with reduced nitrogen application (8.8 t·hm-2) was significantly lower than that with conventional nitrogen application (9.1 t·hm-2). When soil organic matter content was more than 30 g·kg-1, rice yield with reduced nitrogen application (6.9 t·hm-2) was significantly higher than that with conventional nitrogen application (6.7 t·hm-2), but soil organic matter content were 10-20 g·kg-1 and more than 20 g·kg-1, the reducing nitrogen application significantly reduced wheat yield. When soil pH was lower than 6.5, rice yield with reduced nitrogen application (6.6 t·hm-2) was significantly higher than that with conventional nitrogen application (6.4 t·hm-2). Wheat yield (6.6 t·hm-2) with reducing nitrogen application under single cropping was significantly higher than that with conventional nitrogen application (5.9 t·hm-2); maize yield (8.9 t·hm-2) with reducing nitrogen application under double cropping was significantly lower than that with conventional nitrogen application (9.1 t·hm-2). Based on common fertilizer, wheat yield with reducing nitrogen application (6.8 t·hm-2) was significantly lower than that with conventional nitrogen application (7.1 t·hm-2). Under rainfed, wheat yield with reducing nitrogen application (5.9 t·hm-2) was significantly lower than that with conventional nitrogen application (6.6 t·hm-2). 【Conclusion】 The yield of three major cereals in China can be maintained by reducing conventional nitrogen application rate by 30% although crop yield varied to certain extent with soil properties and management measures. Therefore, the reduced application of nitrogen fertilizer needed to be adjusted according to soil properties and management practices to achieve high yield and high nitrogen efficiency.

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    Genome-Wide Association Study of Yield Component Traits in Upland Cotton (Gossypium hirsutum L.)
    WANG Juan, MA XiaoMei, ZHOU XiaoFeng, WANG Xin, TIAN Qin, LI ChengQi, DONG ChengGuang
    Scientia Agricultura Sinica    2022, 55 (12): 2265-2277.   DOI: 10.3864/j.issn.0578-1752.2022.12.001
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    【Objective】The loci, elite alleles and candidate genes associated with yield component traits, such as boll weight, lint percentage, number of bolls per plant and seed index, were explored using a genome-wide association analysis (GWAS), which provided a theoretical reference for the molecular breeding of cotton yield.【Method】The GWAS based on a mixed linear model was performed on 408 upland cotton accessions grown in six different environments using the Cotton SNP 80K chip for the four yield component traits, and the significant SNP loci (SNPs) and elite allele were also detected. Finally, on the basis of the gene expression levels of the transcriptome, candidate genes related to the target traits were mined within a 1 Mb genome range of the flanking sequences of the significant SNPs. 【Result】The four yield component traits showed wide phenotypic variations in different environments, with the maximum coefficient of variation for number of bolls per plant being 16.67%-22.66%. The heritability of each trait was between 48.4% and 92.2%. The correlations among traits were significant or highly significant, except between boll weight and lint percentage. A total of 23 significant SNPs distributed in seven different genomic regions associated with the four traits were identified across the 408 cotton accessions in the BLUP. The numbers of loci associated with boll weight, lint percentage, number of bolls per plant and seed index were 5, 1, 9 and 8, respectively, and three loci (TM21094, TM21102, and TM57382) were associated with multiple target traits simultaneously. Seven elite allele types, TM21099(TT), TM57382(GG), TM78920(CC), TM53448(TT), TM59015(AA), TM43412(GG) and TM69770(AA), were identified. A total of 158 candidate genes potentially related to yield formation were selected through an analysis of gene expression patterns in RNA-Seq data. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that the functions and metabolic pathways of most genes were varied.【Conclusion】In this study, 23 significant SNPs associated with four yield component traits were identified across 408 cotton accessions, and 158 candidate genes were predicted using RNA-Seq.

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    Genome-Wide Identification of DIR Family Genes in Tomato and Response to Abiotic Stress
    CHEN FengQiong, CHEN QiuSen, LIN JiaXin, WANG YaTing, LIU HanLin, LIANG BingRuoShi, DENG YiRu, REN ChunYuan, ZHANG YuXian, YANG FengJun, YU GaoBo, WEI JinPeng, WANG MengXue
    Scientia Agricultura Sinica    2022, 55 (19): 3807-3821.   DOI: 10.3864/j.issn.0578-1752.2022.19.010
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    【Objective】 The aim of this study was to identify all members of tomato DIR gene family, and to predict and analyze their gene structures, physicochemical properties of proteins, phylogenetic relationship, chromosome location, collinearity analysis, promoter elements, expression pattern, prediction of interacting transcription factors and endogenous competitive RNA, so as to provide a reference for exploring the role of DIR in tomato growth and development and response to environmental stresses. 【Method】 The family members of DIR were identified in the whole genome level by bioinformatics methods. The chromosome location, conserved motif, cis-acting element, transcription factors, miRNA and circRNA were analyzed with Phytozome, MEME, PlantCARE, opsRNATarget and plantcircnet, respectively. Chromosome location map, evolutionary tree, relationship map between DIR and transcription factors, ceRNA network, and etc., were drown using Maptea, TBtools, Cytoscape and Omicshare. The expression level of DIR under environmental stresses was studied by NCBI gene database, transcriptome sequencing and qRT-PCR. 【Result】 27 members of DIR family were identified from the whole genome of the tomato, which were named SlDIR1-SlDIR27, and DIR genes of the tomato were located on 12 chromosomes, most of which were located at the end of chromosomes. The gene structures, motifs and domains were relatively conservative, and the classical structure of one exon existed in 22 SlDIR genes. The collinear relationship of DIR genes between tomato and Arabidopsis was much higher than that of rice and soybean. Based on the phylogenetic relationship, 27 DIR members of tomato were divided into three different subfamilies. The tissue specific expression analysis revealed that transcription levels of DIR members of tomato were higher in root. In addition, the promoter region of these genes contained multiple cis-acting elements related to abiotic stress, including drought, low temperature, and hormone induction, such as MeJA, ABA and SA. Hormone, growth and abiotic stress related to transcription factors (ERF, E2F / DP and MYB) were also predicted. Combined with our transcriptome data of pesticide stress and published transcriptome data analysis, the expression level of 5, 10, 10 and 13 SlDIR genes was significantly up-regulated after pesticide, drought, salt and cold stress. And SlDIR23 was induced by all the four stresses, while SlDIR8, SlDIR13 and SlDIR20 were specifically responded to the induction of cold stress, and SlDIR17 specifically responded to salt stress. Finally, the ceRNA regulation of tomato DIR showed that miR-156 might interacted with the target gene SlDIR8 to regulate tomato against stresses. 【Conclusion】 A total of 27 DIR gene family members were identified from the tomato genome and unevenly distributed on 12 chromosomes, with high expression in roots. The expression of SlDIR1, SlDIR13, SlDIR14 and other genes was included by MeJA, ABA and SA and other hormone response elements, among which SlDIR6 only contained MeJA element, and SlDIR27 only contained SA response element. In addition, SlDIR2, SlDIR14, SlDIR23 and other genes were participated in drought, salt, low temperature and other stresses. Especially for SlDIR23, it could be activated under different stress treatments. In addition, DIR genes interacted with transcription factors and noncoding RNA to regulate the responses of tomato plants under stresses.

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    Cloning, Expression and Anti-TMV Function Analysis of Nicotiana benthamiana NbMBF1c
    YuXia WEN,Jian ZHANG,Qin WANG,Jing WANG,YueHong PEI,ShaoRui TIAN,GuangJin FAN,XiaoZhou MA,XianChao SUN
    Scientia Agricultura Sinica    2022, 55 (18): 3543-3555.   DOI: 10.3864/j.issn.0578-1752.2022.18.006
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    【Objective】Tobacco mosaic virus (TMV) is an important virus that harms crops such as Solanaceae, Cruciferae and Cucurbitaceae, causing great losses to agricultural production. The objective of this study is to obtain Nicotiana benthamiana multiprotein bridging factor 1c (MBF1c) by molecular cloning, clarify the antiviral function and mechanism of NbMBF1c by bioinformatics, cell biology and molecular biology methods, and to provide a theoretical basis for the antiviral breeding of crops.【Method】Based on the full-length NbMBF1c sequence reported in Sol Genomics Network, primers were designed to clone the full-length sequence of NbMBF1c. GeneDoc and MEGA X were employed to align the homologous protein sequences of NbMBF1c and other species. The gene characteristics and protein structure of NbMBF1c were analyzed by bioinformatics. The tissue expression and its expression after TMV infection were detected by real-time fluorescence quantitative PCR (qRT-PCR). Tobacco rattle virus (TRV)-induced gene silencing technology was used to silence NbMBF1c and determine its effect on TMV-GFP infection. The transient overexpression vectors of pART27-GFP-NbMBF1c and pART27-Myc-NbMBF1c were constructed and the fusion protein GFP-NbMBF1c was expressed in N. benthamiana leaf to observe its subcellular localization under confocal microscope. Myc-NbMBF1c was expressed and the changes of TMV-GFP infection after NbMBF1c expressed were observed. qRT-PCR was employed to detect the expression of hormone related genes after NbMBF1c silencing, and the mechanism of NbMBF1c affecting virus infection was analyzed.【Result】NbMBF1c, which is 441 bp in full length, encodes 146 amino acids and contains a conserved domain HTH (helix-turn-helix). Phylogenetic analysis showed that NbMBF1c had the most closely relationship with Nicotiana tomentosiformis MBF1c (XP_009614458.1). NbMBF1c was localized in the cytoplasm and nucleus and had specific tissue expression, with the highest expression in roots, followed by stems, leaves and flowers. Silencing of NbMBF1c in N. benthamiana significantly reduced the tobacco plant height and promoted TMV-GFP infection, on the 5th day after TMV-GFP inoculation, the virus content of new leaf in the silencing treatment was higher than that in the control group. Transient overexpression of Myc-NbMBF1c suppressed TMV-GFP infection, after inoculation with TMV-GFP, virus infection was reduced. However, NbMBF1c did not interact with TMV components, but silencing NbMBF1c up-regulated the expression of abscisic acid (ABA) related gene NCED3, PYL1, ABAI, and SnRK2E and jasmonic acid (JA) synthesis pathway AOS1, while down-regulated the expression of JA signaling pathway receptor COI1.【Conclusion】NbMBF1c is mainly located in cytoplasm and nucleus, and acts as a positive regulator to inhibit TMV infection in N. benthamiana. NbMBF1c does not inhibit viral infection by directly interacting with TMV components, but by regulating phytohormone production and signal transduction.

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    The Genetic Basis of Flavonoid Contents in Wheat and Its Application in Functional Wheat Variety Breeding
    CHEN Jie, CHEN Wei
    Scientia Agricultura Sinica    2023, 56 (13): 2431-2442.   DOI: 10.3864/j.issn.0578-1752.2023.13.001
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    Accompanying the elevated expenses on consumption, people’s urge upon food has been gradually changed from “eat to be fed” to “eat to be satisfied” and further to “eat to gain nutrition” and “eat to be healthy”. Accordingly, breeders considered the wheat breeding goals should be set as breeding wheat with better quality along with higher yield, wherein the phrase “functional wheat variety” was recently raised. Flavonoids comprise one of the most widely reported categories of metabolites, the contents of which have been included within the “functional wheat variety” breeding program for its connection with plant phenotypes and its contribution to human health. The combination of metabolomics approach and genetics design has been proved to be efficient in identifying the candidates that responsible for metabolite contents, that said its application in wheat was lagged behind due to the lately released wheat reference genome. Further, the deficient knowledge upon the genetic basis of metabolites has in turn constrained the application of breeding “functional wheat variety”. In the current manuscript, the research progresses on genetic basis of flavonoids are briefly summarized, and its application for wheat breeding is highlighted. Meanwhile, the metabolomics-assisted breeding frame is concepted. Ultimately, the “functional wheat variety” breeding program will be achieved through the combination of the fundamental researches and breeding applications.

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    Non-Starch Polysaccharide Enzymes Cocktail of Corn-Miscellaneous Meal-Based Diet Optimization by In Vitro Method and Its Effects on Intestinal Microbiome in Finishing Pigs
    DENG FuLi,SHEN Dan,ZHONG RuQing,ZHANG ShunFen,LI Tao,SUN ShuDong,CHEN Liang,ZHANG HongFu
    Scientia Agricultura Sinica    2022, 55 (16): 3242-3255.   DOI: 10.3864/j.issn.0578-1752.2022.16.014
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    【Objective】 The objective of this study was to optimize the non-starch polysaccharide (NSP) enzymes cocktail of the corn-miscellaneous meal-based diet for finishing pigs by using in vitro simulation method, and to analyze the effects of the optimal NSP enzymes cocktail (OEC) on dietary nutrient digestibility and intestinal microbial composition and structure of finishing pigs. Finally, it could provide data support and theoretical reference for efficient utilization of diets and precise feeding. 【Method】 In experiment 1, different levels of six NSP enzymes (xylanase, β-glucanase, cellulase, α-galactosidase, β-mannanase, and pectinase) were individually and respectively added to the corn-miscellaneous meal-based diet of finishing pigs. Then, in vitro ileal dry matter digestibility (IVIDMD) was determined by gastric-small intestinal simulation digestion method in vitro. When IVIDMD reached the maximum, the supplemental level of each NSP enzyme was the coding level of NSP enzyme 0. In vitro digestion experiments were carried out according to the six-element quadratic regression orthogonal rotation combination design. Meanwhile, the optimal NSP enzymes cocktail (OEC) of the corn-miscellaneous meal-based diet was selected by establishing the six-element quadratic regression equation between IVIDMD and the supplemental level of NSP enzymes. The in vitro dry matter digestibility (IVDMD), in vitro gross energy digestibility (IVGED) and in vitro digestible energy (IVDE) of diets before and after OEC addition were determined by gastric-small intestinal-large intestinal simulation digestion method in vitro to verify the effect of OEC. In experiment 2, 16 healthy castrated barrows (117.8 ± 1.66 kg) with similar body weight were randomly divided into two groups with eight pigs in each group. The pigs in the control group were fed the corn-miscellaneous meal-based diet, and the pigs in the enzyme-addition group were fed the basal diet supplemented with OEC. On the 18th day of the experiment, the fresh feces of pigs were collected by rectal wiping method, and the diversity and relative abundance of fecal microbiome were analyzed by high-throughput sequencing analysis of 16S rRNA gene, and the function was predicted. 【Result】 (1) Under the conditions of this experiment, the optimized NSP enzymes cocktail of corn-miscellaneous meal-based diet was as follows: cellulase 1 003 U·kg-1, xylanase 18 076 U·kg-1, β-glucanase 1 377 U·kg-1, β-mannanase 14 765 U·kg-1, α-galactosidase 337 U·kg-1, and pectinase 138 U·kg-1. (2) Adding NSP enzymes cocktail optimized by in vitro method in corn-miscellaneous meal-based diet significantly increased the IVDMD from 73.44% to 76.26% (P<0.01), the IVGED from 74.03% to 76.45% (P = 0.01), and the IVDE from 14.97 MJ·kg-1 to 15.58 MJ·kg-1 (P<0.01). (3) At the phylum level, a total of 12 phyla with relative abundances greater than 0.1% were selected, among which Bacteroidetes, Firmicutes, and Spirochetes were the dominant phyla, and the sum of these three phyla accounted for more than 96% in the group. (4) At the genus level, adding OEC in the diet significantly increased the relative abundance of Norank_F_F082, Norank_F_Bacteroidales_ RF16_group, Bacteroides and Roseburia (P<0.05), and Eubacterium_ruminantium_group (P = 0.083) had an increasing trend, while the relative abundance of Oscillibacter decreased significantly (P<0.05), and Clostridium_Sensu_Stricto_1 and Norank_F__Norank_O__ WCHB1-41 (P = 0.083) showed a decreasing trend (P = 0.052). 【Conclusion】 Dietary non-starch polysaccharide enzymes cocktail optimization by in vitro method increased in vitro digestibility of dry matter and energy and in vitro digestible energy of corn-miscellaneous meal-based diets in finishing pigs. It also increased the proportion of beneficial bacteria in intestinal microorganism, such as fiber decompose bacteria and butyric acid producing bacteria, and reduced the number of harmful bacteria to a certain extent, and optimized intestinal microecology.

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    Genome-Wide Identification and Expression Analysis of XTH Gene Family in Peach Fruit During Storage
    GUO ShaoLei, XU JianLan, WANG XiaoJun, SU ZiWen, ZHANG BinBin, MA RuiJuan, YU MingLiang
    Scientia Agricultura Sinica    2022, 55 (23): 4702-4716.   DOI: 10.3864/j.issn.0578-1752.2022.23.011
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    【Objective】 The aim of this study was to identify members of the XTH gene family from peach, and to analyze the expression of PpXTHs in peach fruit with different textures during storage, which not only provided data for the research on the candidate PpXTHs involved in peach fruit softening, but also laid the foundation for further study on the PpXTHs function in peach fruit softening.【Method】 The HMM profiles of the Glyco_hydro_16 domain and XET_C domain were used to search all XTH proteins with the Hmmer 3.1 software in the peach protein database. The molecular weight, theoretical isoelectric point and other physicochemical properties were then predicted by the online tool ProtParam. PpXTHs subcellular localization were predicted by the online software Plant-mPLoc. The MEGA 11 software was used to construct a phylogenetic tree. The online tool MEME was used to analyze conserved motifs, the conserved motifs, conserved protein domains and gene structure maps were draw by Tbtools. According to the PpXTH gene family location information, chromosome mapping was carried out with MapChart software. The expressions of PpXTHs in peach fruit with different textures during storage were monitored by qRT-PCR..【Result】 A total of 27 PpXTH genes were systematically identified from peach, which were distributed on seven chromosomes. Based on the phylogenetic tree, the ancestral group, Ⅰ/Ⅱ subfamily, ⅢA subfamily and ⅢB subfamily were classified. In addition, according to the analysis of protein domains, all PpXTH gene family proteins had Glyco_hydro_16 and XET_C conserved domain. The results from qRT-PCR analysis showed that PpXTH33 belonging to the ⅢB subfamily was upregulated as the storage period increased in melting peach fruit, with the expression being markedly higher than that during the storage period of stony hard peach fruit. The positive clone sequencing was consistent with the coding sequence of the Prunus persica reference genome with a length of 924 bp for a 307 amino acid sequence. The PpXTH33 combined with green fluorescent protein may mainly located in the cell wall and nucleus detected by confocal laser scanning microscopy..【Conclusion】 All 27 PpXTHs protein structures contained two highly XTH conserved domains and the genes were distributed on seven chromosomes. The expression characteristics of PpXTH33 in peach fruit with different flesh textures during storage suggested that PpXTH33 was closely associated with peach fruit softening during storage.

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    Comprehensive Evaluation and Breeding Evolution of Early Maturing Upland Cotton Varieties in the Northwest Inland of China
    WANG CaiXiang,YUAN WenMin,LIU JuanJuan,XIE XiaoYu,MA Qi,JU JiSheng,CHEN Da,WANG Ning,FENG KeYun,SU JunJi
    Scientia Agricultura Sinica    2023, 56 (1): 1-16.   DOI: 10.3864/j.issn.0578-1752.2023.01.001
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    【Objective】This paper evaluated comprehensively early maturity upland cotton varieties in northwest inland cotton-growing region of China, and uncovered the evolution rules of the main traits from the breeding cultivars in the region. It provides a useful reference for recommendation and breeding of main cotton varieties in northwest inland region. 【Method】A total of 110 early-maturing upland cotton varieties which were approved in northwest inland cotton-growing region from 1988 to 2021 were applied, and phenotypic identification of 12 main traits related to early maturity, yield, fiber quality and plant architecture was carried out in Dunhuang, Gansu province and Shihezi, Xinjiang Production and Construction Corps in 2020 and 2021, respectively. Clustering analysis, correlation analysis and principal component analysis were respectively used to evaluate the phenotypic characteristics of the cultivars, and carry out the breeding evolution analysis of their main traits. 【Result】The phenotype value of 12 main traits had large distribution range from 110 early-maturing upland cotton varieties in northwest inland cotton-growing region of China. The variation coefficient in descending order is: fruit branch length (FBL), boll number per plant (BN), boll opening rate (BOR), boll weight (BW), fiber micronaire (FM), fiber strength (FS), lint percentage (LP), fiber length (FL), flowering time (FT), fruit branch angle (FBA), fiber elongation (FE), and fiber uniformity (FU). By cluster analysis, these cultivars were divided into four groups: Ⅰ, Ⅱ, Ⅲ and Ⅳ, which were the population of high fiber quality, early maturity, loose plant type and high yield, respectively. Correlation analysis showed that early maturity was negatively correlated with yield and fiber quality related to traits, while the yield related to traits were positively correlated with the fiber quality traits, and most of them reached significant or extremely significant level. The 12 main traits were simplified into four principal components which had cumulative contribution rate of 66.92%. Based on the comprehensive evaluation results of these varieties by principal components, an excellent cultivar Zhongmian 113 ranked the first in the 110 early-maturing upland cotton varieties with a score of 0.67, which was characterized by early maturity, high yield and excellent fiber quality, and relatively loose plant type. Additionally, it was found that the early maturity character of cotton varieties approved in Gansu province was significantly better than that of varieties approved in northwest inland region and Xinjiang province, and the traits related to yield and fiber quality of cotton varieties approved in Gansu province were significantly lower than those of varieties approved in northwest inland region and Xinjiang province. During the breeding evolution of early maturing upland cotton varieties in northwest of China for more than 30 years, most of the traits related to yield and fiber quality showed significant upward trends, and the plant type was becoming more compact. BN was negatively correlated with BW, LP, FL and FS in early cultivars, while BN was positively correlated with BW, LP, FL and FS in recent cultivars. 【Conclusion】In the process of breeding and improvement of early maturing upland cotton varieties in northwest of China, the main traits related to yield and fiber quality had wide distribution, and they had significant improvement trends year by year. In the recently developed varieties, BN, FL and FS had been improved cooperatively.

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    Epidemiological Investigation of Respiratory Pathogens in Deceased Fattening Pigs in Major Pig Farming Area of Middle and Eastern China and Characterization of Pasteurella multocida
    LUO SuXian, ZHOU Hong, LIN HuiXing, FAN HongJie
    Scientia Agricultura Sinica    2024, 57 (11): 2254-2264.   DOI: 10.3864/j.issn.0578-1752.2024.11.016
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    【Objective】This study aims to isolate and identify prominent bacterial respiratory pathogens from samples collected from fattening pigs that have died from respiratory diseases in major domestic pig farming area of middle and eastern China. And identifying these bacterial pathogens will offer valuable evidence for preventing and controlling the significantly prevalent respiratory diseases in recent years. Moreover, the characteristics of Pm were identified, providing reference for the development of Pm vaccines.【Method】The lungs of pigs died from respiratory disease were collected from large-scale farms in major pig farming area of middle and eastern China from 2021 to 2023. Blood agar and TSA were employed for the isolation of pathogens, which were then identified through microbiological and molecular biology methods. Additionally, MLST typing and virulence testing in mice were conducted on Pm isolates. The primers for PCR against seven housekeeping genes of adk, est, gdh, mdh, pgi, pmi and zwf of Pm were designed. Then the productions of amplicons were sequenced and submitted to perform MLST typing. The capsule and lipopolysaccharide typing were detected by PCR. The virulence factor genes were detected by PCR. Single isolates of A type and selected D and F types of Pm were evaluated for virulence in ICR mice. LD50 of JS-65, JS-51 and JS-34 were detected in ICR mice.【Result】A total of 73 Pm isolates were obtained, with an isolation rate of 15.53%. Additionally, 71 SS isolates, 29 APP isolates, and 10 GPS isolates were obtained, with isolation rates of 15.11%, 6.17%, and 2.13% respectively. The typing results indicated that the prevailing subtype among Pm isolates was A:L3, accounting for 55%. Among SS isolates, subtype 9 was the prevailing type, accounting for 38.03%. Among APP isolates, subtype 15 was the prevailing type, accounting for 51.72%. Among GPS isolates, subtype 5/12 was the prevailing type, accounting for 60.00%. Co-infection included Pm+SS, Pm+APP, SS+APP and Pm+APP+GPS, accounting for 16.67% of the total pig population. Three capsule types were isolated: A (67%), D (30%), and F (3%). Two lipopolysaccharide types were found: L3 (56%) and L6 (44%). Nine ST genotypes were identified: ST79, ST50, ST7, ST74, ST13, ST27, ST9, ST287, and ST370, with proportions of 33%, 26%, 16%, 10%, 4%, 4%, 3%, 3%, and 1%, respectively. The results of virulence gene detection showed that the positivity rates of ptfA, fimA, hsf-2, exbB, exbD, tonB, fur, nanH, sodA, and sodC genes were greater than 95%. The positivity rates of hsf-1, pfhA, tadD, hgbA, hgbB, pmHAS, ompA, ompH, oma87, and plpB genes ranged from 40% to 90%. The positivity rates of tbpA and nanB genes were between 10% and 30%; the toxA gene was not detected. The virulence test results indicated that all mice died when exposed to less than 102 CFU of strain A, the mortality rate of mice was between 60% and 100% when exposed to 103 CFU of strain D, and the mortality rate of mice was 60% when exposed to 5×103 CFU of strain F. LD50 of JS-65, JS-51, and JS-34 were detected in ICR mice, and the results showed that JS-65 LD50<10 CFU, and JS-51 LD50=6.3 × 102 CFU, JS-34 LD50=3.98 × 103 CFU.【Conclusion】Based on the bacterial pathogen isolates from 2021 to 2023, the primary pathogen bacterium of the respiratory tract in dead fattening pigs were Pm, SS, APP, and GPS. Pm had the highest number of isolates and isolation rate from lung tissue. The RIRDC identified a Pm strain of ST370 and extended MLST typing data in pigs. PCR typing results showed that the dominant serotype of Pm was A:L3:ST79, which exhibited the highest virulence in ICR mice with a minimum lethal dose of less than 10 CFU. These results serve as the foundation for the development of an inactivated Pm vaccine.

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    Genome-Wide Association Study of Cold Tolerance at the Germination Stage of Rice
    PANG HongBo, CHENG Lu, YU MingLan, CHEN Qiang, LI YueYing, WU LongKun, WANG Ze, PAN XiaoWu, ZHENG XiaoMing
    Scientia Agricultura Sinica    2022, 55 (21): 4091-4103.   DOI: 10.3864/j.issn.0578-1752.2022.21.001
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    【Objective】Rice is an important food crop, and its growth and development are most vulnerable at the germination stage. Under cold stress, direct-seeded rice exhibited significantly reduced germination rates (GRs) and yield compared with normally grown plants. Thus, a better understanding of genetic mechanisms regulating cold tolerance will enable to develop rice varieties with improved tolerance during germination. 【Method】238 representative rice germplasm resources from 14 countries worldwide were tested in phenotypic identification in Shenyang in 2021 and 2022; the low-temperature germination rate and relative low-temperature germination rate (LTGR and relative LTGR; 1-10 days under 15℃) were evaluated in an artificial climate incubator, and a 5-10 day LTGR histogram was constructed using R. The day suitable for GWAS was determined by phenotypic variation (Hill) and a mixed linear model combining LTGR and relative LTGR phenotype data with resequencing data. 【Result】LTGR histogram and phenotypic variation showed optimal GR on day 8 (Hill=0.84), i.e., it was higher than on other days (Hill=0.48-0.83), which could be used for GWAS. The principal component analysis results divided all germplasms into five groups—indica, aus, temperate japonica, tropical japonica, and aromatic. GWAS analysis of two indicators detected three identical significant single nucleotide polymorphisms (SNPs) related to cold tolerance in rice at the germination stage. These were located on chromosome 4, which could explain 11.9%-25.4% of the phenotype. In addition, 24 candidate genes were screened in the 50-kb region upstream and downstream of these three SNPs. Further linkage disequilibrium analysis and haplotype analysis were carried out and highly significant differences were found between different haplotypes of the LOC_Os04g24840 and LOC_Os04g25140 genes for cold tolerance. LOC_Os04g24840 was divided into five haplotypes by the coding region SNP, and Hap_3 was significantly more cold tolerant than Hap_1; LOC_Os04g25140 was divided into 18 haplotypes by the coding region SNP and the amino acid variation (S>L) at 77 bp was different in japonica and indica rice. These results showed that the genes encoding glycosyltransferases (LOC_Os04g24840) and F-box protein (LOC_Os04g25140) might be closely related to cold tolerance in rice.【Conclusion】 A total of three SNP loci were detected in 238 rice germplasm resources, and two candidate genes were screened for their association with cold tolerance during germination in rice.

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    Identification of Pathogenic Fusarium spp. Causing Maize Ear Rot and Susceptibility of Some Strains to Fungicides in Jilin Province
    CHAI HaiYan,JIA Jiao,BAI Xue,MENG LingMin,ZHANG Wei,JIN Rong,WU HongBin,SU QianFu
    Scientia Agricultura Sinica    2023, 56 (1): 64-78.   DOI: 10.3864/j.issn.0578-1752.2023.01.005
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    【Objective】The objective of this study is to clarify the population distribution of Fusarium spp. of maize ear rot in Jilin Province and the inhibitory effect of fungicides on the growth of Fusarium mycelium, and to provide a basis for the targeted control of maize ear rot. 【Method】149 samples of maize ear rot collected from 36 cities and counties in Jilin Province in 2020 were isolated and identified by tissue isolation and molecular biology methods. The specific toxin synthesis primers of related genes were synthesized using Fusarium graminearum species complex (FGSC) toxin. The toxigenic chemotypes were detected, and the pathogenicity of some FGSC was determined. The inhibitory effect of 7 fungicides on FGSC was determined by the mycelial growth rate method. 【Result】A total of 233 Fusarium strains were isolated, belonging to 4 Fusarium complex species, including 9 Fusarium species, which were F. verticillioides, F. boothii, F. graminearum, F. proliferatum, F. asiaticum, F. chlamydosporum, F. fujikuroi, F. equiseti and F. subglutinans. The isolation frequencies were 33.05%, 26.18%, 25.32%, 12.45%, 0.86%, 0.86%, 0.43%, 0.43% and 0.43%, respectively. The isolate frequency of FGSC was the highest, which was 52.36%, and it was the dominant pathogen of maize ear rot in Jilin Province. The proportions of F. boothii, F. graminearum and F. asiaticum in FGSC were 50.00%, 48.36% and 1.46%, respectively. The phylogenetic tree showed that the interspecific and intraspecific genetic diversity of FGSC was rich. The results of pathogenicity assay showed that 52.73% of FGSC were medium pathogenic strains. F. graminearum isolated from the main maize producing areas in the east had the strongest pathogenicity. Toxigenic chemotype detection showed that F. asiaticum produced nivalenol (NIV) chemotype, F. graminearum and F. boothii produced 15-acetyl-deoxynivalenol (15-AcDON) chemotype. The EC50 of the 7 fungicides for inhibiting the growth of FGSC ranged from 0.02 to 19.45 μg·mL-1. Fludioxonil (FS), imazalil (FS), flusilazole (EC), tebuconazole (TC) and myclobutanil (EW) had good inhibitory effects on FGSC and the difference was not significant. The EC50 of FGSC was less than 1.20 μg·mL-1 and EC90 was less than 100 μg·mL-1. The difference of EC50 between F. graminearum and F. boothii was significant under 30% pyraclostrobin treatment. The EC50 of F. graminearum was 10.24 times higher than that of F. boothii. 【Conclusion】The dominant pathogenic Fusarium of maize ear rot in different maize producing areas of Jilin Province is different. F. graminearum and F. boothii are dominant species in the east and west, and F. verticillioides is dominant species in the middle. The interspecific and intraspecific genetic diversity of FGSC is rich. Fludioxonil, imazalil, flusilazole, tebuconazole and myclobutanil have better antifungal effect on FGSC. There is no significant difference in the fungicides susceptibility among FGSC.

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    Identification of Adult Plant Stripe Rust Resistance Candidate Genes of YrZ501-2BL by Gene Association and Transciptome Analysis in Wheat (Triticum aestivum L.)
    ZHANG Xu, HAN JinYu, LI ChenChen, ZHANG DanDan, WU QiMeng, LIU ShengJie, JIAO HanXuan, HUANG Shuo, LI ChunLian, WANG ChangFa, ZENG QingDong, KANG ZhenSheng, HAN DeJun, WU JianHui
    Scientia Agricultura Sinica    2023, 56 (8): 1429-1443.   DOI: 10.3864/j.issn.0578-1752.2023.08.001
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    【Objective】Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), significantly reduced wheat production worldwide. Identification of stripe rust resistance genes is the foundation of improving wheat resistance breeding and revealing its genetic mechanism.【Method】A multi-omics approach combined with genome-wide association study (GWAS) was used for dissecting adult plant stripe rust resistance for wheat advanced breeding lines collected from International Maize and Wheat Improvement Center (CIMMYT) and International Centre for Agricultural Research in the Dry Areas (ICARDA) bread-wheat breeding programs. In the present study, a diversity panel of 411 wheat lines from CIMMYT and ICARDA was used for genome-wide association study and a major locus on chromosome arm 2BL was identified. In order to verify the stability of the locus, the resistant line Z501 with the resistance allele of the locus was crossed by the susceptible line Jinmai 79, and the locus tentatively named YrZ501 was successfully confirmed using linkage mapping based on F2:3 genetic population of Jinmai 79×Z501. Then we performed candidate gene analysis based on gene annotation, comparative genome, transcriptome and gene-based association analysis. 【Result】Combining GWAS and linkage mapping results, the YrZ501-2BL was located in the physical interval of 0.26 Mb (575.706-576.587 Mb) on chromosome 2B. According to the annotation information of Chinese Spring reference genome IWGSC v1.1, there were six high confidence genes of 12 genes in this region. Using online website, the target interval in the Chinese spring reference genome was compared with other published different ploidy wheat genomes. The six high-confidence genes within this interval can basically be found homologous in other wheat lines, and the genes arranged in the same order, indicating that the interval may not have large fragment insertions, deletions and inversions. The above results showed that we can perform candidate gene prediction analysis based on the reference genome information. After analysis of their transcriptomic data between the resistant parent Z501 and susceptible parent Jimai 79, only three genes, TraesCS2B02G406400, TraesCS2B02G406500 and TraesCS2B02G406600 showed variable expression levels and were induced by stripe rust infection. Further, they encode GATA transcription factor, SH3 domain-containing protein 2 and zinc finger protein, respectively. Gene-based association analysis revealed that there was a significant SNP (G1369A) in TraesCS2B02G406500 that was associated with stripe rust responses. Although this SNP (G1369A) did not cause amino acid coding changes (both TCG and TCA encode serine), it may be associated with alternative splicing. Moreover, it showed significant differences of the stripe rust responses between the different haplotypes (G1369A). Further analysis revealed two other variants G1377A and G1431A, that caused amino acid changes, i. e. valine (GTT) to isoleucine (ATT) and valine (GTG) to methionine (ATG), respectively. However, the two SNPs were rare variants as they accounting for only 0.87% of the 455 re-sequencing wheat accessions and they were not tested for significance. In summary, TraesCS2B02G406500 was preliminarily considered as an important candidate gene of YrZ501-2BL. In addition, the corresponding AQP markers were developed based on the SNPs among the YrZ501 candidate regions, which can be used to marker-assisted selection in molecular breeding application of wheat stripe rust resistance.【Conclusion】A candidate causal gene TraesCS2B02G406500 associated with stripe rust resistance was successfully identified on wheat chromosome 2B using an integrated method of multi-omics and association analysis, which laid a solid foundation for further gene cloning and functional verification.

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    The Relationship Between Mastication and Development of Segment Membranes in Citrus Fruits
    LI FeiFei, LIAN XueFei, YIN Tao, CHANG YuanYuan, JIN Yan, MA XiaoChuan, CHEN YueWen, YE Li, LI YunSong, LU XiaoPeng
    Scientia Agricultura Sinica    2023, 56 (2): 333-344.   DOI: 10.3864/j.issn.0578-1752.2023.02.010
    Abstract618)   HTML39)    PDF (5045KB)(166)       Save

    【Objective】 This study aimed to reveal the development of segment membrane, which contributed to citrus fruit mastication, so as to provide the theoretical basis for fruit mastication trait improvement. 【Method】 Using different citrus types (hybrid citruses including Ehime No. 30 and Nova, Okitsu Wase satsuma mandarin, navel oranges including Yuanfeng and Newhall, and pumeloes including Anjiang and Jiangyong) as reseach materials, the main physiological and biochemical properties of segment membrane were analyzed by comparisons in tissue development and cell ultrastructure. 【Result】 The rough outside but smooth inside of segment membrane occurred in all citrus types. Obviously waxy layer grew on the inside of segment membrane under which one or two cell layers with thickened cell wall arranged neatly. Cell density decreased gradually from inside to outside in segment membrane. Occurrence of wax layer in the inside and morphological changes of cells under the wax layer emblematized the maturation of citrus segment membrane. For pomelo, the thickest segment membrane linked with the worst mastication was caused from a large number of cell layers, enlarged cell size and more pectin in segment membrane. At early fruit development from squaring stage to flower withering stage, the ventricles differentiated already in the ovary, and the intervals between ventricles would develop into segment membranes. In the period, parenchyma cells in the intervals exhibited equal cell size and arranged neatly, having no segment membrane characteristics. With fruit enlargement and maturation, the segment membranes of Shatian pomelo had the most cell layers and the longest cell wall thickening period. Segment membranes of Shatian pomelo showed significantly higher pectin content than that of Yuanfeng navel orange and Juxiangzao Satsuma mandarin. Segment membranes of Yuanfeng navel orange had medium cell layers and moderate cell wall thickening period, in which protopectin was higher than that of Juxiangzao Satsuma mandarin. The segment membranes of Juxiangzao exposed the least cell layers and the shortest cell wall thickening period. In October when Juxiangzao matured, segment membrane protopectins in Shatian pomelo, Yuanfeng navel orange and Juxiangzao Satsuma mandarin were 364.22, 208.48 and 165.39 mg·g-1, respectively, with Shatian pomelo reaching 74.7% and 120.2% higher than another two varieties. 【Conclusion】 Segment membrane thickness, cell layers in segment membrane and degree of cell wall thickening associated with citrus fruit mastication. Pectin content could reflect the mastication of citrus segment membranes.

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    Screening of Mycobacterium Avium Subsp. Paratuberculosis Immunogenic Proteins and Its Evaluation of Immunological Effect
    CHEN FanRuo, ZHANG JiaJun, LU Ping, CUI Ning, CUI YingYing, CUI ZiYin, DANG GuangHui, LIU SiGuo
    Scientia Agricultura Sinica    2024, 57 (6): 1204-1214.   DOI: 10.3864/j.issn.0578-1752.2024.06.014
    Abstract616)   HTML12)    PDF (3113KB)(300)       Save

    【Background】 Paratuberculosis (PTB) is a chronic, wasting infectious disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) in ruminants. PTB causes huge economic losses to the livestock industry and poses a serious threat to public health safety. Since the current clinical methods for the detection and control of PTB are inadequate, and the PTB vaccine used is ineffective and interferes with the diagnosis of bovine tuberculosis, there is a need for developing a vaccine with strong immunogenicity, good safety, and excellent protection for the prevention and control of PTB. 【Objective】 The immunogenic protein of MAP was screened and its immunoprotective effect was evaluated, so as to provide the data support for the prevention and control of PTB. 【Method】 Five recombinant plasmids were constructed based on six genes of MAP: p22, map1272c, map3531c, map3783, map3701c, and map3527. The five recombinant proteins were combined with MONTANIDE ISA 61 VG adjuvant to immunize mouse by subcutaneous injection, and the best immunogen was screened by IFN-γ ELISPOT assay. The best immunogen was then mixed with the reported 66NC fusion protein. Mouse were immunized by subcutaneous multi-point injection. At 3 weeks after the second immunization, mice were immunized with 1×108 CFU of the MAP K-10 strain intraperitoneally. The immunogenicity and immunoprotective effect of the candidate subunit vaccine were comprehensively evaluated by IFN-γ ELISPOT assay, monitoring antibody titers and serum cytokines, as well as detecting weight changes, liver pathological and histopathological observations and charge count differences of infected mouse. 【Result】 Five recombinant proteins, such as 58F, 62F, 69F, 46F, and 52F, were expressed based on the genes p22, map1272c, map3531c, map3783 and map3701c. 58F produced the highest level of IFN-γ after immunization and was the most promising candidate immunogen. The fusion protein combination 66NC+58F induced persistent high titers of IgG, IgM, IgG1 and IgG2a, and also induced specific release of IFN-γ, TNF-α, and IL-17A. In the evaluation of protective effects, the fusion protein combination 66NC+58F resisted the weight loss caused by MAP infection, significantly reduced pathological damage in the liver, and decreased MAP colonization in the liver. 【Conclusion】 The fusion protein combination 66NC+58F induced Th1 and Th17-type immune responses in mouse, provided immune protection against MAP infection and was an important candidate subunit vaccine for PTB.

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    Spatial-Temporal Variation of Cultivated Land Soil Basic Productivity for Main Food Crops in China
    LI YuHao,WANG HongYe,CUI ZhenLing,YING Hao,QU XiaoLin,ZHANG JunDa,WANG XinYu
    Scientia Agricultura Sinica    2022, 55 (20): 3960-3969.   DOI: 10.3864/j.issn.0578-1752.2022.20.008
    Abstract615)   HTML56)    PDF (473KB)(267)       Save

    【Objective】 Soil basic productivity is the cornerstone of realizing high and stable yield for food crops. The temporal change trends and spatial variation characteristics of cultivated land productivity for main food crops were defined, so as to provide the important theoretical support for ensuring food security and improve cultivated land quality in China. 【Method】 In this study, based on the national long-term positioning monitoring network of cultivated land quality from 1988 to 2019, the long-term monitoring data of the check area were selected with non-fertilization treatment and the conventional area with farmers' fertilization treatment in the first 3-5 years since the establishment of each monitoring point. The temporal and spatial changes in yield of maize, rice and wheat and soil productivity contribution rates were analyzed in China. 【Result】 In the past 30 years, the grain crops’ yield and soil productivity contribution rates showed an overall increasing trend with time, and the annual growth rate of crop yield showed the change law of non-fertilizer area < conventional area, rice < wheat < maize. The yield of maize, wheat and rice in the non-fertilizer area increased from 2 370, 1 712 and 3 111 kg·hm-2 in 1988 to 4 852, 3 258 and 4 167 kg·hm-2 in 2019, respectively, and increased by 104.7%, 90.2% and 34.0%, respectively. The yield of maize, wheat and rice in the conventional area increased from 5 356, 3 296 and 5 970 kg·hm-2 in 1988 to 8 859, 6 515 and 7 825 kg·hm-2 in 2019, respectively, with the increment of 65.4%, 97.6% and 31.0%, respectively. The contribution rate of soil productivity for the three major food crops in China from 2015 to 2019 was 52.7%, which was significantly increased by 7.3% compared with 45.4% in 1988-1994. Among them, the contribution rate from maize was 54.3%, which was 12.2% higher than that of 42.1% in 1988-1994. The contribution rate from rice was 53.3%, which was 6.7% higher than that of 46.6% in 1988-1994. The soil productivity contribution rate from wheat increased with the year as a whole, and was lower than that in maize and rice as a whole. The spatial distribution of soil productivity contribution rate for the three major grain crops was quite different. The Northeast region and Yellow River and Huaihai region were higher, which were 56.5% and 54.1%, respectively, followed by the Southwest region and South region, which were 53.7% and 52.9%, respectively. Gan Xin region and Qinghai-Tibet region were the lowest, only 38.7% and 40.4%, respectively. The random forest model was used to rank the soil factors affecting the basic soil productivity contribution rate in the three major grain crop systems. Among them, soil available potassium, organic matter content and soil bulk density were the key factors affecting the spatial distribution of maize basic soil fertility contribution rate; soil available phosphorus, available potassium and organic matter content were the key factors affecting the spatial distribution of wheat basic soil fertility contribution rate; soil pH, soil available phosphorus and organic matter content were the key factors affecting the spatial distribution of rice basic soil fertility contribution rate.【Conclusion】 Over the past 30 years, the soil basic productivity for three major grain crops in China has been continuously improved, but there were great differences among regions and the overall level was still low, which was far lower than that of developed countries in Europe and United States. Soil available potassium content, soil available phosphorus content and soil pH are the most key factors affecting the spatial distribution of basic soil fertility contribution rate of maize, wheat and rice, respectively.

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    Mining of Genetic Locus of Maize Stay-Green Related Traits Under Multi-Environments
    CHANG LiGuo,HE KunHui,LIU JianChao
    Scientia Agricultura Sinica    2022, 55 (16): 3071-3081.   DOI: 10.3864/j.issn.0578-1752.2022.16.001
    Abstract600)   HTML270)    PDF (2062KB)(580)       Save

    【Objective】 Functional stay-green is generally considered a desirable trait in major crop varieties including maize. Finding new loci and candidate genes related to stay-green, and providing new theoretical basis for the genetic research on stay-green. 【Method】Using 150 recombinant inbred lines (RIL) populations derived from the cross between Xu 178 and K12, QTL mapping of three stay-green related traits (visual stay green (VSG), green leaf number at silking stage (GLNS) and green leaf number at mature stage (GLNM) were performed by the composite interval mapping(CIM)method of Windows QTL Cartographer V2.5. Besides, an association population, which composed of 139 natural materials genotyped with 50790 high-quality SNP markers, was used to dissect genetic locus of three traits by genome-wide association study (GWAS) based on the mixed linear model MLM). 【Result】Based on CIM, three traits (GLNM, GLNS and VSG)were mapped using phenotypic values in a single environment and best linear unbiased prediction (BLUP) value. A total of 37 QTLs were detected on all chromosomes except Chromosome 10, and the LOD score ranged from 2.58-11.36, with a phenotypic variation contribution rate of 4.34%-22.40%. Among them, 14, 12 and 11 loci were detected for GLNM, GLNS and VSG traits, respectively. Four of the QTLs, qGLNS2-1, qVSG1-1, qVSG1-2 and qVSG7-1, were genetically stable and were detected simultaneously in three or more different single environments. GWAS was performed on three stay-green related traits using MLM, and a total of 44 significant SNPs above the threshold line were detected. According to the physical position of SNP markers in the B73 reference genome, a total of 15 SNP were found to fall into the QTL interval mapped by linkage analysis. 【Conclusion】Combined with the results of QTL mapping and genome-wide association study, a total of 4 genetically stable colocalization genetic regions were detected (the corresponding physical position intervals on the B73 reference genome version 4 are 6.2-8.2 Mb on chromosome 1, 209.1-221.4 Mb on chromosome 2, 96.8-102.1 Mb on chromosome 6, and 4.9-11.4 Mb on chromosome 7), and four important candidate genes (Zm00001d006119, Zm00001d018975, Zm00001d006535 and Zm00001d036763) related to photosynthesis and stress response were mined.

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    QTN Mining and Candidate Gene Screening of Upland Cotton (Gossypium hirsutum L.) Seed-Related Traits
    BAI BingNan, QIAO Dan, GE Qun, LUAN YuJuan, LIU XiaoFang, LU QuanWei, NIU Hao, GONG JuWu, GONG WanKui, ELAMEER ELSAMMAN, YAN HaoLiang, LI JunWen, LIU AiYing, SHI YuZhen, WANG HaiZe, YUAN YouLu
    Scientia Agricultura Sinica    2024, 57 (15): 2901-2913.   DOI: 10.3864/j.issn.0578-1752.2024.15.001
    Abstract597)   HTML119)    PDF (3621KB)(564)       Save

    Objective】Exploring the genetic loci and related genes that control cottonseed size traits to lay a foundation for subsequent study on the molecular mechanism cottonseed size formation. 【Method】The upland cotton recombinant inbred line (RIL) population composed of 300 lines was used as the research material. Seven phenotypic traits including cottonseed index (SI), seed length-cutting acreage (SLA), seed length-cutting perimeter (SLP), seed length (SL), seed width (SW), length-width ratio (LWR) and seed roundness (SR) were evaluated in four environments. The RIL population was genotyped by liquid phase chip strategy. The high-quality single nucleotide polymorphism (SNP) markers and phenotypic data were subjected to perform genome-wide association study (GWAS), and quantitative trait nucleotides (QTNs) associated with cottonseed size-related traits were mined. The genetic effects of QTNs were analyzed to identify candidate genes. 【Result】Seven cottonseed size-related traits showed a continuous normal distribution in four environments, which expressed a sizable phenotypic variation. The coefficient of variation ranged from 1.82% to 10.70%. The influencing effect on trait formation were basically as genotype>environment>genotype × environment, indicating suitability for GWAS analysis of these results. Correlation analysis showed that the seed index was significantly correlated with SLA, SLP, SL and SW, and LWR was significantly correlated with SR, indicating the possible existence of pleiotropic loci. GWAS was performed using the 3VmrMLM model, and a total of 47 QTNs were associated with these seven traits. A total of 11 QTNs were associated on chromosome A07, of which three physical loci in the region of 71.99-72.87 Mb, A07:71993462, A07:72067994 and A07:72198802 were very close and simultaneously associated with SI, SLA, SLP, SL and SW in four environments. The average value of R2 between markers was>0.8 (P<0.001), showing a large linkage disequilibrium. Genetic effect analysis showed that there were two haplotypes in this region. Among these cottonseed size relating traits, haplotype Ⅱ and haplotype I were significantly different, indicating that these loci directly affected cottonseed size traits and could be used for molecular marker-assisted selection. The expression patterns of the genes in the interval were analyzed using TM-1 transcriptome data. The results revealed that Gh_A07G1767 was preferentially expressed and Gh_A07G1766 specifically expressed at the stage of cottonseed development. These results speculated that these genes may play an important role in the growth and development of cottonseed.【Conclusion】47 QTNs were identified, and two candidate genes related to cottonseed development were screened.

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    Combined Effects of High Temperature and Drought on Yield and Photosynthetic Characteristics of Summer Maize
    XiaoFan LI, JingYi SHAO, WeiZhen YU, Peng LIU, Bin ZHAO, JiWang ZHANG, BaiZhao REN
    Scientia Agricultura Sinica    2022, 55 (18): 3516-3529.   DOI: 10.3864/j.issn.0578-1752.2022.18.004
    Abstract587)   HTML23)    PDF (587KB)(330)       Save

    【Objective】Climate change has led to global warming, with frequent occurrences of high temperatures and droughts, and high temperatures often accompany droughts during production. This study aimed to explore the physiological mechanism of the compound stress of high temperature and drought in different growth periods affecting the yield and photosynthetic characteristics of summer maize.【Method】DH605 was selected as the experimental hybrid. High temperature treatment (T), drought treatment (D) and the compound stress (T-D) treatment were set in different growth periods. In 2019, it was carried out at the third leaf stage (V3), the sixth leaf stage (V6) and flowering stage (VT); In 2020, it was carried out at the third leaf stage (V3), the twelfth leaf stage (V12) and flowering stage (VT). This experiment took natural temperature and normal moisture treatment as control (CK). The effects of high temperature and drought compound treatments on yield, photosynthetic characteristics, dry matter accumulation and distribution of summer maize were studied, and the differences of photosynthetic characteristics and yield between single treatment and compound treatment were compared.【Result】 After the combined stress treatment of high temperature and drought in different growth stages, the LAI and SPAD of summer maize decreased significantly, which affected the net photosynthetic rate (Pn) and it decreased significantly. Among that, the compound stress during the VT period had the most significant effect on Pn. The Pn under T-D treatment in the VT period decreased by 39.0% on average compared with CK, while the net photosynthetic rate of summer maize after the combined treatment of high temperature and drought decreased more than that under single stress such as high temperature and drought. The combined treatment of high temperature and drought caused the photosynthetic performance of summer maize to decrease, and it led to the decrease of dry matter accumulation capacity and distribution ratio of summer maize to grains, which in turn led to a significant decrease in yield. In 2019, the output of T-D at V3, V6, and VT decreased by 27.4%, 18.3%, and 66.5%, respectively, compared with CK; in 2020, the output of T-D treatment at V3, V12, and VT decreased by 14.5%, 14.6% and 68.7%, respectively, compared with CK.【Conclusion】After the combined stress of high temperature and drought, the leaf area index and chlorophyll content was decreased, gas exchange was inhibited, leading to the decrease of photosynthetic performance, and thus hindered the accumulation and distribution of photosynthetic compounds, resulting in a significant yield reduction of summer maize. The combined stress of high temperature and drought during the flowering stage had the greatest impact on the yield and photosynthetic characteristics of summer maize, and the combined stresses had greater impacts than that of single stress.

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    Provincial Agricultural Ecological Efficiency and Its Influencing Factors in China from the Perspective of Grey Water Footprint
    DENG YuanJian,CHAO Bo
    Scientia Agricultura Sinica    2022, 55 (24): 4879-4894.   DOI: 10.3864/j.issn.0578-1752.2022.24.008
    Abstract585)   HTML43)    PDF (617KB)(111)       Save

    【Objective】This paper evaluated Chinese provincial agricultural ecological efficiency from the perspective of gray water footprint, revealed the spatial distribution characteristics of agricultural ecological efficiency, analyzed the main factors affecting agricultural ecological efficiency, and put forward policy suggestions to improve Chinese provincial agricultural ecological efficiency. 【Method】Based on the provincial panel data of China from 2000 to 2019, this paper comprehensively evaluated the agricultural ecological efficiency of Chinese provinces with the super efficiency SBM model considering the unexpected output, and used the spatial Dobbin model to analyze the spatial differences and influencing factors of agricultural ecological efficiency. 【Result】(1) In general, the agricultural grey water footprint showed a downward trend, but in some provinces (cities and districts), it showed an upward trend. From the ranking of grey water footprint from low to high, it could be seen that the provinces (cities and districts) in the forefront (i.e. with less grey water footprint) had a high level of economic development or a relatively low proportion of agricultural output value; the provinces (cities and districts) in the rear row (i.e. with more grey water footprint) had low economic development level or high agricultural output value. (2) During the observation period, the agricultural ecological efficiency fluctuated greatly in some years in the stable trend, and the average difference among provinces (cities and districts) was obvious and the distribution was extremely unbalanced. (3) Economic development level, fiscal expenditure for supporting agriculture, technological progress, agricultural disaster rate, planting structure and other factors had different impacts on Chinese agricultural ecological efficiency. With the improvement of both economic development level and people's living quality, both agricultural operators and consumers paid more attention to the protection of agricultural ecological environment and the quality of agricultural products, which have improved the level of regional agricultural ecological efficiency to a certain extent. But the pollution caused by regional economic and social development might also have a negative impact on agricultural ecological efficiency. Most of the financial support for agriculture was used to subsidize production links, such as pesticides, chemical fertilizers, and agricultural machinery. Although the agricultural production conditions have been improved and the agricultural economic productivity and efficiency have been improved, the improvement of agricultural ecological efficiency was not significant. The development of technology was very important in the agricultural production process, and the proper use of it would improve the agricultural ecological efficiency. The estimated results of agricultural disaster rate failed to pass the significance test, which might be because the expansion of agricultural disaster area would lead to the decline of agricultural ecological efficiency, but the annual disaster situation was not regular. The coefficient of planting structure was negative, which had a negative impact on agricultural production efficiency. This might be due to the high proportion of grain crop planting area in the total planting area of crops, and the high consumption of nitrogen fertilizer. 【Conclusion】As the evolution trend and difference of agricultural gray water footprint in various provinces (cities and districts) in China were obvious, the overall level of agricultural ecological efficiency was not high, and various factors have different impacts on agricultural ecological efficiency, it was necessary to improve the governance mechanism of agricultural gray water footprint; optimize the agricultural industrial structure and establish a compensation mechanism for agricultural water resources protection based on gray water footprint; improve the ways and policies of financial support for agriculture, and guide business entities to actively improve agricultural ecological efficiency.

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    Comparison of Shell Mechanical Property, Ultrastructure and Component Between Chicken and Duck Eggs
    ZHANG YaNan,JIN YongYan,ZHUANG ZhiWei,WANG Shuang,XIA WeiGuang,RUAN Dong,CHEN Wei,ZHENG ChunTian
    Scientia Agricultura Sinica    2022, 55 (24): 4957-4968.   DOI: 10.3864/j.issn.0578-1752.2022.24.013
    Abstract582)   HTML44)    PDF (3716KB)(270)       Save

    【Objective】The research was conducted to study the comparison of shell mechanical property, ultrastructure and component between chicken and duck eggs. 【Method】160 eggs at the average weight from laying hens (Hy-Line grey) or ducks (Longyan Shanma) in aged 45 weeks were randomly divided into 2 groups, respectively. Each group had 20 eggs with 8 replicates. The laying hens and ducks were fed with maize-soybean meal basal diet, and the nutritional levels were formulated according to the national standard. The eggshell strength was measured by eggshell strength analyzer, the thickness of eggshell membrane and calcified eggshell was measured by digital micrometer, and then the eggshell ratio and toughness were calculated. Scanning electron microscope (SEM) was used to observe the ultrastructure of eggshell and to measure the effective thickness, mammillary thickness and width, and then to calculate the total thickness, the ratio of effective or mammillary thickness relative to total thickness. The mammillary structure was also observed by SEM and the degree of variation was scored. After crushing and extracting the eggshell, the content of matrix protein was determined by Coomassie brilliant blue method. After microwave digestion, the content of calcium, phosphorus, magnesium, manganese, copper and zinc in eggshell were determined according to the national standard method. 【Result】In comparison with chicken eggshell, the weight of duck egg and eggshell were increased (P<0.01), but the shell ratio was not changed (P>0.05); the eggshell breaking strength, toughness and eggshell membrane thickness were increased (P<0.01), but the thickness of the calcified eggshell (without shell membrane) was not changed (P>0.05). In respect to the ultrastructure, the thickness of mammillary layer and the number of mammillary knobs in per unit were decreased, but the mammillary knob width and mammillary layer ratio in duck eggshell were increased in relative to those of chicken eggs (P<0.001). No differences were observed in total and effective thickness (P>0.05), but the ratio of effective layer relative to total thickness was increased in duck eggshell (P<0.001). About the ultrastructure of mammillary knobs, there were no significant differences in the mammillae density, type B, type A, aragonite, cuff and pitted structure scores of the duck eggshell (P>0.05), the scores of the variations such as caps, early fusion and late fusion, and the total score of knobs were decreased in duck eggshell compared with chicken eggshell (P<0.05). There was higher frequency of mammillary structure variation in the chicken eggshell than the duck eggshell. The groove-like traces on the cap structure of the duck eggshell were deeper and clearer, the early fusion was more extensive, and the bonding between the knobs and the shell membrane fibers were denser than that in chicken eggshell. The contents of phosphorus, copper and manganese in duck eggshell were increased (P < 0.05), but the magnesium and matrix protein contents were decreased in duck eggshells relative to those in chicken eggshell (P<0.001), and there were no significant differences in calcium and zinc content (P>0.05). 【Conclusion】Above all, the eggshell quality of chicken and duck eggs were similar, and there were no differences in eggshell ratio, thickness of calcified layer, calcium and zinc content in eggshells. Compared with the chicken eggshell, the mechanical properties of duck eggshell were better, for shell breaking strength and toughness of duck eggshell were increased, which mainly due to the improvement of shell ultrastructure by increasing effective thickness and the ameliorate of mammillary knobs in duck eggshell. In addition, the phosphorus, copper and manganese content in duck eggshell were increased, but the content of magnesium and matrix proteins were decreased. In some content, the quality of duck eggshell could be improved by regulating the mineral elements and matrix protein content in eggshell, and modulated the process of eggshell formation, especially the deposition of calcium carbonate in the mammillary and palisade layers, and increased effective thickness and improved structure of the mammillary layer.

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