Scientia Agricultura Sinica

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

Abstract ( 453 )

HTML ( 78 )

PDF (5768KB) ( 293 )

Save

Figures and Tables | References | Related Articles | Metrics

【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 F_2:3 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.

Development of A Set of Matrix Reference Materials in Different Mass Fractions of Genetically Modified Maize MON87427

LI Jun, SHAN LuYing, XIAO Fang, LI YunJing, GAO HongFei, ZHAI ShanShan, WU Gang, ZHANG XiuJie, WU YuHua

Scientia Agricultura Sinica. 2023, 56(8): 1444-1455. doi:10.3864/j.issn.0578-1752.2023.08.002

Abstract ( 237 )

HTML ( 26 )

PDF (568KB) ( 105 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】The GMO (genetically modified organism) reference materials (RMs) are the material basis for GMO safety supervision and labeling policy implementation. During GMO detection the utilization of RMs guarantees the traceability of quantitative results within laboratory and the comparability of quantitative results between laboratories. GM (genetically modified) maize MON87427 has been approved to be imported as raw material in China, it’s urgent to develop certified reference materials (CRMs) for safety supervision and quantification. 【Method】 The GM maize MON87427 hybrid seeds and non-GM counterparts provided by the developer were used as raw materials to perform washing, drying, freeze-grinding, particle size measurement, and moisture content measurement, sequentially. The matrix RMs of MON87427a, MON87427b and MON87427c were produced by blending the seed powder of the GM maize MON87427 and a non-GM counterpart in GMO mass fractions of 60.0 mg·g^-1, 99.5 mg·g^-1 and 1 000.0 mg·g^-1 on a dry basis. The real-time quantitative PCR was used to conduct an initial assessment of homogeneity before packing. The MON87427/zSSIIb duplex digital PCR (ddPCR) was used to evaluate the homogeneity and stability of the RMs as well as the collaborative characterization by 8 qualified laboratories. The data processing of homogeneity, stability, collaborative characterization together with uncertainty evaluation of RMs were carried out according to the standard "General and Statistical Principles for Characterization of Reference Materials" (JJF 1343). 【Result】 This batch of RMs contains three RMs of MON87427a, MON87427b, and MON87427c in different mass fractions, with more than 80% of particle size of less than 200 μm and less than 5% of moisture content. The RMs were packed in brown glass bottles, nitrogen flushed before capping, bottling amount was not less than 1.0 g/bottle, a total of 400 bottles were produced for each mass fraction RM. The calculated F values of the homogeneity test were all less than the critical value of F_{0.05 (14, 30)} (2.04) for the three RMs, displaying good homogeneity within and between bottles, and the minimum intake was determined to be 100 mg. The RMs can be stored stably at 25℃, 37℃, and 60℃ for 14 days, the property value of the RMs does not change significantly after 14 days of transportation at room temperature; the long-term stability can reach 12 months at 4℃ and -20℃; The property value of the samples taken from the same bottle of RM after 5 opening-capping cycles, does not deviate significantly from that of the first taken sample. The collaborative characterization data by eight qualified laboratories displayed normal distribution without outliers and outlying standard deviations. The standard value and expanded uncertainty of MON87427a, MON87427b, Mon87427c were certified to be (2.92±0.44)%, (4.89±0.57)%, (52.1±3.4)%. 【Conclusion】The developed GM maize MON87427 matrix RMs in different mass fractions have good homogeneity, and can be stably transported and stored. This batch of RMs meets the requirements of qualitative and quantitative detection of MON87427 event, providing reliable CRMs for the safety supervision and implementation of quantitative labeling policy for GMO-derived products.

Study on the Dynamics of Root Length Density in Soil Layers of Single Plant Wheat Under Controlled Seed-to-Seed Distance

SUN QiBin, WANG JianNan, LI YiNian, HE RuiYin, DING QiShuo

Scientia Agricultura Sinica. 2023, 56(8): 1456-1470. doi:10.3864/j.issn.0578-1752.2023.08.003

Abstract ( 283 )

HTML ( 51 )

PDF (4264KB) ( 261 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】In order to quantify the influence of seed-to-seed distance on wheat root development in soil layers under single seed precision sowing, an integrated technique combining root architecture digitizer and MATLAB simulation was developed to quantify wheat root length density (RLD) and relative root length density (NRLD), as well as related models in each soil layer in the field.【Method】Ningmai 13 was used as experiment marital and the seed was sown with single seed precision sowing method in no-till paddy soil. The experiment was carried out in 2020 and 2021, respectively. Five treatments (JT1.5, JT3, JT4.5, JT6.7, and JT9) with row spacing of 1.5, 3.0, 4.5, 6.7 and 9.0 cm were introduced for field stand control. RLD was analyzed with combined technologies, i.e. root architecture digitizer and 3D root system architecture reconstruction with Pro-E, supplemented with MATLAB simulation, which facilitated fine segmentation and analysis of the rhizosphere dynamics under soil space voxel resolution of 3 mm³, and this further results quantified RLD distribution dynamics and the development of NRLD models along soil layers.【Result】The post-paddy wheat RLD decreased gradually along the soil layers under different treatments. As much as 95% of the root system was confined within the top soil layer in 0-9 cm, below which, root length decreased rapidly. The wheat root expansion area of a single plant first increased along the soil layers and then decreased. Root expansion started from the seed site as its central point, and revealed an obvious directional and constraining effects induced by the soil environment. With the increase of seed-to-seed distance, wheat RLD experienced first an increasing and then a decreasing trend, and the maximum value of which was found at JT4.5. The expansion area of wheat RLD increased with the increased seed-to-seed distance, and the maximum value of which was 22 972 mm². Either the too high or the too low density stand was found adversely impacts the efficiency of root configuration. Only the most suitable sowing density led to the best 3D distribution of wheat root system, which has been considered as the primary mechanism for efficient utilization of soil spatial resources. The NRLD distribution within 0-20 cm soil layers satisfied both cubic polynomial and exponential models well (R²>0.99, RMSE<0.1), but when considered the field state root system architecture, it was found that the exponential model was more realistic and fit the field wheat RLD the best along the soil layers.【Conclusion】An integrated technique combining root architecture digitizer and MATLAB simulation was developed to quantify wheat RLD and NRLD in the field, which satisfactorily illustrated the influence of seed-to-seed distance on RLD and NRLD along the soil layers. The results showed that the proposed method could be applicable for studies of wheat precision cultivation, precise water and fertilizer management, root configuration regulation and so on in the future.

Mepiquat Chloride Increases the Cry1Ac Protein Content Through Regulating Carbon and Amino Acid Metabolism of Bt Cotton Under High Temperature and Drought Stress

XING YuTong, TENG YongKang, WU TianFan, LIU YuanYuan, CHEN Yuan, CHEN Yuan, CHEN DeHua, ZHANG Xiang

Scientia Agricultura Sinica. 2023, 56(8): 1471-1483. doi:10.3864/j.issn.0578-1752.2023.08.004

Abstract ( 232 )

HTML ( 27 )

PDF (1190KB) ( 146 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】The effects of mepiquat chloride (DPC) on the insecticidal protein contents in Bt (Bacillus thuringiensis) cotton shell under high temperature and drought stress were investigated to provide a theoretical reference for the Bt cotton breeding as well as high-yield and high-efficiency cotton cultivation.【Method】The study was undertaken on the Bt cotton cultivar Sikang 3 during the 2020 and 2021 growing seasons at the Yangzhou University Farm, Yangzhou, China. The potted cotton plants were exposed to high temperature and drought stress, and 20 mg·L^-1DPC and water (CK) were sprayed to cotton plants. Seven days after treatment, the insecticidal protein content, α-ketoglutarate content, pyruvic acid content, glutamate synthase activity, glutamic oxaloacetic transaminase activity, soluble protein content, free amino acid content in boll shell were analyzed, and the transcriptome sequencing was performed. DESeq was used for differential gene analysis. The GO and KEGG pathway databases were used to analyze the differentially expressed genes involved in regulating the insecticidal protein content through DPC.【Result】Compared with the water treatment (CK), the insecticidal protein contents under DPC treatment increased by 4.7%-11.9%. In terms of carbon metabolism, the contents of α-ketoglutarate and pyruvic acid were increased by 46%-57% and 25%-29%, respectively. In terms of amino acid metabolism, the activities of glutamate synthase and glutamic oxaloacetic transaminase, and the contents of soluble protein and free amino acid were increased by 32%-44%, 30%-40%, and 28%, 22%-27%, respectively. The transcriptome analysis revealed that there were 7 542 upregulation genes and 10 449 downregulation genes for DPC vs water. The GO and KEGG analysis showed that the differentially expressed genes were mainly involved in biological process such as amino acid metabolism and carbon metabolism. The genes coding 6-phosphofructokinase, pyruvate kinase, glutamic pyruvate transaminase, pyruvate dehydrogenase, citrate synthase, isocitrate dehydrogenase, 2-oxoglutarate dehydrogenase, glutamate synthase, 1-pyrroline-5-carboxylate dehydrogenase, glutamic oxaloacetic transaminase, amino-acid N-acetyltransferase, and acetylornithine deacetylase were all significantly up-regulated. 【Conclusion】 Under the stress of high temperature and drought, the DPC treatment increased the contents of α-ketoglutarate and pyruvic acid, and improved the synthesis ability of aspartic acid, glutamic acid, pyruvate and arginine, then enhanced the insecticidal protein contents in boll shell by regulating the carbon and amino acid metabolism.

Expression Pattern of csi-miR399 in Response to Xanthomonas citri subsp. citri Infection and Its Disease Resistance Analysis

WANG ZhaoHao, GUO XingRu, ZHANG LeHuan, HE YongRui, CHEN ShanChun, YAO LiXiao

Scientia Agricultura Sinica. 2023, 56(8): 1484-1493. doi:10.3864/j.issn.0578-1752.2023.08.005

Abstract ( 224 )

HTML ( 33 )

PDF (1605KB) ( 104 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】The objective of this study is to identify the expression pattern of csi-miR399 in response to the infection of citrus canker bacteria (Xanthomonas citri subsp. citri, Xcc), screen its target genes, analyze the correlation between csi-miR399 and Xcc resistance in host plants, and to lay a foundation for the creation of citrus canker resistant germplasms.【Method】In order to clarify the expression pattern of csi-miR399 in response to Xcc infection, Xcc-resistant variety Calamondin (Citrus microcarpa) Xcc-sensitive variety Newhall Navel Orange (Citrus sinensis) were used as materials, and changes in the relative expression of csi-miR399 were analyzed by stem-loop qPCR after their leaves were injected with Xcc at 1, 3 and 5 d in vitro. The online software psRNATarget was used to predict the target genes of csi-miR399, which were further confirmed by qPCR in citrus leaves infected with Xcc and transiently over-expressed with csi-miR399. The viral expression vector pCLBV202-MIR399 was constructed by in-fusion cloning through csi-miR399 precursor sequence being inserted into pCLBV202, and transferred into Eureka Lemon (Citrus limon) by Agrobacterium tumefaciens-mediated vacuum infiltration. The lemon over-expressed with csi-miR399 was evaluated for resistance against Xcc through being stab-inoculated with the pathogen and investigated disease index.【Result】After inoculation with Xcc, the expression of csi-miR399 in Calamondin showed a downward trend and then an upward trend, while that in Newhall Navel Orange continued to decrease. At 5 d, the expression of csi-miR399 in Calamondin and Newhall Navel Orange was 4.64 times and 7.61% as its expression in healthy leaves, respectively, preliminary indicating that csi-miR399 was related to citrus canker resistance. Thirteen predicted target genes were screened from citrus genome. Three of them were confirmed because of the opposite expression trends with csi-miR399, which were Cs2g06030 (PHO2), Cs7g03830 (unknown protein), and Cs8g18800 (laccase). Three lemon strains (Y37, Y41 and Y57) with over-expressed csi-miR399 were obtained. Comparing with L35 (empty vector pCLBV202), csi-miR399 was significantly up-regulated in the Y37, Y41 and Y57 strains. The area of canker lesions in Y37, Y41 and Y57 was also significantly reduced, and the disease index was significantly decreased after inoculation with Xcc (P<0.01). It indicated that overexpression of csi-miR399 significantly enhanced the resistance to citrus canker.【Conclusion】csi-miR399 is closely related to the resistance of citrus to canker disease. Overexpression of csi-miR399 significantly improves the resistance, which can be applied to the molecular breeding of citrus against canker disease.

Construction of an Infectious Clone of Tobacco Mild Green Mosaic Virus Isolate Infecting Pepper from Jiangsu Based on Genomic Clone

GAO XiaoXiao, TU LiQin, YANG Liu, LIU YaNan, GAO DanNa, SUN Feng, LI Shuo, ZHANG SongBai, JI YingHua

Scientia Agricultura Sinica. 2023, 56(8): 1494-1502. doi:10.3864/j.issn.0578-1752.2023.08.006

Abstract ( 307 )

HTML ( 36 )

PDF (2317KB) ( 187 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】Tobamovirus is one of the main viruses that infect Solanaceae crops such as pepper and tobacco, which seriously affects the cultivation and production of crops. The purpose of this study is to investigate the genomic structural characteristics, phylogenetic relationship and pathogenicity of tobacco mild green mosaic virus (TMGMV) isolate infected pepper in Nanjing City of Jiangsu Province (TMGMV-JS), and to provide a scientific basis for the prevention and control of TMGMV. 【Method】Total RNA was extracted from disease pepper samples, then the positive samples were confirmed by specific detection primers of TMGMV. Subsequently, a pair of primers were designed and used to amplify the full-length genome sequence of TMGMV-JS isolate. The infectious cDNA clone of TMGMV-JS isolate was obtained by cloning the amplified products into pCB301 vector by homologous recombination. Then the homology of TMGMV-JS isolate with reported isolates was analyzed by BLAST and the neighbor-joining method of MEGA7 software was used for the phylogenetic analysis. Nicotiana benthamiana and Capsicum annuum were infiltrated with the infectious cDNA clone mediated by Agrobacterium tumefaciens. Furthermore, RT-PCR and Western blot were determined to define the pathogenicity of TMGMV-JS isolate.【Result】TMGMV-JS isolate contains 6 356 nt, encoding four functional proteins, 126K replication-associated protein, 183K replicase, movement protein MP, and coat protein CP. Homology analysis showed that TMGMV-JS isolate shared the highest identity with Chongqing TMGMV-TN29 isolate (MF139550), followed by Xiamen isolate (JX534224). Phylogenetic analysis showed that TMGMV-JS was clustered in a big branch with other TMGMV isolates and relatively closed to Chongqing and Xiamen isolates in a small branch. Furthermore, the constructed pCB301-TMGMV-JS infectious cDNA clone can systematically infect N. benthamiana, causing leaf yellow and systemic necrosis symptoms. It can also systematically infect C. annuum, causing symptoms such as leaf mottle, curling and dwarfing symptoms. 【Conclusion】The full-length genome of TMGMV-JS isolate infecting C. annuum from Nanjing City, Jiangsu Province is 6 356 nt, which is closely related to Chongqing and Xiamen isolates and belongs to the same branch. Significantly, the constructed infectious clone of TMGMV-JS can systemically infect N. benthamiana and C. annuum, causing systemic necrosis symptoms on N. benthamiana.

Synergistic Effects of Organic Carbon and Nitrogen Content in Water-Stable Aggregates as well as Microbial Biomass on Crop Yield Under Long-Term Straw Combined Chemical Fertilizers Application

HAN ZiXuan, FANG JingJing, WU XuePing, JIANG Yu, SONG XiaoJun, LIU XiaoTong

Scientia Agricultura Sinica. 2023, 56(8): 1503-1514. doi:10.3864/j.issn.0578-1752.2023.08.007

Abstract ( 339 )

HTML ( 85 )

PDF (3128KB) ( 278 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】The effects of long-term straw combined application of chemical fertilizers on the content of aggregates, distributions of aggregate-associated organic carbon and nitrogen, and soil microbial biomass were studied to reveal the promotion of soil fertility and productivity. 【Method】Soil samples were collected from a 40-year long-term experiment. The research was conducted with 4 treatments: pure chemical fertilizer (NP), straw with chemical fertilizer (S+NP), straw with 1/2 chemical fertilizer (S+1/2NP), and straw with 1/4 chemical fertilizer (S+1/4NP), and the straw was returned with the amount of 3 000 kg·hm^-2, chemical fertilizer NP was pure N 150 kg·hm^-2 and P₂O₅ 150 kg·hm^-2 conducted. All soils samples were separated into four aggregate-size classes (>2 mm, 0.25-2 mm, 0.053-0.25 mm, and <0.053 mm) by wet sieving. Organic carbon and total nitrogen content of aggregates and soil microbial biomass content were measured. 【Result】(1) Long-term application of chemical fertilizers with straw reduced soil bulk density, while improved the stability of aggregates. Compared with NP, the bulk density of S+NP decreased by 4.7%, while the proportion of aggregates >2 mm in size, the average weight diameter (MWD) and geometric weight diameter (GWD) increased by 254.4%, 76.5% and 91.3%, respectively. (2) In the three chemical fertilizers combined with straw return, the percentage of aggregates >2 mm, MWD and GWD under S+NP and S+1/2NP were significantly increased by 49.1%-52.4%, 19.43%-22.4% and 24.2%-33.3%, compared with S+1/4NP, respectively. (3) Compared with NP, S+NP, S+1/2NP and S+1/4NP increased the contribution rate of aggregates >2 mm and >0.25 mm to SOC and total nitrogen, and significantly improved the SOC, SMBC and SMBN content in bulk soil. Among them, the SOC content was the highest under S+NP, which was 6.3% and 12.6% higher than that under S+1/2NP and S+1/4NP, respectively. (4) The yield was showed that S+NP>NP>S+1/2NP>S+1/4NP, and S+NP increased wheat yield by 5.83%-83.6% compared with other treatments. (5) Positive correlation was revealed between soil aggregate stability, carbon and nitrogen content and crop yield, and >2 mm aggregate content, while MWD and GWD were significantly or extremely significant with the total soil SOC, SMBC content and wheat yield, respectively.【Conclusion】In the dark brown soil area, the long-term straw returning and fertilizer application of 150 kg N·hm^-2 and 150 kg P₂O₅·hm^-2could improve aggregate stability, soil organic carbon content, microbial biomass and yield, and achieve the synergistic effect of soil structure improvement, fertility improvement and crop yield increase.

Effects of Drip Irrigation Under Film and Trickle Furrow Irrigation on Maize Growth and Yield

LIU MengJie, LIANG Fei, LI QuanSheng, TIAN YuXin, WANG GuoDong, JIA HongTao

Scientia Agricultura Sinica. 2023, 56(8): 1515-1530. doi:10.3864/j.issn.0578-1752.2023.08.008

Abstract ( 326 )

HTML ( 29 )

PDF (2187KB) ( 238 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】The aim of this study was to investigate the effects of drip irrigation and trickle furrow irrigation on maize growth, yield and water use efficiency. 【Method】 Taking Zhengdan 958 as the research object, a field experiment was conducted from 2015 to 2021. The soil water content of 0-50 cm under narrow row, root zone and wide row was measured by a tubular moisture meter to study the effects of drip irrigation and trickle furrow irrigation under film on soil water distribution and its effects on maize plant height, leaf area index, chlorophyll content, biomass, yield and water use efficiency.【Result】Drip irrigation under mulch gave priority to supplement soil moisture in narrow row and root zone, while trickle furrow irrigation gave priority to supplement surface moisture in wide row. The water consumption of maize was mainly concentrated in 0-30 cm soil layer, and the soil water content in narrow row and 0-30 cm root zone of drip irrigation under mulch was higher than that of trickle furrow irrigation; with the increase of depth, the effect of irrigation on soil water content decreased, and the 40-50 cm water dynamics was less affected by irrigation methods. Drip irrigation under mulch could significantly promote the growth of maize at flowering and maturation stages, and increase leaf area index compared with trickle furrow irrigation. Compared with trickle irrigation, the plant height and leaf area index of drip irrigation under mulch increased by 4.3% and 8.3% at flowering stage, and increased by 4.9% and 15.1% at maturation stage, respectively. The total biomass of maize at flowering stage and maturation stage was drip irrigation under mulch>trickle furrow irrigation treatment, with an increase of 12.2% at flowering stage, and the maturation stage increased by 11.5%. The amount of dry matter transfer, the rate of dry matter transfer and the contribution rate of dry matter transfer of maize under drip irrigation were significantly higher than those under trickle irrigation, with increasing by 17.8%, 3.8% and 3.5% respectively. Drip irrigation under mulch significantly increased maize yield and irrigation water utilization efficiency, with an average yield increase of 14.4%, and irrigation water utilization efficiency increased by 14.6%.【Conclusion】Under the condition of equal irrigation volume, the drip irrigation under mulch could increase the water content in maize root zone, promote the growth of maize, facilitate the accumulation and transportation of dry matter of maize, improve the yield, and achieve water saving and efficiency increasing. Compared with trickle furrow irrigation, the average yield increased by 2 131.68 kg·hm^-2, and the irrigation water use efficiency increased by 8.8%-24.1%. Therefore, the drip irrigation under plastic mulch was a high-yield and efficient irrigation method for maize planting in Northern Xinjiang.

Effects of Combined Application of Organic Manure and Chemical Fertilizer Ratio on Water and Nitrogen Use Efficiency of Cotton Under Water Deficit

WANG Ning, FENG KeYun, NAN HongYu, CONG AnQi, ZHANG TongHui

Scientia Agricultura Sinica. 2023, 56(8): 1531-1546. doi:10.3864/j.issn.0578-1752.2023.08.009

Abstract ( 233 )

HTML ( 31 )

PDF (1078KB) ( 165 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】The aim of this study was to explore the effects of combined application of organic manure and chemical fertilizer on water and nitrogen use efficiency and yield of cotton under different water conditions, so as to provide a theoretical basis for the rational use of organic fertilizer in the cotton area of Hexi corridor.【Method】Field experiments were carried out from 2020 to 2021. The experiment was designed by split block, the main plot treatment consisted of full irrigation (W1) and deficit irrigation(W2), and the split-plot treatment was composed of five fertilizer treatments: no fertilizer (CK), single application of chemical fertilizer (CF), 25% organic manure with 75% chemical fertilizer (OF1), 50% organic manure with 50% chemical fertilizer (OF2) and 75% organic manure with 25% chemical fertilizer (OF3), while the nutrient content of each fertilization treatment was equal. The effects of fertilization under different water conditions on soil water content, periodical evapotranspiration, dry matter accumulation, nitrogen accumulation, transport and distribution, water and nitrogen use efficiency, seed cotton yield and economic benefits were analyzed. 【Result】The seed cotton yield, water and nitrogen utilization characteristics of cotton were significantly affected by different water and fertilizer treatments and interactions. Soil water content, total evapotranspiration, dry matter accumulation, total nitrogen uptake and seed cotton yield decreased significantly, while water use efficiency increased significantly under deficit irrigation. The suitable combined application of organic manure and chemical fertilizer treatment could increase the soil water content of 0-40 cm soil layer, and reduce the evapotranspiration at seedling stage and budding stage, while increase the evapotranspiration at flower-boll stage, increase dry matter and nitrogen accumulation, and promote distribution to reproductive organs. Under the condition of full irrigation, the yield of the OF1 treatment was the highest in all fertilization treatments, with an average increase of 10.5% over single application of chemical fertilizer in two years, there was no significant difference between OF2 and CF, while the treatment of OF3 was significantly lower than that under single application of chemical fertilizer. The treatment of OF1 had the highest water and nitrogen use efficiency in each fertilization treatment, in which water use efficiency, nitrogen use efficiency and nitrogen agronomic use efficiency were 8.9%, 14.3% and 28.9% higher than CF, respectively. Under the condition of deficit irrigation, the seed cotton yield of the combined application of organic manure and chemical fertilizer treatments were higher than that of CF among which OF2 was the highest, and the average seed cotton yield of two years was 12.9% higher than that of CF, meanwhile, the treatment of OF2 also had the highest water and nitrogen use efficiency, in which the water use efficiency, nitrogen use efficiency and nitrogen agronomic use efficiency were 6.3%, 35.5% and 31.6% higher than that of CF, respectively.【Conclusion】The appropriate proportion of combined application of organic manure and chemical fertilizer could coordinate the supply and demand relationship of soil and crop for water and nutrients, and improve the seed cotton yield and the water and nitrogen use efficiency. Considering yield, water and nitrogen use efficiency and economic benefits, the treatment of 25% organic manure was the suitable mode of organic fertilizer application in Hexi corridor.

Population Genomic Structure of Pomelo Germplasm and Fruit Acidity Associated Genes Identification by Genotyping-by-Sequencing Technology

JIANG Dong, WANG Xu, LI RenJing, ZHAO XiaoDong, DAI XiangSheng, LIU ZhengWei

Scientia Agricultura Sinica. 2023, 56(8): 1547-1560. doi:10.3864/j.issn.0578-1752.2023.08.010

Abstract ( 261 )

HTML ( 33 )

PDF (3083KB) ( 184 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】 To reveal the phylogeny, population genetic structure and diversity level of pomelo (Citrus grandis (L.) Osbeck) germplasm, and to efficiently utilize them to explore genes related to important fruit quality traits, this research provided an insight into the population genetic structure and phylogeny of pomelo germplasm and facilitated the pomelo varieties innovation.【Method】 A total of 282 pomelo accessions including landraces from different geographical regions and hybrid offspring of kiyomi tangor and pomelo were contained in this study. GBS library was constructed with genomic DNAs digested by EcoR I restriction endonuclease and sequenced on Illumina HiSeq PE150 platform, the clean short reads were then mapped to pomelo reference genome by BWA, and SNPs were called out with SAMTOOLS pipeline. Based on 121 726 SNPs genotyping data, principal component analysis (PCA) and population genetic structure analysis were carried out and phylogenetic trees were constructed with Neighbor-joining method. Furthermore, two sub-populations containing high-acid accessions (32) and low-acid accessions (23) were used to identify candidate genes related to fruit acidity by Fst and XP-CLR selective sweeping analysis. Meanwhile, the genotype data of 282 pomelo accessions and the phenotypic data of titratable acid content in fruit were used for GWAS.【Result】 A total of 201.66 Gb original reads were generated from 282 pomelo germplasm by GBS approach, in average each sample produced 0.72 Gb reads. After the screening conditions of sequencing depth of dp5, the miss less than 0.2 and minor alleles frequency (MAF)>0.01, and a total of 121 726 SNPs were selected out for subsequent analysis. The PCA, structure and phylogenetic analysis all supported that the 282 pomelo germplasm could be divided into 6 subgroups, among which pomelo and kiyomi hybrid population, grapefruits and other pomelo hybrid populations could be obviously different from true-to-type pomelo populations, pomelos originated from different geographical region displayed unique genetic feature. The pomelo germplasm from Thailand and Vietnam formed a relatively unique group different from other domestic groups, such as ShaTian pomelo, Wen Dan pomelo, and Dian Jiang pomelo in China. The genetic introgression from Vietnam pomelos were exhibited in most pomelo germplasm in southern China, suggested that Vietnam was the origin center for pomelo. In addition, some pomelo germplasm with unknown origin have been identified accurately by GBS technology. This study showed that different geographical distribution and artificial selection pressure had great effect on the genomic composition of pomelo. Besides, Fst, XP-CLR selective sweeping analysis revealed a strong selection signal region on chromosome 7 contained genes annotated as dihydrolipoyl transacetylase (DLT-E2) of pyruvate dehydrogenase complex (PDC) and aluminum-activated malate transporter (ALMT9), which involved in the synthesis and transportation of citric acid. In additional GWAS genome-wide association analysis identified another region on chromosome 2, which was also highly associated with fruit acidity. 【Conclusion】GBS technology provided reliable and efficient method for studying the phylogeny and evolution of pomelo. The study showed that artificial cross breeding, long-term artificial selection, geography isolation and domestication were the major driving forces for the formation of different types of pomelo germplasm. In addition, it clearly showed that Southeast Asian was primary center for pomelo origin and China mainland was secondary evolutionary center. Several candidate genes related to citric acid content in pomelo fruits were identified by Fst, XP-CLR selective sweeping and GWAS. This study provided important gene resources for the further genetic improvement and breeding of pomelo fruits.

Genome-Wide Association Studies for Grape Berry Weight Related Traits

WANG HuiLing, YAN AiLing, WANG XiaoYue, LIU ZhenHua, REN JianCheng, XU HaiYing, SUN Lei

Scientia Agricultura Sinica. 2023, 56(8): 1561-1573. doi:10.3864/j.issn.0578-1752.2023.08.011

Abstract ( 326 )

HTML ( 46 )

PDF (2665KB) ( 203 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】Grape berry size is one of important factors affecting grape appearance and the final productivity. It is a complex quantitative trait regulated by multiple genes. Mining the key genetic regulatory loci and the underlying genes for berry size related traits would help to improve grape yield. 【Method】In this study, 150 diverse grapevine varieties were selected as materials. The berry weight, seed number per berry, and seed weight were measured in 2019 and 2020, respectively. Based on high-density genotype data obtained by resequencing, the genome-wide association studies (GWAS) were carried out to detect significantly associated SNPs and to predict important candidate genes.【Result】The three measured traits exhibited extensive phenotypic variation with 39.55%-68.89% of phenotypic variation coefficients; the phenotypic distribution of the observed three traits in the population showed continuous quantitative genetic characteristics; a significant positive correlation between each trait were observed in two years; based on the phenotypic data collected in two years, a total of 150 significant SNPs were detected for berry weight. In 2019, 99 SNPs were detected, each of which contributed the phenotypic variation from 14.48% to 25.59%; in 2020, 73 SNPs were detected, explaining 16.08%-26.83% of phenotypic variation; among these SNPs, 24 were detected repeatedly in both two years, mainly located on chromosome 1, 5, 11 and 16. Compared with the trait of berry weight, less SNPs significantly associated with the seed number were detected. A significant SNP was detected in 2019, and the phenotypic explanation value was 24.29%; in 2020, 17 significant SNPs were detected, which all located on chromosome 18; 1 and 2 SNPs located on chromosome 18 significantly associated with seed weight were detected in 2019 and 2020, respectively, accounting for 23.59%-48.29% of phenotypic variation. Within the genomic region of SNPs detected repeatedly for two years, 11 candidate genes related to berry weight were screened out based on the functional annotation, including ethylene signal pathway genes (VIT_05s0049g00490, VIT_05s0049g00500, VIT_05s0049g00510 and VIT_16s0100g00400), gibberellin signal pathway genes (VIT_11s0016g04630 and VIT_16s0022g02310), auxin responsive protein gene (VIT_11s0016g05640) and some important transcription factor genes (VIT_05s0049g00460, VIT_11s0016g05660 and VIT_16s0022g02330). A candidate gene VIT_18s0041g01880 (encoding a MADS box protein VviAGL11) associated with seed content was identified on chromosome 18, and different SNP genotypes on this gene significantly affected the grape berry seed number and weight. 【Conclusion】A total of 150 SNPs significantly associated with berry weight were detected in two years, mainly located on chromosomes 1, 5, 11 and 16; A total of 19 significant SNPs associated with seed content were detected, mainly located on chromosome 18. Based on the results of gene annotation and genotype analysis, 11 candidate genes that might be involved in the regulation of grape berry weight including VIT_11s0016g04630 and VIT_16s0022g02310 were selected; the candidate gene VIT_18s0041g01880 was determined significantly correlated with seed content.

Preparation of Ultrasound-Assisted Zein Ethylene Scavenger Film and Its Preservation Property of Bananas

FAN Xin, LI YuXin, KUANG JiWei, YANG Ting, LIU MiaoMiao, CAO YunGang, HUANG JunRong

Scientia Agricultura Sinica. 2023, 56(8): 1574-1584. doi:10.3864/j.issn.0578-1752.2023.08.012

Abstract ( 163 )

HTML ( 25 )

PDF (1605KB) ( 82 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】 Ethylene is an important plant hormone that has a key influence on the quality and shelf life of fruit. In this study, zein was modified to transform into a stretched structure and consequently expose its internal active functional groups by the high-field intensity ultrasound treatment (HIU). Numerous functional groups (-SH) exposed in modified zein film could rapidly react with ethylene via a click reaction, resulting in an extended shelf life of the fruit. 【Method】 The 5 g zein was dissolved in acetic acid-DI water (4:1) solution. The zein solutions were sonicated for 0, 5, 15, and 30 min at an ultrasonic power of 400 W and dried in a drying oven at 40℃ for 24 h to obtain the zein-0 film, zein-5 film, zein-15 film, and zein-30 film. The structures of zein before and after HIU treatment were analyzed by circular dichroism spectroscopy, endogenous fluorescence, particle size potentiometer, and scanning electron microscope. The mechanical and ethylene adsorption properties of zein-based films were characterized by the texture analyzer and the VOC detector. Bananas were used as the climacteric fruit samples to investigate the effectiveness of the zein films as ethylene scavengers. The ultrasonic treated zein film and banana samples were placed in the same plastic sealing bag and then stored at room temperature for 10 d. The performance for extending shelf life was evaluating by browning rate, the flesh hardness, and the weight loss rate of bananas. 【Result】 The HIU treatment (20 kHz, 400 W, 15 min) could effectively stretch the structure of zein. The particle size of the zein and the content of the α-helix were decreased to 1 013.3±6.9 nm, and 45.86%, respectively, and the content of the β-sheet increased to 12.20%. Compared with the zein-0 film, the ethylene adsorption capacity and oxygen resistance of the zein-15 film were increased by 9.486 mg·m^-3·h^-1and 0.75×10^-16 kg·m·m^-2·s^-1·Pa^-1, respectively. The results including the browning rate, the flesh hardness, and the weight loss rate of bananas indicated that the zein-15 film could effectively extend the shelf-life of bananas. 【Conclusion】 The HIU treatment (20 kHz, 400 W, 15 min) could effectively induce to stretch the zein structure and expose more functional groups, resulting in an improved ethylene adsorption performance of zein. The zein-15 film presented a better ethylene adsorption capacity, oxygen permeability, and mechanical property, leading to an extended shelf life of bananas and its life as the ethylene scavenger.

Comparison of Imputation Accuracy for Different Low-Density SNP Selection Strategies

LIN YuNong, WANG ZeZhao, CHEN Yan, ZHU Bo, GAO Xue, ZHANG LuPei, GAO HuiJiang, XU LingYang, CAI WenTao, LI YingHao, LI JunYa, GAO ShuXin

Scientia Agricultura Sinica. 2023, 56(8): 1585-1593. doi:10.3864/j.issn.0578-1752.2023.08.013

Abstract ( 195 )

HTML ( 21 )

PDF (1310KB) ( 88 )

Save

Figures and Tables | References | Related Articles | Metrics

【Objective】 To facilitate the low-cost genomic selection in Huaxi Cattle, the present study represented the first attempt to designed a new low-density Genotype chip to support imputation to higher density genotypes. The representative SNP markers with different density gradients were selected from high-density SNP chips in the Huaxi cattle reference population by using two SNP selection methods. And then, these marker sets were imputed to high-density sets with the same imputation parameters for subsequent genomic studies. Meanwhile, the current study compared the differences in imputation accuracy and concordance among SNP panels and illustrated the effects of four factors on imputation results, including marker screening method, marker density, minor allele frequency, and the number of reference population. This study could provide insights about the methods to select the low-density SNP markers for imputation in the current population and the representative SNPs, and aid in designing low-density SNP chip for Huaxi cattle.【Method】Totally 1,233 Huaxi cattle after genotypes filtered was randomly divided into reference (986) and validation (247) populations., Based on Equidistance (EQ) and high MAF (HM), two SNP selection strategies were used to make 16 SNP sets with different densities from the Illumina Bovine HD chip in the reference population, respectively. Each of the 32 low-density set was then imputed to the 770K density level in the validation population by using Beagle (v5.1), while the imputation accuracy and concordance were calculated as the mean correlation between true and imputed genotypes. Finally, a comprehensive set of factors that influence the imputation performance were analyzed.【Result】The number of markers in the 32 low-density SNP sets ranged from 100 to 16 000, with a maximum window of 24 176 kb and a minimum window of 151 kb. The imputation accuracy and concordance of both EQ and HM methods went up with increasing marker densities. The imputation accuracy of both methods was the highest at 16k SNP density (r2 EQ=0.8801, r2 MAF=0.8696). When the marker density was below 11k, the imputation concordance of HM was higher than EQ for all marker density gradients. However, when the SNP density exceeded 11 k, EQ showed an imputation accuracy advantage over HM. Similar to the imputation concordance results, the HM method still had higher imputation accuracy when the SNP density was lower than 10 k, but the EQ method had higher imputation accuracy when the SNP pool density was higher than 10 k, and the EQ imputation accuracy tended to be stable after the SNP density was greater than 12 k. It was also found that the imputation accuracy of high MAF locus was higher. During the imputation process, it was found that the imputation accuracy and concordance increased with the increase of the reference panel. The imputation accuracy and concordance of loci were higher when the population of the reference panel was 600-800. 【Conclusion】In the Huaxi cattle population, the imputation accuracy and concordance increased with increasing marker density, and a better imputation effect could be obtained in the marker density of 10 k-12 k interval. The HM method was preferred when the marker density was less than 10 k, and the EQ method was better at high marker density. High MAF loci were more accurate for imputation. When the imputation strategy for low-density marker imputation was used, the number of reference panel should be at least 400 heads for better imputation effect.

Screening of Candidate Genes for Green Shell Egg Shell Color Traits in Chishui Black Bone Chicken Based on Transcriptome Sequencing

XIAO Tao, LI Hui, LUO Wei, YE Tao, YU Huan, CHEN YouBo, SHI YuShi, ZHAO DePeng, WU Yun

Scientia Agricultura Sinica. 2023, 56(8): 1594-1605. doi:10.3864/j.issn.0578-1752.2023.08.014

Abstract ( 244 )

HTML ( 41 )

PDF (1311KB) ( 228 )

Save

Figures and Tables | References | Related Articles | Metrics

【Background】Green shell eggs are loved by consumers, and the green color of eggshell is an important reference index affecting the pricing and sales of green shell eggs in the market. The formation of green shell eggs is regulated by multiple genes, and the color of green shell varies. However, the molecular mechanism of green shell eggs is still unclear. In this study, transcriptomic sequencing was conducted on the eggshell gland tissue of Chishui black bone chicken, and the candidate genes and key signal pathways that regulated the depth and depth of eggshell color of green shell eggs were excavated, so as to explore the heritability of eggshell color, and to develop the seed selection and breeding of green shell eggs and improve economic benefits. 【Objective】The aim of this study was to investigate the genetic basis of Chishui black bone chicken and to identify and then screen them by SLCO1B3 genotyping, in order to provide new insights through molecular markers in the breeding planning of green-shelled hens, and to help control and improve the homogeneity of eggshell quality of Chishui black bone chicken in the later selection strategy. 【Method】A pure 280-day-old Chishui black bone chicken was used as the research object. Three hens were slaughtered to produce light green eggs (QL) and dark green eggs (SL), and the eggshell glands were collected and analyzed by RNA-SEQ technology. Selected differentially expressed genes (DEGs) closely related to eggshell color, and analyzed for GO and KEGG enrichment. Qrt-pcr was used to detect the transcriptional level changes of six candidate genes related to eggshell color to verify the reliability of transcriptomic data. 【Result】A total of 93 DEGs were screened in SL group and QL group, among which 59 genes were up-regulated and 34 genes were down-regulated in SL group. DEGs was annotated to GO database for comparison, and sodium ion transport, negative ion binding, and sarcoplasmic reticulum were mainly enriched significantly. KEGG analysis showed that aldosterone regulated sodium reabsorption, enriched mineral absorption, linoleic acid metabolism and other signal pathways. The results of QRT-PCR showed that the expression trend of these genes was consistent with the transcriptome sequencing results. 【Conclusion】By functional analysis, TF gene, SCNN1 gene, CYP450 gene, SLC gene and FAM gene, as well as the sodium reabsorption signaling pathway regulated by aldosterone, might be involved in eggshell pigment synthesis, transport and deposition. These genes and signal pathways might be candidate genes and key signal pathways affecting the different shades of green in eggshell of Chishui black bone chicken.

Development and Application of Indirect ELISA Kits for Antibody Detection of Haemophilus parasuis

ZHANG PengYun, CHEN Min, LIU MingXing, ZHOU Hong, LIN HuiXing, FAN HongJie

Scientia Agricultura Sinica. 2023, 56(8): 1606-1614. doi:10.3864/j.issn.0578-1752.2023.08.015

Abstract ( 195 )

HTML ( 20 )

PDF (866KB) ( 89 )

Save

Figures and Tables | References | Related Articles | Metrics

【Background】Haemophilus parasuis (HPS) is the pathogen of upper respiratory tract of pigs, causing Glaser’s disease, mainly in pigs before and after weaning and in the nursery stage, which is usually seen in young pigs aged 5-8 weeks, and the incidence rate is generally 10%-15%. There are 15 serotypes of the bacteria and the serotypes currently prevalent in major pig-raising countries are 4, 5, 12 and 13, and it is one of the main bacterial pathogens affecting the development of pig industry. At present, there is no commercial kit for detecting antibody of the bacteria in China.【Objective】The development of a rapid, sensitive and specific antibody detection kit could provide the technical support for the effective prevention and control of the disease.【Method】Three different periplasmic substrate binding proteins of OppA, DppA and HbpA were expressed and purified. The positive and negative serum was used to screen one of the above three proteins with sound immunoreactivity and specificity. Using the screened protein as the coating antigen, an indirect ELISA method for detecting HPS antibody was established, the reaction conditions of indirect ELISA were optimized, and the kit was assembled. On this basis, the sensitivity and specificity of the kit were evaluated; the practicability of the kit was evaluated by testing 2 000 clinical pig serum samples collected at different times and from different pig farms; based on the above clinical serum samples, 200 samples were selected randomly and tested with this kit, indirect hemagglutination test, and imported commercial kit, respectively, and the test results were compared to verify the compliance rate of the kit; finally, the kit developed in this study was used to detect immune and challenge pigs. The collected serum was used to evaluate the growth and decline of antibodies against the bacteria after immunization.【Result】Three proteins of OppA, DppA and HbpA were successfully expressed and purified, and it was found that OppA had the best immunoreactivity and specificity. After optimizing the reaction conditions, the coating concentration of OppA was determined to be 1 μg·mL^-1, the blocking solution was 0.5% BSA-PBS solution, the sample dilution was 1% BSA-PBST solution, the sample incubation time was 30 min, the sample dilution was 1:50, the enzyme labeled secondary antibody incubation time was 30min, the substrate action time was 15min, and the cut-off value was 0.18; the sensitivity and specificity of the kit were 96.67%, and the kit could detect the HPS positive sera against HPS with common serotypes prevalent in China and no cross-reaction with positive sera of other common pathogens in pigs; the positive rate of 2 000 clinical serum samples was 34.65%; 200 serum samples were randomly selected, the coincidence rate with indirect hemagglutination test was 92.50%, and the coincidence rate with imported commercial kit was 87.00%; using the kit to detect the swine serum collected at different times after immunization and challenge, the HPS antibody fluctuation rule was in line with expectations.【Conclusion】The ELISA antibody detection kit for Haemophilus parasuis developed in this study had high specificity and sensitivity, and hads a high coincidence rate with the commercial kit and indirect hemagglutination test, so it could be used for clinical HPS antibody detection and vaccine immunity evaluation.

Pathological Changes of a Novel Pigeon Adenovirus Type A Infection

YANG ZhiYuan, ZHOU YuTing, LIN Jian, HUANG Cheng, GAO Jie, DUAN HuiJuan, CHENG ShuiSheng, ZHAO JiCheng, LUO WeiJue, LIU YueHuan

Scientia Agricultura Sinica. 2023, 56(8): 1615-1616. doi:10.3864/j.issn.0578-1752.2023.08.016

Abstract ( 192 )

HTML ( 31 )

PDF (1866KB) ( 174 )

Save

Figures and Tables | Related Articles | Metrics

Table of Content