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Comparative transcriptome and lipidome reveal that a low K+ signal effectively alleviates the effect induced by Ca2+ deficiency in cotton fibers
GUO Kai, GAO Wei, ZHANG Tao-rui, WANG Zu-ying, SUN Xiao-ting, YANG Peng, LONG Lu, LIU Xue-ying, WANG Wen-wen, TENG Zhong-hua, LIU Da-jun, LIU De-xin, TU Li-li, ZHANG Zheng-sheng
2023, 22 (8): 2306-2322.   DOI: 10.1016/j.jia.2023.01.002
Abstract194)      PDF in ScienceDirect      
Calcium (Ca2+) plays an important role in determining plant growth and development because it maintains cell wall and
membrane integrity. Therefore, understanding the role of Ca2+ in carbon and lipid metabolism could provide insights
into the dynamic changes in cell membranes and cell walls during the rapid elongation of cotton fibers. In the present
study, we found that the lack of Ca2+ promoted fiber elongation and rapid ovule expansion, but it also caused tissue
browning in the ovule culture system. RNA-sequencing revealed that Ca2+ deficiency induced cells to be highly oxidized,
and the expression of genes related to carbon metabolism and lipid metabolism was activated significantly. All gene
members of nine key enzymes involved in glycolysis were up-regulated, and glucose was significantly reduced in Ca2+
deficiency-treated tissues. Ca2+ deficiency adjusted the flowing of glycolysis metabolic. However, low K+ recovered
the expression levels of glycolysis genes and glucose content caused by Ca2+ deficiency. Electrospray ionizationtandem
mass spectrometry technology was applied to uncover the dynamic profile of lipidome under Ca2+ and K+
interacted conditions. Ca2+ deficiency led to the decrease of fatty acid (FA), diacylglycerol (DAG), glycolipid and the
significant increase of triacylglycerol (TAG), phospholipid phosphatidylethanolamine (PE), phosphatidylglycerol (PG),
and PC (phosphatidylcholine). Low K+ restored the contents of FA, phospholipids, and glycolipids, effectively relieved
the symptoms caused by Ca2+ deficiency, and recovered the development of fiber cells. This study revealed dynamic
changes in transcript and metabolic levels and uncovered the signaling interaction of Ca2+ deficiency and low K+ in
glycolysis and lipid metabolism during fiber development.
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Improvement of soil fertility and rice yield after long-term application of cow manure combined with inorganic fertilizers
GAO Peng, ZHANG Tuo, LEI Xing-yu, CUI Xin-wei, LU Yao-xiong, FAN Peng-fei, LONG Shi-ping, HUANG Jing, GAO Ju-sheng, ZHANG Zhen-hua, ZHANG Hui-min
2023, 22 (7): 2221-2232.   DOI: 10.1016/j.jia.2023.02.037
Abstract249)      PDF in ScienceDirect      
Fertilization is an effective technique to improve soil fertility and increase crop yield. The long-term effects of different fertilizers on soil considerably vary. Over 38 consecutive years of different fertilization positioning experiments in a double cropping rice field of Qiyang Red Soil Experimental Station, seven different fertilization treatments including CK (no fertilization), NPK (nitrogen, phosphorus, and potassium fertilizer), M (cow manure), NPKM (nitrogen, phosphorus, and potassium with cow manure), NPM (nitrogen and phosphorus with cow manure), NKM (nitrogen and potassium with cow manure), and PKM (phosphorus and potassium with cow manure) were applied to study the effects on rice yield, soil fertility, and nutrient apparent balance in a paddy field. The results showed that the annual average yields of rice in NPKM, NPM, NKM, PKM, M, NPK and CK treatments ranged from 6 214 to 11 562 kg ha–1. Yields under longterm organic and inorganic treatments (NPKM, NPM, NKM and PKM) were 22.58, 15.35, 10.53 and 4.41%, respectively, greater than under the NPK treatment. Soil organic carbon (SOC), total nitrogen (TN), available nitrogen (AN) and available potassium (AK) concentration with long-term organic and inorganic treatment (NPKM, NPM, NKM and PKM) were significantly higher than in inorganic fertilizer (NPK) treatments. Soil total phosphorus (TP) and available phosphorus (AP) contentration with organic fertilizer combined with inorganic N and P fertilizer treatment (NPKM, NPM and PKM) were significantly higher than with inorganic fertilizer alone (NPK treatments). The average annual rice yield (11 562 kg ha–1), SOC (20.88 g kg–1), TN (2.30 g kg–1), TP (0.95 g kg–1), TK (22.50 g kg–1) and AP (38.94 mg kg–1) concentrations were the highest in the NPKM treatment. The soil AN concentration (152.40 mg kg–1) and AK contentration (151.00 mg kg–1) were the highest in the NKM treatment. N and P application led to a surplus of nitrogen and phosphorus in the soil, but NPKM treatment effectively reduced the surplus compared with other treatments. Soils under all treatments were deficient in potassium. Correlation analysis showed that SOC, TN, AN, TP, and AP contentration was significantly correlated with rice yield; the correlation coefficients were 0.428, 0.496, 0.518, 0.501, and 0.438, respectively. This study showed that the combined application of N, P, and K with cow manure had important effects on rice yield and soil fertility, but balanced application of N, P, and K with cow manure was required.
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Identification of two novel linear epitopes on the p30 protein of African swine fever virus
YU Si-hui, SHAN Zhao-meng, YANG Jing-jing, LIU Yi-ning, WU Chang-de, ZHANG Zhen-jiang, ZHU Yuan-mao, MENG Bo, ZHAN Jia-xing, WEN Xue-xia, ZHANG Ying
2023, 22 (6): 1945-1949.   DOI: 10.1016/j.jia.2023.04.012
Abstract233)      PDF in ScienceDirect      
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Effects of sowing date and ecological points on yield and the temperature and radiation resources of semi-winter wheat
ZHANG Zhen-zhen, CHENG Shuang, FAN Peng, ZHOU Nian-bing, XING Zhi-peng, HU Ya-jie, XU Fang-fu, GUO Bao-wei, WEI Hai-yan, ZHANG Hong-cheng
2023, 22 (5): 1366-1380.   DOI: 10.1016/j.jia.2022.08.029
Abstract225)      PDF in ScienceDirect      

Exploring the effects of sowing date and ecological points on the yield of semi-winter wheat is of great significance.  This study aims to reveal the effects of sowing date and ecological points on the climate resources associated with wheat yield in the Rice–Wheat Rotation System.  With six sowing dates, the experiments were carried out in Donghai and Jianhu counties, Jiangsu Province, China using two semi-winter wheat varieties as the objects of this study.  The basic seedlings of the first sowing date (S1) were planted at 300×104 plants ha−1, which was increased by 10% for each of the delayed sowing dates (S2–S6).  The results showed that the delay of sowing date decreased the number of days, the effective accumulated temperature and the cumulative solar radiation in the whole growth period.  The yields of S1 were higher than those of S2 to S6 by 0.22–0.31, 0.5–0.78, 0.86–0.98, 1.14–1.38, and 1.36–1.59 t ha–1, respectively.  For a given sowing date, the growth days increased as the ecological point was moved north, while both mean daily temperature and effective accumulative temperature decreased, but the cumulative radiation increased.  As a result, the yields at Donghai County were 0.01–0.39 t ha–1 lower than those of Jianhu County for the six sowing dates.  The effective accumulative temperature and cumulative radiation both had significant positive correlations with yield.  The average temperature was significantly negatively correlated with the yield.  The decrease in grain yield was mainly due to the declines in grains per spike and 1 000-grain weight caused by the increase in the daily temperature and the decrease in the effective accumulative temperature.

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Millet/peanut intercropping at a moderate N rate increases crop productivity and N use efficiency, as well as economic benefits, under rain-fed conditions
LIU Zhu, NAN Zhen-wu, LIN Song-ming, YU Hai-qiu, XIE Li-yong, MENG Wei-wei, ZHANG Zheng, WAN Shu-bo
2023, 22 (3): 738-751.   DOI: 10.1016/j.jia.2022.08.078
Abstract298)      PDF in ScienceDirect      

Cereal and legume intercropping has been widely adopted to increase crop productivity in sustainable farming systems worldwide.  Among different intercropping combinations, millet and peanut intercropping can be adapted to most water-limited areas.  However, there are few studies on the differences in yield characteristics and nitrogen use efficiency between millet/peanut intercropping and monocultures under different nitrogen (N) application rates.  The objective of this study was to determine the yield advantages and economic benefits, as well as the appropriate N application rate, of millet/peanut intercropping.  A two-year field experiment was conducted with three cropping patterns (monoculture millet, monoculture peanut and millet/peanut intercropping) and four N rates (0, 75, 150 and 225 kg ha−1).  The results showed that the land equivalent ratio (LER) and net effect (NE) of the intercropping system reached their highest levels at the N input of 150 kg ha−1 in 2018 and 2019 (1.04 for LER, 0.347 Mg ha−1 for NE, averaged across two years).  Millet was the dominant crop in the intercropping system (aggressivity of millet and peanut (Amp)>0, competitive ratio of millet and peanut (CRmp)>1), and millet yields achieved their highest values at N inputs of 225 kg ha−1 for monoculture and 150 kg ha−1 for intercropping.  NUE reached its highest levels with N inputs of 150 kg ha−1 for all planting patterns over the two years.  Intercropping combined with an N input of 150 kg ha−1 achieved the highest net income of 2 791 USD ha−1, with a benefit-cost ratio of 1.56, averaged over the two years.  From the perspective of economics and agricultural sustainable development, millet/peanut intercropping at 150 kg N ha−1 seems to be a promising alternative to millet or peanut monoculture.

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Occurrence pattern and morphological polymorphism of weedy rice in China
WANG Hao-quan, DAI Wei-min, ZHANG Zi-xu, LI Meng-shuo, MENG Ling-chao, ZHANG Zheng, LU Huan, SONG Xiao-ling, QIANG Sheng
2023, 22 (1): 149-169.   DOI: 10.1016/j.jia.2022.08.001
Abstract303)      PDF in ScienceDirect      
Rice, the main food crop in China, has been sporadically reported to suffer from weedy rice infestation.  However, the overall occurrence and distribution pattern of Chinese weedy rice remains unclear because a systematic survey has not been conducted.  In order to reveal the infestation of Chinese weedy rice, a field survey was conducted in 999 sampling sites all over the rice-growing regions in China from 2009 to 2016 using seven-scale visual scoring of the level of weed infestation.  Weedy rice was found 39% occurrence incidence in a total of 387 sites.  The sampling sites with 50% or higher overall weedy rice infestation index mainly radiated from Jiangsu, Heilongjiang, Ningxia and Guangdong to the whole East China, Northeast China, Northwest China and South China.  A total of 45 morphological characters from 287 populations (collected simultaneously with the field survey) out of those occurred sites were observed and analyzed using multivariate analysis in common gardens with the same cultivation conditions in 2017 and 2019.  Canonical correlation analysis showed that 45 morphological characters were significantly related to the latitude, mean temperature, minimum temperature, precipitation and mean diurnal range factors.  The 287 weedy rice populations were divided into three morphological groups with climate-dependent geographical differentiation: strong tiller type only in Jiangsu, large leaf type in South China and Central China and large grain type mainly in North China.  Weedy rice seriously infested rice fields and had a geography, climate and cultivated rice type-dependent morphological and biotype differentiation in China.  It is suggested to pay attention to the harmfulness of weedy rice and adopt comprehensive control strategies.
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Incorporating genomic annotation into single-step genomic prediction with imputed whole-genome sequence data
TENG Jin-yan, YE Shao-pan, GAO Ning, CHEN Zi-tao, DIAO Shu-qi, LI Xiu-jin, YUAN Xiao-long, ZHANG Hao, LI Jia-qi, ZHANG Xi-quan, ZHANG Zhe
2022, 21 (4): 1126-1136.   DOI: 10.1016/S2095-3119(21)63813-3
Abstract197)      PDF in ScienceDirect      
Single-step genomic best linear unbiased prediction (ssGBLUP) is now intensively investigated and widely used in livestock breeding due to its beneficial feature of combining information from both genotyped and ungenotyped individuals in the single model.  With the increasing accessibility of whole-genome sequence (WGS) data at the population level, more attention is being paid to the usage of WGS data in ssGBLUP.  The predictive ability of ssGBLUP using WGS data might be improved by incorporating biological knowledge from public databases.  Thus, we extended ssGBLUP, incorporated genomic annotation information into the model, and evaluated them using a yellow-feathered chicken population as the examples.  The chicken population consisted of 1 338 birds with 23 traits, where imputed WGS data including 5 127 612 single nucleotide polymorphisms (SNPs) are available for 895 birds.  Considering different combinations of annotation information and models, original ssGBLUP, haplotype-based ssGHBLUP, and four extended ssGBLUP incorporating genomic annotation models were evaluated.  Based on the genomic annotation (GRCg6a) of chickens, 3 155 524 and 94 837 SNPs were mapped to genic and exonic regions, respectively.  Extended ssGBLUP using genic/exonic SNPs outperformed other models with respect to predictive ability in 15 out of 23 traits, and their advantages ranged from 2.5 to 6.1% compared with original ssGBLUP.  In addition, to further enhance the performance of genomic prediction with imputed WGS data, we investigated the genotyping strategies of reference population on ssGBLUP in the chicken population.  Comparing two strategies of individual selection for genotyping in the reference population, the strategy of evenly selection by family (SBF) performed slightly better than random selection in most situations.  Overall, we extended genomic prediction models that can comprehensively utilize WGS data and genomic annotation information in the framework of ssGBLUP, and validated the idea that properly handling the genomic annotation information and WGS data increased the predictive ability of ssGBLUP.  Moreover, while using WGS data, the genotyping strategy of maximizing the expected genetic relationship between the reference and candidate population could further improve the predictive ability of ssGBLUP.  The results from this study shed light on the comprehensive usage of genomic annotation information in WGS-based single-step genomic prediction.

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Construction of a telomerase-immortalized porcine tracheal epithelial cell model for swine-origin mycoplasma infection
XIE Xing,  HAO Fei, WANG Hai-yan, PANG Mao-da, GAN Yuan, LIU Bei-bei, ZHANG Lei, WEI Yan-na, CHEN Rong, ZHANG Zhen-zhen, BAO Wen-bin, BAI Yun, SHAO Guo-qing, XIONG Qi-yan, FENG Zhi-xin
2022, 21 (2): 504-520.   DOI: 10.1016/S2095-3119(21)63644-4
Abstract166)      PDF in ScienceDirect      
Primary porcine tracheal epithelial cells (PTECs) are an appropriate model for studying the molecular mechanism of various porcine respiratory diseases, including swine-origin mycoplasmas, which are isolated from respiratory tract of pigs and mainly found on the mucosal surface surrounding swine trachea.  However, the short proliferation ability of primary PTECs greatly limits their lifespan.  In this study, primary PTECs were carefully isolated and cultured, and immortal PTECs were constructed by transfecting primary PTECs with the recombinant constructed plasmid pEGFP-hTERT containing human telomerase reverse transcriptase (hTERT).  Immortal PTECs (hTERT-PTECs) maintained both the morphological and functional characteristics of primary PTECs, as indicated by the expression of cytokeratin 18, cell-cycle analysis, proliferation assay, Western blotting, telomerase activity assay, karyotype analysis and quantitative RT-PCR.  Compared to primary PTECs, hTERT-PTECs had an extended replicative lifespan, higher telomerase activity, and enhanced proliferative activity.  In addition, this cell line resulted in a lack of transformed and grown tumors in nude mice, suggesting that it could be safely applied in further studies.  Moreover, hTERT-PTECs were vulnerable to all swine-origin mycoplasmas through quantitative analysis as indicated by 50% color changing unit (CCU50) calculation, and no significant differences of adhesion ability between primary and immortal PTECs were observed.  For the representative swine mycoplasma Mycoplasma hyopneumoniae (Mhp), except for DNA copies quantitative real-time PCR assay, indirect immunofluorescence assay and Western blotting analysis also depicted that hTERT-PTECs was able to adhere to different Mhp strains of different virulence.  In summary, like primary PTECs, hTERT-PTECs could be widely used as an adhesion cell model for swine-origin mycoplasmas and in infection studies of various porcine respiratory pathogens.  
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The water-saving potential of using micro-sprinkling irrigation for winter wheat production on the North China Plain
ZHAI Li-chao, Lü Li-hua, DONG Zhi-qiang, ZHANG Li-hua, ZHANG Jing-ting, JIA Xiu-ling, ZHANG Zheng-bin
2021, 20 (6): 1687-1700.   DOI: 10.1016/S2095-3119(20)63326-3
Abstract175)      PDF in ScienceDirect      
The shortage of groundwater resources is a considerable challenge for winter wheat production on the North China Plain.  Water-saving technologies and procedures are thus urgently required.  To determine the water-saving potential of using micro-sprinkling irrigation (MSI) for winter wheat production, field experiments were conducted from 2012 to 2015.  Compared to traditional flooding irrigation (TFI), micro-sprinkling thrice with 90 mm water (MSI1) and micro-sprinkling four times with 120 mm water (MSI2) increased the water use efficiency by 22.5 and 16.2%, respectively, while reducing evapotranspiration by 17.6 and 10.8%.  Regardless of the rainfall pattern, MSI (i.e., MSI1 or MSI2) either stabilized or significantly increased the grain yield, while reducing irrigation water volumes by 20–40%, compared to TFI.  Applying the same volumes of irrigation water, MSI (i.e., MSI3, micro-sprinkling five times with 150 mm water) increased the grain yield and water use efficiency of winter wheat by 4.6 and 11.7%, respectively, compared to TFI.  Because MSI could supply irrigation water more frequently in smaller amounts each time, it reduced soil layer compaction, and may have also resulted in a soil water deficit that promoted the spread of roots into the deep soil layer, which is beneficial to photosynthetic production in the critical period.  In conclusion, MSI1 or MSI2 either stabilized or significantly increased grain yield while reducing irrigation water volumes by 20–40% compared to TFI, and should provide water-saving technological support in winter wheat production for smallholders on the North China Plain.
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Identifying the complex genetic architecture of growth and fatness traits in a Duroc pig population
ZHANG Zhe, CHEN Zi-tao, DIAO Shu-qi, YE Shao-pan, WANG Jia-ying, GAO Ning, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi
2021, 20 (6): 1607-1614.   DOI: 10.1016/S2095-3119(20)63264-6
Abstract185)      PDF in ScienceDirect      
In modern pig breeding programs, growth and fatness are vital economic traits that significantly influence porcine production.  To identify underlying variants and candidate genes associated with growth and fatness traits, a total of 1 067 genotyped Duroc pigs with de-regressed estimated breeding values (DEBV) records were analyzed in a genome wide association study (GWAS) by using a single marker regression model.  In total, 28 potential single nucleotide polymorphisms (SNPs) were associated with these traits of interest.  Moreover, VPS4B, PHLPP1, and some other genes were highlighted as functionally plausible candidate genes that compose the underlying genetic architecture of porcine growth and fatness traits.  Our findings contribute to a better understanding of the genetic architectures underlying swine growth and fatness traits that can be potentially used in pig breeding programs. 
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Exploring the genetic features and signatures of selection in South China indigenous pigs
DIAO Shu-qi, XU Zhi-ting, YE Shao-pan, HUANG Shu-wen, TENG Jin-yan, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi, ZHANG Zhe
2021, 20 (5): 1359-1371.   DOI: 10.1016/S2095-3119(20)63260-9
Abstract152)      PDF in ScienceDirect      
To explore the genetic features and signatures of selection in indigenous pigs from South China and Duroc pigs, 259 pigs from six populations were genotyped using single-nucleotide polymorphism (SNP) BeadChips.  Principal component analysis (PCA), effective population size (Ne), linkage disequilibrium (LD), and signatures of selection were explored and investigated among the six pig populations.  The results showed the Ne of five South China indigenous pig populations has been decreasing rapidly since 100 generations ago.  The LD between pairwise SNP distance at 100 kb ranged from 0.16 to 0.20 for the five indigenous pig populations, while it was 0.32 for the Duroc population.  However, the LD of all six pig populations showed the opposite order at long distances (>5 Mb).  Furthermore, 15 potential signatures of selection associated with meat quality and age at puberty were exclusively detected in South China indigenous pigs, while eight potential signatures of selection associated with growth traits were detected in Duroc pigs.  Our work provides valuable insights for the utilization and conservation of South China indigenous pigs.
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Improving winter wheat grain yield and water-/nitrogen-use efficiency by optimizing the micro-sprinkling irrigation amount and nitrogen application rate
LI Jin-peng, ZHANG Zhen, YAO Chun-sheng, LIU Yang, WANG Zhi-min, FANG Bao-ting, ZHANG Ying-hua
2021, 20 (2): 606-621.   DOI: 10.1016/S2095-3119(20)63407-4
Abstract174)      PDF in ScienceDirect      
Available irrigation resources are becoming increasingly scarce in the North China Plain (NCP), and nitrogen-use efficiency of crop production is also relatively low. Thus, it is imperative to improve the water-use efficiency (WUE) and nitrogen fertilizer productivity on the NCP. Here, we conducted a two-year field experiment to explore the effects of different irrigation amounts (S60, 60 mm; S90, 90 mm; S120, 120 mm; S150, 150 mm) and nitrogen application rates (150, 195 and 240 kg ha–1; denoted as N1, N2 and N3, respectively) under micro-sprinkling with water and nitrogen combined on the grain yield (GY), yield components, leaf area index (LAI), flag leaf chlorophyll content, dry matter accumulation (DM), WUE, and nitrogen partial factor productivity (NPFP). The results indicated that the GY and NPFP increased significantly with increasing irrigation amount, but there was no significant difference between S120 and S150; WUE significantly increased first but then decreased with increasing irrigation and S120 achieved the highest WUE. The increase in nitrogen was beneficial to improving the GY and WUE in S60 and S90, while the excessive nitrogen application (N3) significantly reduced the GY and WUE in S120 and S150 compared with those in the N2 treatment. The NPFP significantly decreased with increasing nitrogen rate under the same irrigation treatments. The synchronous increase in spike number (SN) and 1 000-grain weight (TWG) was the main reason for the large increase in GY by micro-sprinkling with increasing irrigation, and the differences in SN and TGW between S120 and S150 were small. Under S60 and S90, the TGW increased with increasing nitrogen application, which enhanced the GY, while N2 achieved the highest TWG in S120 and S150. At the filling stage, the LAI increased with increasing irrigation, and greater amounts of irrigation significantly increased the chlorophyll content in the flag leaf, which was instrumental in increasing DM after anthesis and increasing the TGW. Micro-sprinkling with increased amounts of irrigation or excessive nitrogen application decreased the WUE mainly due to the increase in total water consumption (ET) and the small increase or decrease in GY. Moreover, the increase in irrigation increased the total nitrogen accumulation or contents (TNC) of plants at maturity and reduced the residual nitrate-nitrogen in the soil (SNC), which was conducive to the increase in NPFP, but there was no significant difference in TNC between S120 and S150. Under the same irrigation treatments, an increase in nitrogen application significantly increased the residual SNC and decreased the NPFP. Overall, micro-sprinkling with 120 mm of irrigation and a total nitrogen application of 195 kg ha–1 can lead to increases in GY, WUE and NPFP on the NCP.
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Effects of deep vertical rotary tillage on the grain yield and resource use efficiency of winter wheat in the Huang-Huai-Hai Plain of China
WU Fen, ZHAI Li-chao, XU Ping, ZHANG Zheng-bin, Elamin Hafiz BAILLO, Lemessa Negasa TOLOSA, Roy Njoroge KIMOTHO, JIA Xiu-ling, GUO Hai-qian
2021, 20 (2): 593-605.   DOI: 10.1016/S2095-3119(20)63405-0
Abstract130)      PDF in ScienceDirect      
Tillage represents an important practice that is used to dynamically regulate soil properties, and affects the grain production process and resource use efficiency of crops. The objectives of this 3-year field study carried out in the Huang-Huai-Hai (HHH) Plain of China were to compare the effects of a new deep vertical rotary tillage (DVRT) with the conventional shallow rotary tillage (CT) on soil properties, winter wheat (Triticum aestivum L.) grain yield and water and nitrogen use efficiency at different productivity levels, and to identify a comprehensive management that optimizes both grain yield and resource use efficiency in the HHH Plain. A split-plot design was adopted in field experiments in the winter wheat growing seasons of 2016–2017 (S1), 2017–2018 (S2) and 2018–2019 (S3), with DVRT (conducted once in June 2016) and CT performed in the main plots. Subplots were treated with one of four targeted productivity level treatments (SH, the super high productivity level; HH, the high productivity and high efficiency productivity level; FP, the farmer productivity level; ISP, the inherent soil productivity level). The results showed that the soil bulk density was reduced and the soil water content at the anthesis stage was increased in all three years, which were due to the significant effects of DVRT. Compared with CT, grain yields, partial factor productivity of nitrogen (PFPN), and water use efficiency (WUE) under DVRT were increased by 22.0, 14.5 and 19.0%. Path analysis and direct correlation decomposition uncovered that grain yield variation of winter wheat was mostly contributed by the spike numbers per area under different tillage modes. General line model analysis revealed that tillage mode played a significant role on grain yield, PFPN and WUE not only as a single factor, but also along with other factors (year and productivity level) in interaction manners. In addition, PFPN and WUE were the highest in HH under DVRT in all three growth seasons. These results provided a theoretical basis and technical support for coordinating the high yield with high resource use efficiency of winter wheat in the resource-restricted region in the HHH Plain of China.
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Cultivar selection can increase yield potential and resource use efficiency of spring maize to adapt to climate change in Northeast China
SU Zheng-e, LIU Zhi-juan, BAI Fan, ZHANG Zhen-tao, SUN Shuang, HUANG Qiu-wan, LIU Tao, LIU Xiao-qing, YANG Xiao-guang
2021, 20 (2): 371-382.   DOI: 10.1016/S2095-3119(20)63359-7
Abstract101)      PDF in ScienceDirect      
Northeast China (NEC) is one of the major maize production areas in China. Agro-climatic resources have obviously changed, which will seriously affect crop growth and development in this region. It is important to investigate the contribution of climate change adaptation measures to the yield and resource use efficiency to improve our understanding of how we can effectively ensure high yield and high efficiency in the future. In this study, we divided the study area into five accumulated temperature zones (ATZs) based on growing degree days (GDD). Based on the meteorological data, maize data (from agro-meteorological stations) and the validated APSIM-Maize Model, we first investigated the spatial distributions and temporal trends of maize potential yield of actual planted cultivars, and revealed the radiation use efficiency (RUE) and heat resource use efficiency (HUE) from 1981 to 2017. Then according to the potential growing seasons and actual growing seasons, we identified the utilization percentages of radiation (PR) resource and heat resource (PH) for each ATZ under potential production from 1981 to 2017. Finally, we quantified the contributions of cultivar changings to yield, PR and PH of maize. The results showed that during the past 37 years, the estimated mean potential yield of actual planted cultivars was 13 649 kg ha–1, ranged from 11 205 to 15 257 kg ha–1, and increased by 140 kg ha–1 per decade. For potential production, the mean values of RUE and HUE for the actual planted maize cultivars were 1.22 g MJ–1 and 8.58 kg (°C d)–1 ha–1. RUE showed an increasing tendency, while HUE showed a decreasing tendency. The lengths of the potential growing season and actual growing season were 158 and 123 d, and increased by 2 and 1 d per decade. PR and PH under potential production were 82 and 86%, respectively and showed a decreasing tendency during the past 37 years. This indicates that actual planted cultivars failed to make full use of climate resources. However, results from the adaptation assessments indicate that, adoption of cultivars with growing season increased by 2–11 d among ATZs caused increase in yield, PR and PH of 0.6–1.7%, 1.1–7.6% and 1.5–8.9%, respectively. Therefore, introduction of cultivars with longer growing season can effectively increase the radiation and heat utilization percentages and potential yield.
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Differentially expressed miRNAs in anthers may contribute to the fertility of a novel Brassica napus genic male sterile line CN12A
Dong Yun, Wang Yi, Jin Feng-wei, Xing Li-juan, Fang Yan, Zhang Zheng-ying, ZOU Jun-jie, Wang Lei, Xu Miao-yun
2020, 19 (7): 1731-1742.   DOI: 10.1016/S2095-3119(19)62780-2
Abstract95)      PDF in ScienceDirect      
In Brassica napus L. (rapeseed), complete genic male sterility (GMS) plays an important role in the utilization of heterosis.  Although microRNAs (miRNAs) play essential regulatory roles during bud development, knowledge of how GMS is regulated by miRNAs in rapeseed is rather limited.  In this study, we obtained a novel recessive GMS system, CN12AB.  The sterile line CN12A has defects in tapetal differentiation and degradation.  Illumina sequencing was employed to examine the expression of miRNAs in the buds of CN12A and the fertile line CN12B.  We identified 85 known miRNAs and 120 novel miRNAs that were expressed during rapeseed anther development.  When comparing the expression levels of miRNAs between CN12A and CN12B, 19 and 18 known miRNAs were found to be differentially expressed in 0.5–1.0 mm buds and in 2.5–3.0 mm buds, respectively.  Among these, the expression levels of 14 miRNAs were higher and the levels of 23 miRNAs were lower in CN12A compared with CN12B.  The predicted target genes of these differentially expressed miRNAs encode protein kinases, F-box domain-containing proteins, MADS-box family proteins, SBP-box gene family members, HD-ZIP proteins, floral homeotic protein APETALA 2 (AP2), and nuclear factor Y, subunit A.  These targets have previously been reported to be involved in pollen development and male sterility, suggesting that miRNAs might act as regulators of GMS in rapeseed anthers.  Furthermore, RT-qPCR data suggest that one of the differentially expressed miRNAs, bna-miR159, plays a role in tapetal differentiation by regulating the expression of transcription factor BnMYB101 and participates in tapetal degradation and influences callose degradation by manipulating the expression of BnA6.  These findings contribute to our understanding of the roles of miRNAs during anther development and the occurrence of GMS in rapeseed.
 
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Genome-wide detection of selective signatures in a Jinhua pig population
XU Zhong, SUN Hao, ZHANG Zhe, Zhao Qing-bo, Babatunde Shittu Olasege, Li Qiu-meng, Yue Yang, Ma Pei-pei, Zhang Xiang-zhe, Wang Qi-shan, Pan Yu-chun
2020, 19 (5): 1314-1322.   DOI: 10.1016/S2095-3119(19)62833-9
Abstract119)      PDF in ScienceDirect      
The aim of this study was to detect evidence for signatures of recent selection in the Jinhua pig genome.  These results can be useful to better understand the regions under selection in Jinhua pigs and might shed some lights on groups of genes that control production traits.  In the present study, we performed extended haplotype homozygosity (EHH) tests to identify significant core regions in 202 Jinhua pigs.  A total of 26 161 core regions spanning 636.42 Mb were identified, which occupied approximately 28% of the genome across all autosomes, and 1 158 significant (P<0.01) core haplotypes were selected.  Genes in these regions were related to several economically important traits, including meat quality, reproduction, immune responses and exterior traits.  A panel of genes including ssc-mir-365-2, KDM8, RABEP2, GSG1L, RHEB, RPH3AL and a signal pathway of PI3K-Akt were detected with the most extreme P-values.  The findings in our study could draw a comparatively genome-wide map of selection signature in the pig genome, and also help to detect functional candidate genes under positive selection for further genetic and breeding research in Jinhua and other pigs.
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Effects of palm fat powder and coated folic acid on growth performance, ruminal fermentation, nutrient digestibility and hepatic fat accumulation of Holstein dairy bulls
ZHANG Zhen, LIU Qiang, WANG Cong, GUO Gang, HUO Wen-jie, ZHANG Yan-li, PEI Cai-xia, ZHANG Shuan-lin
2020, 19 (4): 1074-1084.   DOI: 10.1016/S2095-3119(19)62752-8
Abstract135)      PDF in ScienceDirect      
This study evaluated the effects of palm fat powder (PFP) and coated folic acid (CFA) on growth performance, ruminal fermentation, nutrient digestibility, microbial enzyme activity, microflora, hepatic lipid content and gene expression in dairy bulls.  Forty-eight Chinese Holstein bulls ((362±12.4) days of age and (483±27.1) kg of body weight (BW)) were assigned to four groups in a completely randomized design with a 2×2 factorial arrangements.  Supplemental PFP (0 or 30 g PFP kg–1 dietary dry matter (DM)) and CFA (0 or 120 mg FA d–1 as CFA) were mixed into the top one-third of a total mixed ration.  The study included a 20-day adaptation period and followed by a 90-day collection period.  The lower (P<0.01) feed conversion ratio with PFP or CFA addition resulted from the constant DM intake and the higher (P<0.05) average daily gain.  The higher (P<0.05) ruminal pH, ether extract digestibility, microbial α-amylase activity, Butyrivibrio fibrisolvens copy, and expression of peroxisome-proliferator-activated receptor α (PPARα) and carnitine palmitoyl transferase-1 (CPT1), and lower ruminal total volatile fatty acids (VFA) concentration, acetate to propionate ratio, neutral detergent fibre (NDF) digestibility, copies of total protozoa and Ruminococcus flavefaciens, and expression of sterol regulatory element binding protein-1 (SREBP1) and acetyl-coenzyme A carboxylase α (ACACA) were observed for PFP addition.  Supplementation with CFA increased (P<0.05) ruminal total VFA concentration, acetate to propionate ratio, digestibility of DM, organic matter, crude protein and NDF, activity of cellobiase, pectinase and α-amylase, copies of selected microbial except for total protozoa, as well as expression of PPARα, but decreased (P<0.05) ruminal pH, and expression of SREBP1 and ACACA.  The PFP×CFA interaction (P<0.05) was observed for ammonia N, hepatic TG content, and mRNA expression of CPT1 and FAS.  There had no significant difference in hepatic TG content when CFA was supplemented in the diet without PFP addition, the lower (P=0.001) hepatic TG content was observed when CFA was supplemented in the diet with PFP addition.  The higher (P<0.05) mRNA expression of CPT1, and the lower (P<0.05) mRNA expression of FAS and ammonia N concentration were observed when CFA was supplemented in diet either without or with PFP addition.  The results indicated that supplementation of CFA in PFP diet was more effective on increasing hepatic CPT1 expression, and decreasing ammonia N, hepatic TG content and FAS expression than in diet without PFP.  Supplementation with PFP or CFA improved growth performance of dairy bulls by promoting nutrient utilization, microbial enzyme activity, microflora, and hepatic gene expression.
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Expression and contribution of microphthalmia-associated transcription factor to the melanin deposition in Liancheng white ducks
XIN Qing-wu, MIAO Zhong-wei, LIU Zhao-yuan, LI Li, ZHANG Lin-li, ZHU Zhi-ming, ZHANG Zheng-hong, ZHENG Nen-zhu, WANG Zheng-chao
2020, 19 (3): 800-809.   DOI: 10.1016/S2095-3119(19)62736-X
Abstract101)      PDF in ScienceDirect      
The present study investigates the expression of microphthalmia-associated transcription factor (MITF) and its contribution to the melanin deposition in Liancheng white ducks.  Nested PCR was used to clone the MITF gene sequence from the skin tissue of female Liancheng white ducks.  Ultraviolet spectrophotometry was used to detect the melanin deposition.  MITF mRNA expression and melanin deposition in different tissues and organs were detected and their correlation was analyzed.  The MITF gene (GenBank number: MG516570) was 1 323 bp in length, contains a complete CDS region (34–1 323 bp) and codes 429 amino acids with 100% homology to the MITF of Anas platyrhynchos and over 95% homology to those of Gallus gallus and Coturnix japonica.  Genetic evolution analysis reveals a close relationship of Liancheng white ducks with A. platyrhynchos, and also to lesser extents with Anser cygnoides, silky fowl and G. gallus, as well as Sus scrofa, Ovis aries and other mammals.  Real-time quantitative PCR (qPCR) analysis demonstrated that MITF was expressed in skin, gizzard, liver, kidney and muscle, and of these tissues, its expression was the highest in the skin tissue (skin>gizzard>liver>kidney>muscle).  Ultraviolet spectrophotometry showed that melanin deposition was positively correlated with the MITF expression level in these five tissues and organs (P<0.05).  Together, these results demonstrated a tissue-specific pattern of MITF expression and a positive correlation between MITF expression and melanin deposition, indicating that MITF expression may contribute to the melanin deposition in Liancheng white ducks.
 
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Effects of the severity and timing of basal leaf removal on the amino acids profiles of Sauvignon Blanc grapes and wines
YUE Xiao-feng, JU Yan-lun, TANG Zi-zhu, ZHAO Ya-meng, JIAO Xu-liang, ZHANG Zhen-wen
2019, 18 (9): 2052-2062.   DOI: 10.1016/S2095-3119(19)62666-3
Abstract135)      PDF in ScienceDirect      
The effects of the severity and timing of leaf removal (LR) on the amino acids of Sauvignon Blanc grapes and wines were studied during the 2017 growing season.  High-performance liquid chromatography (HPLC) was used to analyze the amino acids profiles of grape berries and wines.  The basal leaves were removed at three time points (40, 56 and 72 days after flowering, named LR40, LR56 and LR72, respectively) at two severity levels (one at which the first, third, and fifth basal leaves of each shoot were removed (50% level); and another at which the first six basal leaves were removed (100% level)).  The results showed that leaf removal had little impact on total soluble solids (°Brix), titratable acidity, pH or berry weight.  The LR72-50% treated grapes had higher berry weight, titratable acidity and °Brix than those of the other treatments.  The highest concentrations of total amino acids and of total amino acids except proline were detected in LR72-50% treated grapes (2 952.58 and 2 764.36 mg L–1, respectively); the lowest were detected in LR72-100% treated grapes (2 172.82 and 2 038.71 mg L–1, respectively).  LR72-50% treatment significantly promoted the synthesis of aspartic acid, serine, arginine, alanine, aminobutyric acid and proline at both severity levels for grapes, the concentrations of all of these amino acids were increased relative to the control concentrations.  The LR72-50%, LR40-100% and LR72-100% treated wines had higher total amino acids concentrations and higher concentrations of some individual amino acids, such as arginine, alanine and serine, than did the control wines.  Of all the amino acids studied, glycine, tyrosine, cysteine, methionine and lysine were not significantly influenced by the timing or severity basal defoliation in grapes and wines.  The present study reveals the effects of the timing and severity of leaf removal on the amino acids profiles of grapes and wines.
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Effect of tillage and burial depth and density of seed on viability and seedling emergence of weedy rice
ZHANG Zheng, GAO Ping-lei, DAI Wei-min, SONG Xiao-ling, HU Feng, QIANG Sheng
2019, 18 (8): 1914-1923.   DOI: 10.1016/S2095-3119(19)62583-9
Abstract183)      PDF in ScienceDirect      
Weedy rice (Oryza sativa f. spontanea) is one of the three worst paddy weeds in most rice growing areas.  The unexpected heavy infestation is derived from a persistence of soil seed bank of weedy rice, which the shattered seeds chiefly feed back to.  Information on soil seed bank dynamics is imperative to predict the infestation of weeds.  In the present paper, the effect of rotary tillage on weedy rice seed bank structure was studied first, and a burial experiment of marked seeds was conducted to observe the overwintering survival, seed viability and seedling emergence of weedy rice.  The results showed that the proportion of weedy rice seeds in deeper soil increased but seedling emergence decreased with increasing plowing depth.  The viability of weedy rice seeds decreased as the burial duration time extended but more slowly in deeper soil layers.  Additionally, there was no significant effect of burial density on seed viability.  Moreover, the logistic model fitted well (R2≥0.95, P≤0.01) with the depressive trends of seed viability with increasing burial time under all burial depths and densities which can provide us further information about seed survival.  In field experiments, number of seedling emergence significantly decreased as seed burial depth increased, conversely, proportion of seedling emergence increased as seed burial density decreased.  This study has important implications for determining strategies for weedy rice management by exhausting its seed bank through the alteration of tillage practices.
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Genetic diversity and population structure analysis of Capsicum germplasm accessions
GU Xiao-zhen, CAO Ya-cong, ZHANG Zheng-hai, ZHANG Bao-xi, ZHAO Hong, ZHANG Xiao-min, WANG Hai-ping, LI Xi-xiang, WANG Li-hao
2019, 18 (6): 1312-1320.   DOI: 10.1016/S2095-3119(18)62132-X
Abstract234)      PDF in ScienceDirect      
Genetic diversity plays an essential role in plant breeding and utilization.  Pepper is an important vegetable and spice crop worldwide.  The genetic diversity of 1 904 accessions of pepper conserved at the National Mid-term Genebank for Vegetables, Beijing, China was analyzed based on 29 simple sequence repeat (SSR) markers, which were evenly distributed over 12 pepper chromosomes.  The pepper accessions were divided into two groups in a genetic structure analysis, and the two groups showed obvious differences in fruit type and geographical distribution.  We finally selected 248 accessions capturing 75.6% of the SSR alleles as the core collection for further research.  Insights into the genetic structure of pepper provide the basis for population-level gene mining and genetic improvement.
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Genome-wide detection of selective signatures in a Duroc pig population
DIAO Shu-qi, LUO Yuan-yu, MA Yun-long, DENG Xi, HE Ying-ting, GAO Ning, ZHANG Hao, LI Jia-qi, CHEN Zan-mou, ZHANG Zhe
2018, 17 (11): 2528-2535.   DOI: 10.1016/S2095-3119(18)61984-7
Abstract429)      PDF in ScienceDirect      
The Duroc pig has high adaptability and feeding efficiency, making it one of the most popular pig breeds worldwide.  Over long periods of natural and artificial selection, genetic footprints, i.e., selective signatures, were left in the genome.  In this study, a Duroc pig population (n=715) was genotyped with the Porcine SNP60K Bead Chip and the GeneSeek Genomic Profiler (GGP) Porcine Chip.  The relative extended haplotype homozygosity (REHH) method was used for selective signature detection in a subset of the population (n=368), selected to represent a balanced family structure.  In total, 154 significant core regions were detected as selective signatures (P<0.01), some of which overlap with previously reported quantitative trait loci associated with several economically important traits, including average daily gain and backfat thickness.  Genome annotation for these significant core regions revealed a variety of interesting candidate genes including GATA3, TAF3, ATP5C1, and FGF1.  These genes were functionally related to anterior/posterior pattern specification, phosphatidylinositol 3-kinase signaling, embryonic skeletal system morphogenesis, and oxidation-reduction processes.  This research provides knowledge for the study of selection mechanisms and breeding practices in Duroc and other pigs.
 
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Effects of slow or controlled release fertilizer types and fertilization modes on yield and quality of rice
WEI Hai-yan, CHEN Zhi-feng, XING Zhi-peng, ZHOU Lei, LIU Qiu-yuan, ZHANG Zhen-zhen, JIANG Yan, HU Ya-jie, ZHU Jin-yan, CUI Pei-yuan, DAI Qi-gen, ZHANG Hong-cheng
2018, 17 (10): 2222-2234.   DOI: 10.1016/S2095-3119(18)62052-0
Abstract469)      PDF in ScienceDirect      
There is limited information about the influence of slow or controlled release fertilizer (S/CRF) on rice yield and quality.  In this study, japonica rice cultivar Nanjing 9108 was used to study the effects of three different S/CRFs (polymer-coated urea (PCU), sulfur-coated urea (SCU), and urea formaldehyde (UF)) and two fertilization modes (both S/CRF and common urea (CU) as basal fertilizer, S/CRF as basal and CU as tillering fertilizer) on rice yield and quality.  CU only was applied separately as control (CK).  Results showed that, rice grain yield, chalky kernel rate, chalky area, overall chalkiness, and the content of gliadin, glutenin, and protein, all showed the trends of UF>PCU>SCU within the same fertilization mode, and showed the trends of S/CRF as basal and CU as tillering fertilizer>both S/CRF and CU as basal fertilizer within the same type of S/CRF.  In contrast, the contents of amylose, amylopectin, and starch, as well as taste value, and peak and hot viscosity showed trends of SCU>PCU>UF, and the trends of both S/CRF and CU as basal fertilizer>S/CRF as basal and CU as tillering fertilizer.  Among S/CRF treatments and fertilization modes, taste values of cooked rice were positively correlated with amylose, amylopectin, and starch contents, as well as gel consistency, peak viscosity, hot viscosity, and cool viscosity, while negatively correlated with globulin, gliadin, glutenin, and protein contents.  The types of S/CRF and fertilization modes are important for improving rice yield and quality.  Compared to CK, higher yield and similar quality of rice was achieved with UF as basal and CU as tillering fertilizer, and similar yield with improved appearance and eating and cooking quality of rice was achieved with either both UF and CU as basal fertilizer, or PCU as basal and CU as tillering fertilizer.
 
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Effects of leaf removal and cluster thinning on berry quality of Vitis vinifera cultivars in the region of Weibei Dryland in China
SONG Chang-zheng, WANG Chao, XIE Sha, ZHANG Zhen-wen
2018, 17 (07): 1620-1630.   DOI: 10.1016/S2095-3119(18)61990-2
Abstract525)      PDF in ScienceDirect      
Leaf removal and cluster thinning were carried out prior to veraison to evaluate the effects on berry quality of two Vitis vinifera cultivars (Cabernet Sauvignon and Ugni Blanc) in the Weibei Dryland of China in 2013 and 2014, and comprehensive analysis of the chemical and volatile composition in berries was performed.  The results showed that content of reducing sugar in both varieties was not affected while total acid was generally decreased by leaf removal and cluster thinning.  The pH of berry juice was correspondingly higher in most treatment groups.  Meanwhile, promoting effects on accumulation of total phenols, tannin in both varieties and total anthocyanins in Cabernet Sauvignon were found.  As for monomeric anthocyanins, percentage of malvidin and its derivatives was decreased by leaf removal and cluster thinning.  Besides, cinnamylated anthocyanins decreased with the intensity of cluster thinning.  The accumulation of non-anthocyanin phenolics was similarly affected in the two varieties.  Notably, cluster thinning was more effective on enhancing the phenolics content than leaf removal.  The combination of middle level of leaf removal and cluster thinning was the most favor to the accumulation of phenolic acids.  Furthermore, cluster thinning could also significantly enhance the synthesis of flavanols and stilbenes.  Lastly, content and variety of aroma compounds in both grape varieties were also significantly affected by the treatments.  The results provided a theoretical basis for a combination of leaf removal and cluster thinning to improve quality of grapes and wines.
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Identification of miRNAs and target genes regulating catechin biosynthesis in tea (Camellia sinensis)
SUN Ping, ZHANG Zhen-lu, ZHU Qiu-fang, ZHANG Guo-ying, XIANG Ping, LIN Yu-ling, LAI Zhongxiong, LIN Jin-ke
2018, 17 (05): 1154-1164.   DOI: 10.1016/S2095-3119(17)61654-X
Abstract1175)      PDF in ScienceDirect      
MicroRNAs (miRNAs) are endogenous non-protein-coding small RNAs that play crucial and versatile regulatory roles in plants.  Using a computational identification method, we identified 55 conserved miRNAs in tea (Camellia sinensis) by aligning miRNA sequences of different plant species with the transcriptome library of tea strain 1005.  We then used quantitative real-time PCR (qRT-PCR) to analyze the expression of 31 identified miRNAs in tea leaves of different ages, thereby verifying the existence of these miRNAs and confirming the reliability of the computational identification method.  We predicted which miRNAs were involved in catechin synthesis using psRNAtarget Software based on conserved miRNAs and catechin synthesis pathway-related genes.  Then, we used RNA ligase-mediated rapid amplification of cDNA ends (RLM-RACE) to obtain seven miRNAs cleaving eight catechin synthesis pathway-related genes including chalcone synthase (CHS), chalcone isomerase (CHI), dihydroflavonol 4-reductase (DFR), anthocyanidin reductase (ANR), leucoanthocyanidin reductase (LAR), and flavanone 3-hydroxylase (F3H).  An expression analysis of miRNAs and target genes revealed that miR529d and miR156g-3p were negatively correlated with their targets CHI and F3H, respectively.  The expression of other miRNAs was not significantly related to their target genes in the catechin synthesis pathway.  The RLM-RACE results suggest that catechin synthesis is regulated by miRNAs that can cleave genes involved in catechin synthesis. 
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MicroRNA-34c regulates porcine granulosa cell function by targeting forkhead box O3a
XU Yuan, ZHANG Ai-ling, ZHANG Zhe, YUAN Xiao-long, CHEN Zan-mou, ZHANG Hao, LI Jia-qi
2017, 16 (09): 2019-2028.   DOI: 10.1016/S2095-3119(16)61582-4
Abstract880)      PDF in ScienceDirect      
Granulosa cells (GCs) are somatic cells of ovary, the behaviors of GCs are important for ovarian function.  MicroRNAs (miRNAs) are a class of endogenous 18–24 nucleotide (nt) non-coding RNAs, some of which have been shown to be important regulators of GCs function.  miR-34c involved in the regulation of various biological processes and was identified to be a pro-apoptotic and anti-proliferative factor in many cell types.  However, the roles of miR-34c in GCs function remain unknown.  In this study, we used Annexin V-FITC and EdU assays to demonstrate that miR-34c exerted pro-apoptotic and anti-proliferative effects in porcine GCs.  Dual-luciferase reporter assays, quantitative real-time PCR (qRT-PCR) and Western blotting identified Forkhead box O3a (FoxO3a) as a direct target gene of miR-34c.  The overexpression of FoxO3a rescued the phenotypic change caused by miR-34c in porcine GCs.  In conclusion, miR-34c regulate the function of porcine GCs by targeting FoxO3a.
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Penicillin-resistant characterization of Staphylococcus aureus isolated from bovine mastitis in Gansu, China
YANG Feng, LIU Long-hai, WANG Ling, WANG Xu-rong, LI Xin-pu, LUO Jin-yin, ZHANG Zhe, ZHANG Shi-dong, YAN Zuo-ting, LI Hong-sheng
2017, 16 (08): 1874-1878.   DOI: 10.1016/S2095-3119(16)61531-9
Abstract1414)      PDF in ScienceDirect      
    Bovine mastitis caused by Staphylococcus aureus is difficult to treat because of increasing resistance against antibiotics, especially penicillin. β-Lactamase and biofilm are responsible for penicillin resistance of S. aureus. The aim of this study was to investigate the β-lactamase activity and biofilm formation capacity of 37 penicillin-resistant S. aureus strains (35 were blaZ positive and 2 were blaZ negative) from bovine mastitis in Gansu Province, China, as well as to measure the intercellular adhesion genes icaA and icaD of these strains. β-Lactamase Test Kit was used to determine the β-lactamase activity, biofilm formation was tested by semi-quantitative adherence assay method. Moreover, the presence of icaA and icaD were measured by PCR. A total of 32 penicillin-resistant S. aureus strains, including the two blaZ-negative strains, were identified as β-lactamase producers. All tested S. aureus isolates produced biofilm in the microtiter plate assay. Meanwhile, all these strains were PCR-positive for the ica locus, icaA and icaD. The study indicated high prevalence of β-lactamase activity, biofilm-forming capacity, and the ica genes among the penicillin-resistant S. aureus isolates, and implied that S. aureus resistant to penicillin was attributed to multiple mechanisms.
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The diversity and potential function of endophytic bacteria isolated from Kobreasia capillifolia at alpine grasslands on the Tibetan Plateau, China
WANG Ying, YANG Cheng-de, YAO Yu-ling, WANG Yu-qin, ZHANG Zhen-fen, XUE Li
2016, 15 (9): 2153-2162.   DOI: 10.1016/S2095-3119(15)61248-5
Abstract1448)      PDF in ScienceDirect      
A total of 50 endophytic bacterial isolates were obtained from Kobreasia capillifolia at alpine grasslands in the Eastern Qilian Mountains on the Tibetan Plateau in China.  Based on the sequencing and phylogenetic analysis of 16S rDNA genes, all isolates phylogenetically related closely to Bacillus, Acinetobacter, Stenotrophomonas, Brevundimonas, Arthrobacter, Curtobacterium, Paenibacillus, Plantibacter, Promicromonospora, Serratia, and Microbacterium, among which Bacillus was the predominant genus (47.8% of the total number of endophytic isolates).  These isolates possessed different biological functions.  In 50 endophytic bacteria, 42 isolates produced indole acetic acid (IAA) on King medium.  There were seven isolates showing potency of mineral phosphate solubilization in Pikovaskaia’s (PKO) liquid medium.  Seven isolates exhibited antagonistic effect against Fusarium avenaceum, Colletotrichum coccodes and Phoma foveata.  This was the first report on diversity and plant growth promotion of endophytic bacteria from K. capillifolia on alpine grassland in the Eastern Qilian Mountains, Chain.  It is essential for revealing the relationship among plant, microorganism, and the special environment because the potential function of endophytic bacteria made a contribution to the interactions of plants and endophytic bacteria.
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Genetic diversity of pepper (Capsicum spp.) germplasm resources in China reflects selection for cultivar types and spatial distribution
ZHANG Xiao-min, ZHANG Zheng-hai, GU Xiao-zhen, MAO Sheng-li, LI Xi-xiang, Jo?l Chadoeuf, Alain Palloix, WANG Li-hao, ZHANG Bao-xi
2016, 15 (9): 1991-2001.   DOI: 10.1016/S2095-3119(16)61364-3
Abstract1869)      PDF in ScienceDirect      
    Pepper (Capsicum spp.) is an important vegetable crop in the world. Now the pepper in China contributes one-third of the world’s peppers production. Genetic diversity of the pepper germplasm of China is expected interesting to know. To explore the structure of genetic diversity in Chinese pepper germplasm resources and possible relationship with cultivar types or geographic origin, we sampled and compared 372 GenBank pepper accessions (local cultivars and landraces) from 31 provinces, autonomous regions and municipalities of China and 31 additional accessions from other countries. These accessions were genotyped using 28 simple sequence repeat (SSR) markers spanning the entire pepper genome. We then investigated the genetic structure of the sampled collection using model-based analysis in STRUCTURE v2.3.4 and examined genetic relationships by the unweighted pair-group method of mathematical averages (UPGMA) in MEGA. In addition to geographic origin, we evaluated eight plant and fruit traits. In total, 363 alleles were amplified using the 28 SSR primers. Gene diversity, polymorphism information content and heterozygosity of the 28 SSR loci were estimated as 0.09–0.92, 0.08–0.92 and 0.01–0.34, respectively. The UPGMA cluster analysis clearly distinguished Capsicum annuum L. from other cultivated pepper species. Population structure analysis of the 368 C. annuum accessions uncovered three genetic groups which also corresponded to distinct cultivar types with respect to the plant and fruit descriptors. The genetic structure was also related to the geographic origin of the landraces. Overall results indicate that genetic diversity of Chinese pepper landraces were structured by migration of genotypes followed by human selection for cultivar types in agreement with consumption modes and adaptation to the highly diversified agro-climatic conditions.
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p53 and NFκB regulate microRNA-34c expression in porcine ovarian granulosa cells
XU Yuan, ZHANG Ai-ling, XIAO Guang, ZHANG Zhe, CHEN Zan-mou, ZHANG Hao, LI Jia-qi
2016, 15 (8): 1816-1824.   DOI: 10.1016/S2095-3119(15)61178-9
Abstract1514)      PDF in ScienceDirect      
   MicroRNAs (miRNAs) are endogenous 18–24 nucleotide (nt) non-coding RNAs, some of which have been indicated to play key roles in granulosa cells (GCs) function. However, little is known about how the miRNA gene expression itself is regulated in the GCs. Our previous study showed that miR-34c, identified to be a pro-apoptotic and anti-proliferative factor in many cell types, exerted the same effects in porcine GCs. Here, the transcriptional regulation of miR-34c expression in GCs was further investigated. 5´ rapid amplification of cDNA ends (RACE) assay indicated that the pri-miR-34c transcription start site was located in 1 556 bp upstream of pre-miR-34c. With dual-luciferase reporter assay, we confirmed a 69 bp core promoter region (–1 799 bp/–1 730 bp) was indispensable for the transcription of miR-34c. Chromatin immunoprecipitation (ChIP) assay demonstrated that p53, p50, and p65 could bind to the transcription factor binding sites within the 69 bp core promoter region. In addition, deletion of transcripition factor binding sites resulted in obvious change of the miR-34c promoter activity. Finally, using overexpression and knockdown of p53, p50, and p65 strategies, we showed that p53 and p50 could positively regulated miR-34c expression, whereas p65 neletively regulated miR-34c expression in GCs. Our results provide new data about the transcription regulatory mechanism of miRNA genes in GCs.
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