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Genome-wide association with transcriptomics reveals a shade-tolerance gene network in soybean

The Crop Journal 2024年第1期12卷 232-243页

作者： Yanzhu Su Xiaoshuai Hao Weiying Zeng Zhenguang Lai Yongpeng Pan Can Wang Pengfei Guo Zhipeng Zhang Jianbo He Guangnan Xing Wubin Wang Jiaoping Zhang Zudong Sun Junyi Gai soybean research Institute/MARA National center for soybean Improvement MARA Key Laboratory of Biology and Genetic Improvement of soybean/State Key Laboratory for Crop Genetics and Germplasm Enhancement/State Innovation Platform for Integrated Production and Education in soybean Bio-breeding/Jiangsu Collaborative Innovation center for Modern Crop Production Nanjing Agricultural UniversityNanjing 210095JiangsuChina Guangxi Academy of Agricultural Sciences Nanning 530007GuangxiChina

Shade tolerance is essential for soybeans in inter/relay cropping systems.A genome-wide association study(GWAS)integrated with transcriptome sequencing was performed to identify genes and construct a genetic network governing the trait in a set of recombinant inbred lines derived from two soybean parents with contrasting shade *** improved GWAS procedure,restricted two-stage multi-locus genome-wide association study based on gene/allele sequence markers(GASM-RTM-GWAS),identified 140 genes and their alleles associated with shade-tolerance index(STI),146 with relative pith cell length(RCL),and nine with *** of these genes by biological categories allowed the construction of a protein–protein interaction network by 187 genes,of which half were differentially expressed under shading and non-shading conditions as well as at different growth *** the identified genes,three ones jointly identified for both traits by both GWAS and transcriptome and two genes with maximum links were chosen as beginners for entrance into the ***,both STI and RCL gene systems worked for shade-tolerance with genes interacted each other,this confirmed that shadetolerance is regulated by more than single group of interacted genes,involving multiple biological functions as a gene network.

关键词： soybean(Glycine max(L.)Merr.) Shade-tolerance Restricted two-stage multi-locus genomewide association study based on gene/allele sequence markers(GASM-RTM-GWAS) Shade-tolerance index(STI) Relative cell length(RCL) Transcriptome

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Unraveling the regulatory network of flower coloration in soybean:Insights into roles of GmMYBA3 and GmMYBR1

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The Crop Journal 2024年第2期12卷 443-455页

作者： Ruifang Gao Yueqing Li Yanan Wang Xiaotong Shan Siqi Yang Ye Zhang Saiyu Ma Chunbao Zhang Jianchun Qin Li Wang Xiang Gao College of Plant Science Jilin UniversityChangchun 130062JilinChina Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics&Cytology Northeast Normal UniversityChangchun 130024JilinChina soybean research Institute National Engineering Research Center for SoybeanJilin Academy of Agricultural SciencesChangchun 130033JilinChina

Anthocyanins play crucial roles in pollen protection and pollinator attraction in flowering ***,the mechanisms underlying flower color determination and whether floral anthocyanin regulators participate in other processes remain largely unresolved in soybeans(Glycine max).In this study,we investigated the genetic components and mechanisms governing anthocyanin biosynthesis in soybean *** and genetic studies have characterized two antagonistic regulators,the positive activator GmMYBA3 and the negative repressor GmMYBR1,that modulate the gene expression of anthocyanin biosynthesis in soybean *** findings revealed a regulatory interplay between GmMYBA3 and GmMYBR1 bridged by GmTT8a,highlighting the complexity of anthocyanin regulation in different soybean *** of additional soybean cultivars demonstrated the universality of GmMYBA3 and GmMYBR1 in regulating floral anthocyanin biosynthesis-related genes,with GmF3’5’H identified as a crucial determinant of white flower *** study provides a molecular mechanism underlying soybean flower color determination,paving the way for the molecular modification of soybean flowers to probably enhance their resistance to abiotic stresses and attractiveness to pollinators.

关键词： Anthocyanin Flower color determination MBW complex MYB repressor Pleiotropic regulator

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Food-derived protein hydrolysates and peptides:anxiolytic and antidepressant activities,characteristics,and mechanisms

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Food Science and Human Wellness 2024年第3期13卷 1168-1185页

作者： Wenhui Li Yu Xi Junru Wang Yinxiao Zhang He Li Xinqi Liu Beijing Advanced Innovation center for Food Nutrition and Human Health Beijing Engineering and Technology Research Center of Food AdditivesNational Soybean Processing Industry Technology Innovation CenterBeijing Technology and Business UniversityBeijing 100048China

Globally,the prevalence of anxiety and depression has reached epidemic ***-derived protein hydrolysates and peptides delivered through dietary supplementation can avoid the negative risks associated with traditional pharmaceuticals while delivering superior anxiolytic and antidepressant *** review summarizes current research on food-derived anxiolytic and antidepressant protein hydrolysates and peptides,and subsequently analyses their physicochemical characteristics and elaborates on their *** aim of this work is to contribute to the in-depth study and provide a theoretical foundation for the development of related products to better serve patients with anxiety and depression.

关键词： Anxiolytic Antidepressant Peptides Protein hydrolysates Neurotransmitter

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The MADS-box transcription factor GmFULc promotes GmZTL4 gene transcription to modulate maturity in soybean

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Journal of Integrative Plant Biology 2024年第8期66卷 1603-1619页

作者： Jingzhe Sun Yucheng Liu Yuhong Zheng Yongguo Xue Yuhuan Fan Xiaofei Ma Yujia Ji Gaoyuan Liu Xiaoming Zhang Yang Li Shuming Wang Zhixi Tian Lin Zhao Key Laboratory of soybean Biology of Ministry of Education China Northeast Agricultural UniversityHarbin 150030China Qingdao Institute of Bioenergy and Bioprocess Technology The Chinese Academy of SciencesQingdao 266101China State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignThe Chinese Academy of SciencesBeijing 100101China Jilin Academy of Agricultural Sciences China Agricultural Science and Technology Northeast Innovation CenterChangchun 130033China Institute of soybean research Heilongjiang Provincial Academy of Agricultural SciencesHarbin 150086China Depatment of Environmental and Plant Biology Ohio UniversityAthensOhio 45701USA

Flowering time and maturity are crucial agronomic traits that affect the regional adaptability of soybean *** development of soybean cultivars with early maturity adapted to longer days and colder climates of high latitudes is very important for ensuring normal ripening before frost *** belongs to the MADS-box transcription factor family and has several duplicated members in *** this study,we observed that overexpression of GmFULc in the Dongnong 50 cultivar promoted soybean maturity,while GmFULc knockout mutants exhibited late *** immunoprecipitation sequencing(ChIP-seq)and RNA sequencing(RNA-seq)revealed that GmFULc could bind to the CArG,bHLH and homeobox *** investigation revealed that GmFULc could directly bind to the CArG motif in the promoters of the GmZTL3 and GmZTL4 *** of GmZTL4 promoted soybean maturity,whereas the ztl4 mutants exhibited delayed ***,we found that the cis element box 4 motif of the GmZTL4 promoter,a motif of light response elements,played an important role in controlling the growth *** of this motif shortened the growth period by increasing the expression levels of *** investigations revealed that short-day treatment promoted the binding of GmFULc to the promoter of GmZTL4 and inhibited the expression of E1 and E1Lb,ultimately resulting in the promotion of flowering and early *** together,these findings suggest a novel photoperiod regulatory pathway in which GmFULc directly activates GmZTL4 to promote earlier maturity in soybean.

关键词： flowering time GmFULc GmZTL4 maturity photoperiod

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Fermented soybean meal improved laying performance and egg quality of laying hens by modulating cecal microbiota,nutrient digestibility,intestinal health,antioxidant and immunological functions

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Animal Nutrition 2024年第3期18卷 309-321页

作者： Uchechukwu Edna Obianwuna Lingling Huang Haijun Zhang Jing Wang Guanghai Qi Kai Qiu Shugeng Wu National Engineering research center of Biological Feed Institute of Feed ResearchChinese Academy of Agricultural SciencesBeijing 100081China Wilmar(Shanghai)Biotechnology research&Development center Co. Ltd.Shanghai 200137China

Antinutritional factors in feedstuffs may limit their utilization in livestock production,but fermentation process can be used to improve feed quality;however,studies on fermented soybeans for laying hens remain *** investigated the effect of fermented soybean meal(FSBM)at various inclusion levels as a partial replacement for soybean meal(SBM)on egg production,egg quality,amino acid digestibility,gut morphology and microbiota,antioxidant capacity and immune response of young laying hens.A total of 360 Hy-line Brown laying hens aged 18 weeks were selected and divided into 5 groups of 6 replicates each and 12 birds per *** control group received a basal diet while the trial group received the basal diet with FSBM included at 2.5%,5.0%,7.5%and 10.0%,respectively,for 12 *** findings revealed that the nutritional value of FSBM was higher compared to that of SBM in terms of reduced content of trypsin inhibitors and increased contents of crude protein,amino acids and *** enhanced egg production(P<0.05),feed-to-egg ratio(P<0.05),and albumen quality(albumen height and Haugh unit)(P<0.05).Furthermore,FSBM improved apparent fecal amino acid digestibility(P<0.05),gut morphology(increased villus height,villus width,villus height-to-crypt depth ratio and decreased crypt depth)(P<0.05),antioxidant capacity(reduced malondialdehyde and increased catalase,total superoxide dismutase,glutathione peroxidase and total antioxidant capacity)(P<0.05)and immune function(increased concentrations of IgG,IgA,and IgM;increased levels of transforming growth factor beta and Toll-like receptor 2;and reduced levels of interleukin 1βand tumor necrosis factor alpha)(P<0.05).Further analysis showed that FSBM altered the composition of the gut microbiota favoring beneficial *** findings suggest that probiotic fermentation improved the nutritional value of *** inclusion of FSBM in the diets of laying hens at 2.5%or 5.0%improved amino acid digestibility,gut

关键词： Fermented soybean meal Laying hen Egg production Egg quality Immune response

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Searching for plant NLR immune receptors conferring resistance to potyviruses

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The Crop Journal 2024年第1期12卷 28-44页

作者： Xin Hong Shufen Li Xiaofei Cheng Haijian Zhi Jinlong Yin Kai Xu Jiangsu Key Laboratory for Microbes and Functional Genomics Jiangsu Engineering and Technology Research Center for MicrobiologyCollege of Life SciencesNanjing Normal UniversityNanjing 210023JiangsuChina College of Plant Protection Northeast Agricultural UniversityHarbin 150030HeilongjiangChina National center for soybean Improvement National Key Laboratory for Crop Genetics and Germplasm EnhancementKey Laboratory of Biology and Genetic Improvement of Soybean-Ministry of AgricultureNanjing Agricultural UniversityNanjing 210095JiangsuChina

To fight against invasion by pathogens,plants have evolved an elaborate innate immune system,of which the nucleotide-binding domain leucine-rich repeat-containing receptor(NLR)acts as the sensor and immune ***,comprising one of the largest genera of plant viruses,cause severe crop yield losses *** crop resistance to potyviruses can be used in breeding and plant transgenesis to control disease *** review summarizes achievements in mapping and cloning NLR genes conferring dominant resistance against potyvirus in the families Fabaceae,Solanaceae,Brassicaceae,and *** compares mechanisms of potyviral protein recognition and downstream signaling employed by NLRs and discusses strategies for exploiting NLRs to better control diseases caused by potyviruses.

关键词： NLR Potyvirus resistance Genetic diversity Mapping Engineer

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Drought-triggered repression of miR166 promotes drought tolerance in soybean

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The Crop Journal 2024年第1期12卷 154-163页

作者： Chen Zhao Jingjing Ma Chen Yan Yu Jiang Yaohua Zhang Yudan Lu Ye Zhang Suxin Yang Xianzhong Feng Jun Yan School of Life Sciences East China Normal UniversityShanghai 200241China Key Laboratory of soybean Molecular Design Breeding Northeast Institute of Geography and AgroecologyChinese Academy of SciencesChangchun 130102JilinChina

Drought stress limits agricultural productivity *** and characterizing genetic components of drought stress-tolerance networks may improve crop resistance to drought *** show that the regulatory module formed by miR166 and its target gene,ATHB14-LIKE,functions in the regulation of drought tolerance in soybean(Glycine max).Drought stress represses the accumulation of miR166,leading to upregulation of its target *** knockdown of miR166 in the stable transgenic line GmSTTM166 conferred drought tolerance without affecting *** of ABA signaling pathway genes was regulated by the miR166-mediated regulatory pathway,and ATHB14-LIKE directly activates some of these *** is a feedback regulation between ATHB14-LIKE and MIR166 genes,and ATHB14-LIKE inhibits MIR166 *** findings reveal that drought-triggered regulation of the miR166-mediated regulatory pathway increases plants drought resistance,providing new insights into drought stress regulatory network in soybean.

关键词： soybean Drought stress miRNA ABA signaling

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CRISPR/CasRx-mediated resistance to soybean mosaic virus in soybean

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The Crop Journal 2024年第4期12卷 1093-1101页

作者： Le Gao Lijun Xie Yanmin Xiao Xinge Cheng Ruosi Pu Ziheng Zhang Yu Liu Shaopei Gao Zilong Zhang Haoran Qu Haijian Zhi Kai Li MARA Key Laboratory of Biology and Genetics Improvement of soybean Zhongshan Biological Breeding Laboratory(ZSBBL)National Innovation Platform for Soybean Breeding and Industry-Education IntegrationState Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationNanjing Agricultural UniversityNanjing 210095JiangsuChina Department of Horticulture Beijing Vocational College of AgricultureBeijing 102442China College of Agronomy&Biotechnology China Agricultural UniversityBeijing 100193China College of Bioscience and Biotechnology Shenyang Agricultural UniversityShenyang 110866LiaoningChina

soybean mosaic virus(SMV),an RNA virus,is the most common and destructive pathogenic virus in soybean *** newly developed CRISPR/Cas immune system has provided a novel strategy for improving plant resistance to viruses;hence,this study aimed to engineer SMV resistance in soybean using this ***,multiple sgRNAs were designed to target positive-and/or negative-sense strands of the SMV HC-Pro ***,the corresponding CRISPR/CasRx vectors were constructed and transformed into *** inoculation with SMV,39.02%,35.77%,and 18.70%of T_(1)plants were confirmed to be highly resistant(HR),resistant(R),and mildly resistant(MR)to SMV,respectively,whereas only 6.50%were identified as susceptible(S).Additionally,qRT-PCR and DAS-ELISA showed that,both at 15 and 30 d post-inoculation(dpi),SMV accumulation significantly decreased or was even undetectable in HR and R plants,followed by MR and S ***,the expression level of the CasRx gene varied in almost all T_(1)plants with different resistance level,both at 15 and 30 ***,when SMV resistance was evaluated in the T_(2)generation,the results were similar to those recorded for the T_(1)*** findings provide new insights into the application of the CRISPR/CasRx system for soybean improvement and offer a promising alternative strategy for breeding for resistance to biotic stress that will contribute to the development of SMV-immune soybean germplasm to accelerate progress towards greater soybean crop productivity.

关键词： soybean RNA virus soybean mosaic virus Resistance CRISPR/CasRx

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A telomere-to-telomere genome assembly of Zhonghuang 13,a widely-grown soybean variety from the original center of Glycine max

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The Crop Journal 2024年第1期12卷 142-153页

作者： Anqi Zhang Tangchao Kong Baiquan Sun Shizheng Qiu Jiahe Guo Shuyong Ruan Yu Guo Jirui Guo Zhishuai Zhang Yue Liu Zheng Hu Tao Jiang Yadong Liu Shuqi Cao Shi Sun Tingting Wu Huilong Hong Bingjun Jiang Maoxiang Yang Xiangyu Yao Yang Hu Bo Liu Tianfu Han Yadong Wang center for Bioinformatics School of Computer Science and TechnologyHarbin Institute of TechnologyHarbin 150001HeilongjiangChina Ministry of Agriculture Key Laboratory of soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

soybean(Glycine max)stands as a globally significant agricultural crop,and the comprehensive assembly of its genome is of paramount importance for unraveling its biological characteristics and evolutionary ***,previous soybean genome assemblies have harbored gaps and incompleteness,which have constrained in-depth investigations into ***,we present Telomere-to-Telomere(T2T)assembly of the Chinese soybean cultivar Zhonghuang 13(ZH13)genome,termed ZH13-T2T,utilizing PacBio Hifi and ONT ultralong *** employed a multi-assembler approach,integrating Hifiasm,NextDenovo,and Canu,to minimize biases and enhance assembly *** assembly spans 1,015,024,879 bp,effectively resolving all 393 gaps that previously plagued the reference *** annotation efforts identified 50,564 high-confidence protein-coding genes,707 of which are ***13-T2T revealed longer chromosomes,421 not-aligned regions(NARs),112 structure variations(SVs),and a substantial expansion of repetitive element compared to earlier ***,we identified 25.67 Mb of tandem repeats,an enrichment of 5S and 48S rDNAs,and characterized their genotypic *** summary,we deliver the first complete Chinese soybean cultivar T2T *** comprehensive annotation,along with precise centromere and telomere characterization,as well as insights into structural variations,further enhance our understanding of soybean genetics and evolution.

关键词： soybean Telomere-to-Telomere assembly Zhonghuang 13 Structure variations

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A warm temperature-released negative feedback loop fine-tunes PIF4-mediated thermomorphogenesis in Arabidopsis

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Plant Communications 2024年第5期5卷 208-224页

作者： Hui Li Mande Xue Huairen Zhang Fengyue Zhao Xiaoyi Li Shuancang Yu Danhua Jiang Key Laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina University of Chinese Academy of Sciences BeijingChina Beijing Vegetable research center Beijing Academy of Agriculture and Forestry Sciences(BAAFS)BeijingChina National center for soybean Improvement State Key Laboratory of Crop Genetics and Germplasm EnhancementCollege of AgricultureNanjing Agricultural UniversityNanjingChina

Plants can sense temperature changes and adjust their growth *** Arabidopsis,high ambient temperatures stimulate stem elongation by activating a key thermoresponsive regulator,PHYTOCHROME INTERACTING FACTOR 4(PIF4).Here,we show that warmth promotes the nighttime transcription of GI,which is necessary for the high temperature-induced transcription of *** analyses suggest that GI prevents excessive thermoresponsive growth by inhibiting PIF4,with this regulatory mechanism be-ing partially reliant on *** transcription is repressed by ELF3 and HY5,which concurrently inhibit PIF4 expression and *** elevation causes the deactivation or degradation of ELF3 and HY5,leading to PIF4 activation and relief of GI transcriptional repression at high *** allows PIF4 to further activate GI transcription in response to elevated ***,in turn,inhibits PIF4,es-tablishing a negative feedback loop thatfine-tunes PIF4 *** addition,we demonstrate that ELF3,HY5,and PIF4 regulate GI transcription by modulating the enrichment of histone variant H2A.Z at the GI ***,ourfindings suggest that thermal release of a negative feedback loopfinely adjusts plant thermomorphogenesis.

关键词： temperature thermomorphogenesis PIF4 GI TOC1 feedback loop

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