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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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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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GmNF-YC4 delays soybean flowering and maturation by directly repressing GmFT2a and GmFT5a expression

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Journal of Integrative Plant Biology 2024年第7期66卷 1370-1384页

作者： Yupeng Cai Li Chen Xiaoqian Liu Weiwei Yao Wensheng Hou State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Ministry of Agriculture Key Laboratory of soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Flowering time and growth period are key agronomic traits which directly affect soybean(Glycine max(L.)Merr.)adaptation to diverse latitudes and farming *** FLOWERING LOCUS T(FT)homologs GmFT2a and GmFT5a integrate multiple flowering regulation pathways and significantly advance flowering and maturity in *** the genes responsible for regulating GmFT2a and GmFT5a will improve our understanding of the molecular mechanisms governing growth period in *** this study,we identified the Nuclear Factor Y-C(NFY-C)protein GmNF-YC4 as a novel flowering suppressor in soybean under long-day(LD)***-YC4 delays flowering and maturation by directly repressing the expression of GmFT2a and *** addition,we found that a strong selective sweep event occurred in the chromosomal region harboring the GmNF-YC4 gene during soybean *** GmNF-YC4Hap3 allele was mainly found in wild soybean(Glycine soja Siebold&Zucc.)and has been eliminated from *** landraces and improved cultivars,which predominantly contain the GmNF-YC4Hap1 ***,the Gmnf-yc4 mutants displayed notably accelerated flowering and maturation under LD *** alleles may prove to be valuable genetic resources for enhancing soybean adaptability to higher latitudes.

关键词： CRISPR/Cas9 early flowering and maturity GmNF-YC4 regional adaptability soybean

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BBX9 forms feedback loops with PIFs and BBX21 to promote photomorphogenic development

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Journal of Integrative Plant Biology 2024年第9期66卷 1934-1952页

作者： Zhaoqing Song Wanying Ye Qing Jiang Huan Lin Qing Hu Yuntao Xiao Yeting Bian Fengyue Zhao Jie Dong Dongqing Xu State Key Laboratory of Crop Genetics&Germplasm Enhancement and Utilization National Center for Soybean ImprovementCollege of AgricultureNanjing Agricultural UniversityNanjing 210095China institute of Crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China

Light is one of the most essential environmental factors that tightly and precisely control various physiological and developmental processes in plants.B-box CONTAINING PROTEINs(BBXs)play central roles in the regulation of light-dependent *** this study,we report that BBX9 is a positive regulator of light ***9 interacts with the red light photoreceptor PHYTOCHROME B(phyB)and transcription factors PHYTOCHROME-INTERACTING FACTORs(PIFs).phyB promotes the stabilization of BBX9 in light,while BBX9 inhibits the transcriptional activation activity of *** turn,PIFs directly bind to the promoter of BBX9 to repress its *** the other hand,BBX9 associates with the positive regulator of light signaling,BBX21,and enhances its biochemical ***21 associates with the promoter regions of BBX9 and transcriptionally up-regulates its ***,this study unveiled that BBX9 forms a negative feedback loop with PIFs and a positive one with BBX21 to ensure that plants adapt to fluctuating light conditions.

关键词： Arabidopsis BBX21 BBX9 light signaling photo-morphogenesis phyB PIF

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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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The RUBY reporter for visual selection in soybean genome editing

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aBIOTECH 2024年第2期5卷 209-213页

作者： Li Chen Yupeng Cai Xiaoqian Liu Weiwei Yao Shuiqing Wu Wensheng Hou State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China Ministry of Agriculture Key Laboratory of soybean Biology(Beijing) Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijing 100081China

Current systems to screen for transgenic soybeans(Glycine max)involve laborious molecular assays or the expression of fluorescent markers that are difficult to see in soybean ***,a visual system for early screening of transgenic plants would increase the efficiency of crop improvement by genome *** RUBY reporter system,which consists of three genes encoding betalain biosynthetic enzymes,leading to the accumulation of purple pigment in transgenic tissue,has been employed in some plants and dikaryon ***,we assessed the RUBY reporter for visual verification during soybean *** show that RUBY can be expressed in soybean,allowing for visual confirmation of transgenic events without the need for specialized *** with visible accumulation of purple pigment in any tissue were successfully transformed,confirming the accuracy of the RUBY system as a visual *** also assessed the genetic stability of the transgene across generations,which can be performed very early,using the cotyledons of the ***-free seedlings have a distinct green color,facilitating the selection of genome-edited but transgene-free soybean seedlings for *** the RUBY system,we quickly identified a transgene-free Gmwaxy mutant in the T1 *** system thus provides an efficient and convenient tool for soybean genome editing.

关键词： soybean RUBY Visual reporter Genome editing Biotechnology

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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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The GmSTF1/2–GmBBX4 negative feedback loop acts downstream of blue-light photoreceptors to regulate isoflavonoid biosynthesis in soybean

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Plant Communications 2024年第2期5卷 198-214页

作者： Zhaoqing Song Fengyue Zhao Li Chu Huan Lin Yuntao Xiao Zheng Fang Xuncheng Wang Jie Dong Xiangguang Lyu Deyue Yu Bin Liu Junyi Gai Dongqing Xu National Center for soybean Improvement State Key Laboratory of Crop Genetics&Germplasm Enhancement and UtilizationCollege of AgricultureNanjing Agricultural UniversityNanjing 210095China Beijing Key Laboratory of Environmentally Friendly Management of Fruit Diseases and Pests in North China Institute of Plant and Environment ProtectionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China institute of Crop Science College of Agriculture and BiotechnologyZhejiang UniversityHangzhou 310058China State Key Laboratory of Crop Gene Resources and Breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China

Isoflavonoids,secondary metabolites derived from the phenylalanine pathway,are predominantly bio-synthesized in legumes,especially soybean(Glycine max).They are not only essential for plant responses to biotic and abiotic stresses but also beneficial to human *** this study,we report that light signaling controls isoflavonoid biosynthesis in ***-light photoreceptors(GmCRY1s,GmCRY2s,GmPHOT1s,and GmPHOT2s)and the transcription factors GmSTF1 and GmSTF2 promote isoflavonoid accumulation,whereas the E3 ubiquitin ligase GmCOP1b negatively regulates isoflavonoid ***1s and GmPHOT2s stabilize GmSTF1/2,whereas GmCOP1b promotes the degradation of these two proteins in ***1/2 regulate the expression of approximately 27.9%of the genes involved in soybean isoflavonoid biosynthesis,including GmPAL2.1,GmPAL2.3,and *** also repress the expression of GmBBX4,a negative regulator of isoflavonoid biosynthesis in *** addition,GmBBX4 physically interacts with GmSTF1 and GmSTF2 to inhibit their transcriptional activation activity toward target genes related to isoflavonoid ***,GmSTF1/2 and GmBBX4 form a negative feedback loop that acts downstream of photoreceptors in the regulation of isoflavonoid *** study provides novel insights into the control of isoflavonoid biosynthesis by light signaling in soybean and will contribute to the breeding of soybean cultivars with high isoflavonoid content through genetic and metabolic engineering.

关键词： photoreceptor light signaling isoflavonoid GmSTF GmBBX4 soybean

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