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

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 

机构地区：[1]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 University,Nanjing 210095,Jiangsu,China [2]Guangxi Academy of Agricultural Sciences,Nanning 530007,Guangxi,China

出　　处：《The Crop Journal》2024年第1期232-243,共12页作物学报（英文版）

基　　金：This work was financially supported by the grants from the National Key Research and Development Program of China(2021YFF1001204,2021YFD1201602);the MOE 111 Project(B08025);the MOA CARS-04 program,the Program of Jiangsu province(JBGS-2021-014);the Guangxi Scientific Research and Technology Development Plan(14125008-2-16);the Guidance Foundation of Sanya Institute of Nanjing Agricultural University(NAUSY-ZZ02,NAUSY-MS05).

摘　　要：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 tolerance.An 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 both.Annotation 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 stages.From 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 network.Altogether,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 

分 类 号：S565.1[农业科学—作物学]