期刊论文详细信息
Frontiers in Genetics
A Method for Identifying Environmental Stimuli and Genes Responsible for Genotype-by-Environment Interactions From a Large-Scale Multi-Environment Data Set
Jianming Yu1  Akio Onogi2  Seishi Ninomiya3  Satoshi Nakano4  Tetsuya Yamada5  Daisuke Sekine5  Akito Kaga5 
[1] Department of Agronomy, Iowa State University, Ames, IA, United States;Department of Plant Life Science, Faculty of Agriculture, Ryukoku University, Otsu, Japan;Graduate School of Agricultural and Life Science, The University of Tokyo, Nishitokyo, Japan;Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan;Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba, Japan;Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, Tsukuba, Japan;
关键词: genotype-by-environment interactions;    genetic correlation;    genome-wide association;    historical data;    multi-environmental trial;    environmental covariate;   
DOI  :  10.3389/fgene.2021.803636
来源: DOAJ
【 摘 要 】

It has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G × E) interactions, when they occur, and what genes react to them. Large-scale multi-environment data sets are attractive data sources for these purposes because they potentially experienced various environmental conditions. Here we developed a data-driven approach termed Environmental Covariate Search Affecting Genetic Correlations (ECGC) to identify environmental stimuli and genes responsible for the G × E interactions from large-scale multi-environment data sets. ECGC was applied to a soybean (Glycine max) data set that consisted of 25,158 records collected at 52 environments. ECGC illustrated what meteorological factors shaped the G × E interactions in six traits including yield, flowering time, and protein content and when these factors were involved in the interactions. For example, it illustrated the relevance of precipitation around sowing dates and hours of sunshine just before maturity to the interactions observed for yield. Moreover, genome-wide association mapping on the sensitivities to the identified stimuli discovered candidate and known genes responsible for the G × E interactions. Our results demonstrate the capability of data-driven approaches to bring novel insights on the G × E interactions observed in fields.

【 授权许可】

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