AUTHOR=Onogi Akio , Sekine Daisuke , Kaga Akito , Nakano Satoshi , Yamada Tetsuya , Yu Jianming , Ninomiya Seishi 

TITLE=A Method for Identifying Environmental Stimuli and Genes Responsible for Genotype-by-Environment Interactions From a Large-Scale Multi-Environment Data Set

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.803636

DOI=10.3389/fgene.2021.803636

ISSN=1664-8021

ABSTRACT=<p>It has not been fully understood in real fields what environment stimuli cause the genotype-by-environment (G <inline-formula id="inf1"><mml:math id="m1" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math></inline-formula> 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 <inline-formula id="inf2"><mml:math id="m2" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math></inline-formula> E interactions from large-scale multi-environment data sets. ECGC was applied to a soybean (<italic>Glycine max</italic>) data set that consisted of 25,158 records collected at 52 environments. ECGC illustrated what meteorological factors shaped the G <inline-formula id="inf3"><mml:math id="m3" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math></inline-formula> 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 <inline-formula id="inf4"><mml:math id="m4" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math></inline-formula> E interactions. Our results demonstrate the capability of data-driven approaches to bring novel insights on the G <inline-formula id="inf5"><mml:math id="m5" xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>×</mml:mo></mml:math></inline-formula> E interactions observed in fields.</p>