Whole-genome analysis of recombinant inbred rice lines reveals a quantitative trait locus on chromosome 3 with genotype-by-environment interaction effects.

Elucidating genotype-by-environment (GxE) interactions is fundamental for understanding the interplay between genetic and environmental factors that shape complex traits in crops. GxE interactions are of practical importance, as they determine the performance of cultivars grown in different environments, prompting the need for an efficient approach for evaluating GxE interactions. Here, we describe a method for GxE detection that involves comparing linear mixed models. This method successfully detected GxE interactions in rice (Oryza sativa) recombinant inbred lines grown at three locations. We identified a quantitative trait locus (QTL) on chromosome 3 that was associated with heading date, grain number, and leaf length. The effect of this QTL on plant growth-related traits varied with environmental conditions, indicating the presence of GxE interactions. Therefore, our method enables a powerful GxE detection pipeline that should facilitate the production of high-yielding crops in a given environment.