Identification of QTL-by-environment interaction by controlling polygenic background effect

文献类型： 外文期刊

第一作者： Zhao, Fuping

作者： Zhao, Fuping;Wang, Lixian;Xu, Shizhong

作者机构：

关键词： Q x E interaction; Main effect; Meta-analysis; Mixed model; Polygenic background

期刊名称：JOURNAL OF GENETICS AND GENOMICS （ 影响因子：7.1； 五年影响因子：6.4 ）

ISSN： 1673-8527

年卷期： 2025 年 52 卷 7 期

页码：

收录情况： SCI

摘要： The quantitative trait loci (QTL)-by-environment (Q x E) interaction effect is hard to detect because there are no effective ways to control the genomic background. In this study, we propose a linear mixed model that simultaneously analyzes data from multiple environments to detect Q x E interactions. This model incorporates two different kinship matrices derived from the genome-wide markers to control both main and interaction polygenic background effects. Simulation studies demonstrate that our approach is more powerful than the meta-analysis and inclusive composite interval mapping methods. We further analyze four agronomic traits of rice across four environments. A main effect QTL is identified for 1000-grain weight (KGW), while no QTL are found for tiller number. Additionally, a large QTL with a significant Q x E interaction is detected on chromosome 7 affecting grain number, yield, and KGW. This region harbors two important genes, PROG1 and Ghd7. Furthermore, we apply our mixed model to analyze lodging in barley across six environments. The six regions exhibiting Q x E interaction effects identified by our approach overlap with the SNPs previously identified using EM and MCMC-based Bayesian methods, further validating the robustness of our approach. Both simulation studies and empirical data analyses show that our method outperforms all other methods compared. Copyright (c) 2025, The Authors. Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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