Han Linqian, Wang Xiaoming, Benke Ryan, Tibbs-Cortes Laura E, Zhao Peng, Sanguinet Karen A, Zhang Zhiwu, Xu Shengbao, Yu Jianming, Li Xianran
Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA.
State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, College of Agronomy, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Genome Biol. 2025 Aug 28;26(1):256. doi: 10.1186/s13059-025-03740-1.
Wheat has a critical role in global food security. During the improvement of wheat from landraces to cultivars, a suite of traits has been modified for higher yields. However, changing patterns of wheat in response to different environmental conditions, or phenotypic plasticity, during this improvement remain to be elucidated.
We measure 17 agronomic traits for 406 wheat accessions consisting of landraces and cultivars in 10 environments. Analyses reveal varied contributions from genotype and environment to phenotypic variation across the evaluated traits. Using environmental indices identified by Critical Environmental Regressor through Informed Search (CERIS), we model the phenotypic values across environments of each accession with two reaction-norm parameters (intercept and slope). Genome Wide Association Studies (GWAS) identify loci significantly associated with variation in the two parameters, including Ppd-D1 and two Green Revolution genes (Rht-D1 and Rht-B1). Compared with the corresponding wild-type allele, Rht-D1b alters intercept and slope of more traits than Rht-B1b. Among nine possible modes of phenotypic plasticity change from landraces to cultivars, three predominant modes account for 88% of evaluated traits. Generally, two reaction-norm parameters decrease simultaneously for plant architecture traits but increase simultaneously for yield component traits.
We systematically evaluate phenome-wide wheat phenotypic plasticity. Two reaction-norm parameters based on specific environmental indices capture varied degrees of phenotypic plasticity for each trait across wheat accessions. Two Green Revolution genes have different effect spectra in altering phenome-wide phenotypic plasticity. By incorporating the evolutionary dimension, we reveal dominant modes of phenotypic plasticity change during wheat improvement.
小麦在全球粮食安全中起着关键作用。在从地方品种改良为栽培品种的过程中，一系列性状已被改良以提高产量。然而，在这一改良过程中，小麦对不同环境条件的响应模式，即表型可塑性，仍有待阐明。
我们在10种环境中测量了406份由地方品种和栽培品种组成的小麦种质的17个农艺性状。分析揭示了基因型和环境对所评估性状表型变异的不同贡献。使用通过知情搜索的关键环境回归器（CERIS）确定的环境指数，我们用两个反应规范参数（截距和斜率）对每个种质在不同环境中的表型值进行建模。全基因组关联研究（GWAS）确定了与这两个参数变异显著相关的位点，包括Ppd-D1和两个绿色革命基因（Rht-D1和Rht-B1）。与相应的野生型等位基因相比，Rht-D1b比Rht-B1b改变更多性状的截距和斜率。在从地方品种到栽培品种的表型可塑性变化的九种可能模式中，三种主要模式占评估性状的88%。一般来说，株型性状的两个反应规范参数同时降低，而产量构成性状的两个反应规范参数同时增加。
我们系统地评估了全表型组小麦的表型可塑性。基于特定环境指数的两个反应规范参数捕捉了小麦种质中每个性状不同程度的表型可塑性。两个绿色革命基因在改变全表型组表型可塑性方面具有不同的效应谱。通过纳入进化维度，我们揭示了小麦改良过程中表型可塑性变化的主导模式。
