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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Publications at this Location » Publication #422143
Research Project: Wheat and Barley Adaptation to a Changing Climate - Discovery of Genetic and Physiological Processes for Improved Crop Productivity and Quality

Location: Wheat Health, Genetics, and Quality Research

Title: Integrated phenomic and genomic analyses unveil modes of altered phenotypic plasticity during wheat improvement

Author
item HAN, LINQIAN - Washington State University
item WANG, XIAOMING - Northwest A&f University
item Benke, Ryan
item Tibbs, Laura
item ZHANG, PENG - Northwest A&f University
item SANGUINET, KAREN - Washington State University
item ZHANG, ZHIWU - Washington State University
item XU, SHENGBAO - Northwest A&f University
item YU, JIANMING - Iowa State University
item Li, Xianran

Submitted to: Genome Biology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/12/2025
Publication Date: 8/28/2025
Citation: Han, L., Wang, X., Benke, R.L., Tibbs, L.E., Zhang, P., Sanguinet, K.A., Zhang, Z., Xu, S., Yu, J., Li, X. 2025. Integrated phenomic and genomic analyses unveil modes of altered phenotypic plasticity during wheat improvement. Genome Biology. 26. Article 256. https://doi.org/10.1186/s13059-025-03740-1.
DOI: https://doi.org/10.1186/s13059-025-03740-1

Interpretive Summary: Exploiting phenotypic plasticity, a phenomenon of varied performance of the same genotype in different environment, is of great importance in improving crops under the changing climate. Through measuring a suite of 17 traits measured from both wheat landraces and modern cultivars across environments, our study not only presented a global view of phenotypic plasticity from the phenomic perspective, but also considered the time element to evaluating the changing modes of phenotypic plasticity during crop improvement. The trait fluctuations across environments can be adequately captured with two parameters, intercept and slope. Intercept measures the genetic potential, while slope measures the sensitivity to environmental conditions. The results showed that during the wheat improvement from landraces to cultivars, changing the wheat genetic potential intercept also altered the wheat sensitivity. We also found the Rht-D1 had a greater spectrum of pleiotropic effect in altering phenotypic plasticity than Rht-B1.

Technical Abstract: Wheat plays a critical role in global food security. A whole suite of traits have been modified to achieve the goal of higher yield of modern cultivars than landraces. However, changes of wheat capacity in responding to environmental conditions, or phenotypic plasticity, during this improvement remains to be elucidated. A comprehensive understanding of phenotypic plasticity is essential for sustainable wheat improvement under changing environmental conditions. We measured 17 traits from a large wheat population consisting of landraces and modern cultivars over 10 environments. With the identified environmental index for each trait, two reaction-norm parameters (intercept and slope) concisely described the property of each accession responding to external environmental conditions to produce different phenotypic values. Integration of environmental index, intercept and slope, and genomic prediction accurately predicted traits values in various scenarios. GWAS identified loci significantly associated with phenotypic plasticity variations. Between two Green Revolution genes, Rht-D1 significantly altered intercept and slope for more traits than Rht-B1. We found that, out of nine possible modes in changing intercept and slopes during the improvement from landraces to modern cultivars, three modes counted for 88% of evaluated wheat traits. Our comprehensive evaluations shed insights into wheat improvement and underscores the importance of linking phenotypic plasticity with crop improvement to optimize crop in changing climate.