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ARS Home » Pacific West Area » Pullman, Washington » WHGQ » Research » Publications at this Location » Publication #410947
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: Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize

Author
item TIBBS-CORTES, LAURA - Orise Fellow
item GUO, TINGTING - Huazhong Agricultural University
item Andorf, Carson
item Li, Xianran
item YU, JIANMING - Iowa State University

Submitted to: Genome Research
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/6/2024
Publication Date: 9/13/2024
Citation: Tibbs-Cortes, L.E., Guo, T., Andorf, C.M., Li, X., Yu, J. 2024. Comprehensive identification of genomic and environmental determinants of phenotypic plasticity in maize. Genome Research. 34: 1253-1263. https://doi.org/10.1101/gr.279027.124.
DOI: https://doi.org/10.1101/gr.279027.124

Interpretive Summary: Important traits in crops, including maize, are influenced not only by genetics but also by the environment, as well as by their interaction. In this study, we identified genetic and environmental factors that strongly impact traits in maize, which enabled both prediction in new environments and improved understanding of the underlying biology. This systematic inventory of genetic and environmental factors influencing maize traits forms an important community resource and provides context for future studies of plasticity in maize.

Technical Abstract: Maize phenotypes are plastic, determined by the complex interplay of genetics and environmental variables. Uncovering the genes responsible and understanding how their effects change across a large geographic region is challenging. In this study, we conducted systematic analysis to identify environmental indices that strongly influence 19 traits (including flowering time, plant architecture, and yield component traits) measured in the maize Nested Association Mapping (NAM) population in 11 environments. Identified environmental indices based on day length, temperature, moisture, and combinations of these were biologically meaningful. Next, we leveraged a total of more than 20 million SNP and SV markers derived from recent de novo sequencing of the 25 NAM founders for trait prediction and dissection. When combined with identified environmental indices, genomic prediction enabled accurate performance predictions. Genome-Wide Association Studies (GWAS) detected genetic loci controlling the plastic response to the identified environmental indices for all traits. Some of these loci were identified for both intercept (genotypic mean) and slope (plasticity) of a given trait, while others were found to affect only one of these. Systematically uncovering the major environmental and genetic factors underlying plasticity in 19 traits provides a comprehensive framework to facilitate continuing complex trait dissection and prediction in maize and other crops.