Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat

Fei He, Wei Wang, William B. Rutter, Katherine W. Jordan, Jie Ren, Ellie Taagen, Noah DeWitt, Deepmala Sehgal, Sivakumar Sukumaran, Susanne Dreisigacker, Matthew Reynolds, Jyotirmoy Halder, Sunish Kumar Sehgal, Shuyu Liu, Jianli Chen, Allan Fritz, Jason Cook, Gina Brown-Guedira, Mike Pumphrey, Arron Carter, Mark Sorrells, Jorge Dubcovsky, Matthew J. Hayden, Alina Akhunova, Peter L. Morrell, Les Szabo, Matthew Rouse and Eduard Akhunov ()
Additional contact information
Fei He: Kansas State University
Wei Wang: Kansas State University
William B. Rutter: Kansas State University
Katherine W. Jordan: Kansas State University
Jie Ren: Kansas State University
Ellie Taagen: Cornell University
Noah DeWitt: North Carolina State University
Deepmala Sehgal: International Maize and Wheat Improvement Center (CIMMYT)
Sivakumar Sukumaran: International Maize and Wheat Improvement Center (CIMMYT)
Susanne Dreisigacker: International Maize and Wheat Improvement Center (CIMMYT)
Matthew Reynolds: International Maize and Wheat Improvement Center (CIMMYT)
Jyotirmoy Halder: South Dakota State University
Sunish Kumar Sehgal: South Dakota State University
Shuyu Liu: Texas A&M AgriLife Research
Jianli Chen: University of Idaho
Allan Fritz: Kansas State University
Jason Cook: Montana State University
Gina Brown-Guedira: North Carolina State University
Mike Pumphrey: Washington State University
Arron Carter: Washington State University
Mark Sorrells: Cornell University
Jorge Dubcovsky: University of California
Matthew J. Hayden: La Trobe University
Alina Akhunova: Kansas State University
Peter L. Morrell: University of Minnesota
Les Szabo: USDA-ARS Cereal Disease Lab
Matthew Rouse: USDA-ARS Cereal Disease Lab
Eduard Akhunov: Kansas State University

Nature Communications, 2022, vol. 13, issue 1, 1-15

Abstract: Abstract Allopolyploidy greatly expands the range of possible regulatory interactions among functionally redundant homoeologous genes. However, connection between the emerging regulatory complexity and expression and phenotypic diversity in polyploid crops remains elusive. Here, we use diverse wheat accessions to map expression quantitative trait loci (eQTL) and evaluate their effects on the population-scale variation in homoeolog expression dosage. The relative contribution of cis- and trans-eQTL to homoeolog expression variation is strongly affected by both selection and demographic events. Though trans-acting effects play major role in expression regulation, the expression dosage of homoeologs is largely influenced by cis-acting variants, which appear to be subjected to selection. The frequency and expression of homoeologous gene alleles showing strong expression dosage bias are predictive of variation in yield-related traits, and have likely been impacted by breeding for increased productivity. Our study highlights the importance of genomic variants affecting homoeolog expression dosage in shaping agronomic phenotypes and points at their potential utility for improving yield in polyploid crops.

Date: 2022
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DOI: 10.1038/s41467-022-28453-y

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