TY - JOUR
T1 - Genomic variants affecting homoeologous gene expression dosage contribute to agronomic trait variation in allopolyploid wheat
AU - He, Fei
AU - Wang, Wei
AU - Rutter, William B.
AU - Jordan, Katherine W.
AU - Ren, Jie
AU - Taagen, Ellie
AU - DeWitt, Noah
AU - Sehgal, Deepmala
AU - Sukumaran, Sivakumar
AU - Dreisigacker, Susanne
AU - Reynolds, Matthew
AU - Halder, Jyotirmoy
AU - Sehgal, Sunish Kumar
AU - Liu, Shuyu
AU - Chen, Jianli
AU - Fritz, Allan
AU - Cook, Jason
AU - Brown-Guedira, Gina
AU - Pumphrey, Mike
AU - Carter, Arron
AU - Sorrells, Mark
AU - Dubcovsky, Jorge
AU - Hayden, Matthew J.
AU - Akhunova, Alina
AU - Morrell, Peter L.
AU - Szabo, Les
AU - Rouse, Matthew
AU - Akhunov, Eduard
N1 - Funding Information:
This research was supported by Bill and Melinda Gates Foundation (INV-004430) to M.R., E.A., A.A., L.S., by the Agriculture and Food Research Initiative Competitive Grants 2022-68013-36439 (WheatCAP) to J.D. and 2019-67013-29017 from the USDA National Institute of Food and Agriculture to E.A., and by the International Wheat Yield Partnership (IWYP). We thank Dr. Li Lei for comments on an earlier version of the manuscript.
Publisher Copyright:
© 2022, The Author(s).
PY - 2022/12
Y1 - 2022/12
N2 - 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.
AB - 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.
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U2 - 10.1038/s41467-022-28453-y
DO - 10.1038/s41467-022-28453-y
M3 - Article
C2 - 35149708
AN - SCOPUS:85124499672
SN - 2041-1723
VL - 13
JO - Nature communications
JF - Nature communications
IS - 1
M1 - 826
ER -