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

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.

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, Eduard Akhunov