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

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posted on 2022-09-26, 05:52 authored by F He, W Wang, WB Rutter, KW Jordan, J Ren, E Taagen, N DeWitt, D Sehgal, S Sukumaran, S Dreisigacker, M Reynolds, J Halder, SK Sehgal, S Liu, J Chen, A Fritz, J Cook, G Brown-Guedira, M Pumphrey, A Carter, M Sorrells, J Dubcovsky, Matthew HaydenMatthew Hayden, A Akhunova, PL Morrell, L Szabo, M Rouse, E Akhunov
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.

Funding

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).

History

Publication Date

2022-02-11

Journal

Nature Communications

Volume

13

Issue

1

Article Number

826

Pagination

15p.

Publisher

Springer Nature

ISSN

2041-1723

Rights Statement

This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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