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Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton.

You, Jiaqi; Liu, Zhenping; Qi, Zhengyang; Ma, Yizan; Sun, Mengling; Su, Ling; Niu, Hao; Peng, Yabing; Luo, Xuanxuan; Zhu, Mengmeng; Huang, Yuefan; Chang, Xing; Hu, Xiubao; Zhang, Yuqi; Pi, Ruizhen; Liu, Yuqi; Meng, Qingying; Li, Jianying; Zhang, Qinghua; Zhu, Longfu; Lin, Zhongxu; Min, Ling; Yuan, Daojun; Grover, Corrinne E; Fang, David D; Lindsey, Keith; Wendel, Jonathan F; Tu, Lili; Zhang, Xianlong; Wang, Maojun

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Authors

Jiaqi You

Zhenping Liu

Zhengyang Qi

Yizan Ma

Mengling Sun

Ling Su

Hao Niu

Yabing Peng

Xuanxuan Luo

Mengmeng Zhu

Yuefan Huang

Xing Chang

Xiubao Hu

Yuqi Zhang

Ruizhen Pi

Yuqi Liu

Qingying Meng

Jianying Li

Qinghua Zhang

Longfu Zhu

Zhongxu Lin

Ling Min

Daojun Yuan

Corrinne E Grover

David D Fang

Jonathan F Wendel

Lili Tu

Xianlong Zhang

Maojun Wang



Abstract

Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants. [Abstract copyright: © 2023. The Author(s).]

Citation

You, J., Liu, Z., Qi, Z., Ma, Y., Sun, M., Su, L., …Wang, M. (2023). Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton. Nature Genetics, 55, 1987-1997. https://doi.org/10.1038/s41588-023-01530-8

Journal Article Type Article
Acceptance Date Sep 14, 2023
Online Publication Date Oct 16, 2023
Publication Date 2023
Deposit Date Nov 30, 2023
Publicly Available Date Dec 1, 2023
Journal Nature genetics
Print ISSN 1061-4036
Publisher Nature Research
Peer Reviewed Peer Reviewed
Volume 55
Pages 1987-1997
DOI https://doi.org/10.1038/s41588-023-01530-8
Public URL https://durham-repository.worktribe.com/output/1883745

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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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