Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton

Li, Z.; Wang, P.; You, C.; Yu, J.; Zhang, X.; Yan, F.; Ye, Z.; Shen, C.; Li, B.; Guo, K.; Liu, N.; Thyssen, G.N.; Fang, D.D.; Lindsey, K.; Wang, M.; Tu, L.

doi:10.1111/nph.16468

Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton

Li, Z.; Wang, P.; You, C.; Yu, J.; Zhang, X.; Yan, F.; Ye, Z.; Shen, C.; Li, B.; Guo, K.; Liu, N.; Thyssen, G.N.; Fang, D.D.; Lindsey, K.; Wang, M.; Tu, L.

Authors

Z. Li

P. Wang

C. You

J. Yu

X. Zhang

F. Yan

Z. Ye

C. Shen

B. Li

K. Guo

N. Liu

G.N. Thyssen

D.D. Fang

Professor Keith Lindsey keith.lindsey@durham.ac.uk
Professor

M. Wang

L. Tu

Abstract

The cotton fiber serves as a valuable experimental system to study cell wall synthesis in plants, but our understanding of the genetic regulation of this process during fiber development remains limited. We performed a genome‐wide association study (GWAS) and identified 28 genetic loci associated with fiber quality in allotetraploid cotton. To investigate the regulatory roles of these loci, we sequenced fiber transcriptomes of 251 cotton accessions and identified 15,330 expression quantitative trait loci (eQTL). Analysis of local eQTL and GWAS data prioritized 13 likely causal genes for differential fiber quality in a transcriptome‐wide association study (TWAS). Characterization of distal eQTL revealed unequal genetic regulation patterns between two subgenomes, highlighted by an eQTL hotspot (Hot216) that establishes a genome‐wide genetic network regulating the expression of 962 genes. The primary regulatory role of Hot216, and specifically the gene encoding a KIP‐related protein, was found to be the transcriptional regulation of genes responsible for cell wall synthesis, which contributes to fiber length by modulating the developmental transition from rapid cell elongation to secondary cell wall synthesis. This study uncovers the genetic regulation of fiber‐cell development and reveals the molecular basis of the temporal modulation of secondary cell wall synthesis during plant cell elongation.

Citation

Li, Z., Wang, P., You, C., Yu, J., Zhang, X., Yan, F., …Tu, L. (2020). Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton. New Phytologist, 226(6), 1738-1752. https://doi.org/10.1111/nph.16468

Journal Article Type	Article
Acceptance Date	Jan 28, 2020
Online Publication Date	Feb 29, 2020
Publication Date	Jun 30, 2020
Deposit Date	Feb 11, 2020
Publicly Available Date	Feb 12, 2020
Journal	New Phytologist
Print ISSN	0028-646X
Electronic ISSN	1469-8137
Publisher	Wiley
Peer Reviewed	Peer Reviewed
Volume	226
Issue	6
Pages	1738-1752
DOI	https://doi.org/10.1111/nph.16468

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Copyright Statement
This is the accepted version of the following article: Li, Zhonghua, Wang, Pengcheng, You, Chunyuan, Yu, Jiwen, Zhang, Xiangnan, Yan, Feilin, Ye, Zhengxiu, Shen, Chao, Li, Baoqi, Guo, Kai, Liu, Nian, Thyssen, Gregory N., Fang, David D., Lindsey, Keith, Zhang, Xianlong, Wang, Maojun & Tu, Lili (2020). Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton. New Phytologist 226(6): 1738-1752 which has been published in final form at https://doi.org/10.1111/nph.16468. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for self-archiving.