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Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton
Author(s) -
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
Publication year - 2020
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/nph.16468
Subject(s) - expression quantitative trait loci , biology , genome wide association study , transcriptome , quantitative trait locus , gene , genetics , gene regulatory network , regulation of gene expression , computational biology , genome , candidate gene , genetic association , gene expression profiling , gene expression , single nucleotide polymorphism , genotype
Summary The cotton fibre serves as a valuable experimental system to study cell wall synthesis in plants, but our understanding of the genetic regulation of this process during fibre development remains limited. We performed a genome‐wide association study (GWAS) and identified 28 genetic loci associated with fibre quality in allotetraploid cotton. To investigate the regulatory roles of these loci, we sequenced fibre transcriptomes of 251 cotton accessions and identified 15 330 expression quantitative trait loci (eQTL). Analysis of local eQTL and GWAS data prioritised 13 likely causal genes for differential fibre quality in a transcriptome‐wide association study (TWAS). Characterisation of distal eQTL revealed unequal genetic regulation patterns between two subgenomes, highlighted by an eQTL hotspot (Hot216) that established 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 fibre length by modulating the developmental transition from rapid cell elongation to secondary cell wall synthesis. This study uncovered the genetic regulation of fibre‐cell development and revealed the molecular basis of the temporal modulation of secondary cell wall synthesis during plant cell elongation.