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.

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., Ye, Z., Shen, C., Li, B., Guo, K., Liu, N., Thyssen, G., Fang, D., Lindsey, K., Wang, M., & 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
• Public URL: https://durham-repository.worktribe.com/output/1271498