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

Abstract

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.

Unravelling cotton RNAseq repositories to the fiber development specific modules and their alliance with the fiber-related traits

“…The low coverage on draft genome may not be used for the identification of low expressed gene and their variants that might be crucial for fiber development. Similarly in an eQTL identification study, only 10 billion reads were used for 251 cotton accessions (Li et al, 2020). This study was only focused on the initiation of secondary cell wall synthesis at 15 DPA.…”

GWAS Based on RNA-Seq SNPs and High-Throughput Phenotyping Combined with Climatic Data Highlights the Reservoir of Valuable Genetic Diversity in Regional Tomato Landraces

“…The function of Solyc06g066320, together with its simultaneous associations with different traits (i.e., fruit quality, inflorescence, fruit shape and size), suggest a possible pleiotropic role for this gene. Being pleiotropy a target for many GWA studies, variable strategies have been designed for the identification of causal variants and their roles that will help to extract the huge amount of information that is being produced [13,121,122].…”

“…The results of these studies will help in disentangling the role of different genes in the expression of important agronomic traits [2,10,11]. Transcriptomic data, in particular, have been used to both compare expression profiles (expression quantitative trait loci (eQTLs)) in plant populations at different development stages, and genotype (using RNA-Seq-derived single nucleotide polymorphisms (SNPs)) germplasm collections that can be used in genome-wide association studies (GWAS) and genomic selection analyses [10,12,13].…”

Polymorphisms in cis‐elements confer SAUR26 gene expression difference for thermo‐response natural variation in Arabidopsis

“…Expression GWAS is effective in identifying gene regulatory variations in natural accessions While trans-eQTLs, often transcription factors, could influence expression of key regulators of complex phenotype (Fu et al, 2013;Wang et al, 2014;Li et al, 2020), cis-eQTLs, including cisacting nucleotide variants, copy-number variants and gene structural variants (Gan et al, 2011), appear to play a larger role on expression variations in Arabidopsis natural accessions (Keurentjes et al, 2007;Wang et al, 2020). Here we show that eGWAS is a viable approach to identify both trans-acting and cis-acting regulatory variations for gene expression variations.…”