A combination of genome‐wide and transcriptome‐wide association studies reveals genetic elements leading to male sterility during high temperature stress in cotton

Abstract

Global warming has reduced the productivity of many field‐grown crops due to effects on male sterility. The genetic regulation of high temperature (HT) response in the major crop cotton is poorly understood. We determined the functionality and transcriptomes of anther of 218 cotton accessions grown under HT stress. By analyzing transcriptome divergence and implementing genome‐wide association study (GWAS), we identified three thermal tolerance associated loci which contained 75 protein coding genes and 27 long non‐coding RNAs, and provided expression quantitative trait loci (eQTLs) for 13,132 transcripts. A transcriptome‐wide association study (TWAS) confirmed six causal elements for the HT response (three genes overlapped with GWAS results), involved in protein kinase activity. The most susceptible gene, GhHRK1 was confirmed as a previously uncharacterized negative regulator of the HT response both in cotton and in Arabidopsis. These functional variants provided new understanding of genetic basis for HT tolerance in male reproduction organs.