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.

Nanopore-Based Comparative Transcriptome Analysis Reveals the Potential Mechanism of High-Temperature Tolerance in Cotton (Gossypium hirsutum L.)

“…High-temperature stress is one of the most serious challenges for cotton cultivation because high temperatures often occur during the vegetative and flowering stages of cotton, and causes stunting, poor pollination, and losses of fiber quality in cotton [20]. Breeding heat-tolerant cotton varieties is an effective way to cope with this problem.…”

“…In addition to miRNAs, studies reported many functional genes that may be involved in high-temperature resistance in cotton. Ma et al (2021) found that a heat-susceptible gene, designated as heat-related receptor kinase GhHRK1, negatively responds to high-temperature stress in cotton, whereas the Arabidopsis homologous GhHRK1 mutant shows strong high-temperature tolerance, indicating that this gene may play a key role in high-temperature resistance in cotton. Some genes related to cytokinin, abscisic acid, and brassinosteroid signal transduction, such as CRE1, ABF, and CYCD, are considered to participate in the regulation of high-temperature response in cotton, thus contributing to the maintenance of plant growth [9].…”

Fast Anther Dehiscence Status Recognition System Establishing by Deep Learning to Screen Heat Tolerant Cotton

“…HT mainly decreased pollen viability, the anther growth number, and the percentage of dehiscent anther, caused the decreases of male fertility in cotton (Min et al, 2014;Ma et al, 2018). Furthermore, with the development of sequencing technology, a large amount of cotton germplasm resequencing data and transcriptome variation data have been obtained (Wang et al, 2017;Ma et al, 2021). However, no enhancing male reproductive organs HT tolerance genes have been cloned.…”

Rapid Identification of Pollen- and Anther-Specific Genes in Response to High-Temperature Stress Based on Transcriptome Profiling Analysis in Cotton

“…Cotton is cultivated in summer and is commonly affected by high temperatures (HT). Male sterility caused by HT in cotton has been reported in recent years, which has led to yield reductions [ 6 , 7 , 8 , 9 ]. Critical genes in response to HT in the male reproductive organ of cotton are poorly understood.…”