Abstract
BackgroundCotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect its growth and development significantly. It is therefore important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. The development of molecular markers linked to causal genes has provided an effective and efficient approach for improving salt tolerance.ResultsIn this study, a genome-wide association study (GWAS) of salt tolerance related traits at seedling stage was performed based on 2 years of phenotype identification for 217 representative upland cotton cultivars by genotyping-by-sequencing (GBS) platform. A total of 51,060 single nucleotide polymorphisms (SNPs) unevenly distributed among 26 chromosomes were screened across the cotton cultivars, and 25 associations with 27 SNPs scattered over 12 chromosomes were detected significantly (−log10p > 4) associated with three salt tolerance related traits in 2016 and 2017. Among these, the associations on chromosome A13 and D08 for relative plant height (RPH), A07 for relative shoot fresh matter weight (RSFW), A08 and A13 for relative shoot dry matter weight (RSDW) were expressed in both environments, indicating that they were likely to be stable quantitative trait loci (QTLs). A total of 12 salt-induced candidate genes were identified differentially expressed by the combination of GWAS and transcriptome analysis. Three promising genes were selected for preliminary function verification of salt tolerance. The increase of GH_A13G0171-silenced plants in salt related traits under salt stress indicated its negative function in regulating the salt stress response.ConclusionsThese results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.
Highlights
Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands
These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton
Phenotypic diversity analysis In order to evaluate the phenotypic variations of salt tolerance in the genome-wide association study (GWAS) population with 217 upland cotton cultivars (Additional file 1: Table S1), three traits related to salt tolerance including relative plant height (RPH), relative shoot fresh matter weight (RSFW) and relative shoot dry matter weight (RSDW) were determined
Summary
Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. It is important to breed salt tolerance varieties which can help accelerate the improvement of cotton production. Excessive salt in the soil can severely affect the growth and development of cotton plants [1], resulting in a reduction in fiber yield by as much as 60% [2]. Breeding cotton varieties with improved salt tolerance could alleviate the conflict between food crops and cotton by reclaiming and utilizing saline-alkali coastal lands for production. In the northwestern inland cotton production region of China, the availability of salt tolerant varieties would expand the area of cotton production by promoting the synchronous growth of food crops and cotton
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