Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum
文献类型： 外文期刊
作者： Xu, Peng 1 ; Guo, Qi 2 ; Meng, Shan 2 ; Zhang, Xianggui 2 ; Xu, Zhenzhen 2 ; Guo, Wangzhen 1 ; Shen, Xinlian 2 ;
作者机构： 1.Nanjing Agr Univ, Minist Educ, Hybrid Cotton R&D Engn Res Ctr, State Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Peoples R China
2.Minist Agr & Rural Affairs, Key Lab Cotton & Rapeseed, Jiangsu Acad Agr Sci, Inst Ind Crops,Prov Key Lab Agrobiol, Nanjing 210014, Peoples R China
关键词： Gossypium hirsutum; Genome-wide association study; Genotyping-by-sequencing; Salt tolerance; Virus-induced gene silencing assay
期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）
ISSN： 1471-2164
年卷期： 2021 年 22 卷 1 期
页码：
收录情况： SCI
摘要： 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 (-log(10)(p)>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.
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