全基因组关联分析揭示了与陆地棉耐盐相关性状相关的遗传变异和候选基因。

Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum.

机构信息

State Key Laboratory of Crop Genetics & Germplasm Enhancement, Hybrid Cotton R & D Engineering Research Center, Ministry of Education, Nanjing Agricultural University, Nanjing, 210095, China.

Provincial Key Laboratory of Agrobiology, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture and Rural Affairs, Nanjing, 210014, China.

出版信息

BMC Genomics. 2021 Jan 6;22(1):26. doi: 10.1186/s12864-020-07321-3.

BACKGROUND

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. 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.

RESULTS

In 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 > 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.

CONCLUSIONS

These results provided important genetic variations and candidate genes for accelerating the improvement of salt tolerance in cotton.

背景

棉花比其他大田作物更能耐受盐害和干旱胁迫，这使其成为盐碱地的先锋工业作物。然而，非生物胁迫仍然会对其生长和发育产生显著的负面影响。因此，培育具有耐盐性的品种对于加速棉花产量的提高非常重要。与因果基因相关的分子标记的开发为提高耐盐性提供了一种有效和高效的方法。

结果

本研究利用 GBS 平台对 217 个陆地棉品种进行了为期 2 年的幼苗期耐盐相关性状表型鉴定，开展了全基因组关联研究（GWAS）。在棉花品种中筛选出 26 条染色体上不均匀分布的 51,060 个单核苷酸多态性（SNP），并在 2016 年和 2017 年检测到与 3 个耐盐相关性状显著相关（-log > 4）的 27 个 SNP 共 25 个关联，分布在 12 条染色体上。其中，染色体 A13 和 D08 上与相对株高（RPH）相关，A07 上与相对地上部鲜重（RSFW）相关，A08 和 A13 上与相对地上部干重（RSDW）相关的关联在两个环境中均有表达，表明它们可能是稳定的数量性状位点（QTL）。通过 GWAS 和转录组分析相结合，共鉴定出 12 个盐诱导候选基因，这些基因在盐胁迫下差异表达。选择 3 个有前景的基因进行耐盐性初步功能验证。GH_A13G0171 沉默植株在盐胁迫下相关性状的增加表明其在调节盐胁迫响应方面具有负功能。