Table_1_Genome-Wide Association Studies Reveal Genetic Variation and Candidate Genes of Drought Stress Related Traits in Cotton (Gossypium hirsutum L.).xlsx

Cotton is an important industrial crop worldwide and upland cotton (Gossypium hirsutum L.) is most widely cultivated in the world. Due to ever-increasing water deficit, drought stress brings a major threat to cotton production. Thus, it is important to reveal the genetic basis under drought stress and develop drought tolerant cotton cultivars. To address this issue, in present study, 319 upland cotton accessions were genotyped by 55,060 single nucleotide polymorphisms (SNPs) from high-density CottonSNP80K array and phenotyped nine drought tolerance related traits. The two datasets were used to identify quantitative trait nucleotides (QTNs) for the above nine traits using multi-locus random-SNP-effect mixed linear model method. As a result, a total of 20 QTNs distributed on 16 chromosomes were found to be significantly associated with six drought tolerance related traits. Of the 1,326 genes around the 20 QTNs, 205 were induced after drought stress treatment, and 46 were further mapped to Gene ontology (GO) term “response to stress.” Taken genome-wide association study (GWAS) analysis, RNA-seq data and qRT-PCR verification, four genes, RD2 encoding a response to desiccation 2 protein, HAT22 encoding a homeobox-leucine zipper protein, PIP2 encoding a plasma membrane intrinsic protein 2, and PP2C encoding a protein phosphatase 2C, were proposed to be potentially important for drought tolerance in cotton. These results will deepen our understanding of the genetic basis of drought stress tolerance in cotton and provide candidate markers to accelerate the development of drought-tolerant cotton cultivars.

棉花是全球重要的工业经济作物，其中陆地棉（Gossypium hirsutum L.）是当前全球栽培最广泛的棉种。随着水资源短缺问题日益加剧，干旱胁迫已成为制约棉花生产的主要威胁。因此，解析棉花响应干旱胁迫的遗传基础、培育耐旱棉花品种具有重要的理论与实践价值。为解决该问题，本研究利用高密度棉花SNP80K芯片的55060个单核苷酸多态性（Single Nucleotide Polymorphisms，SNPs）位点对319份陆地棉种质资源进行基因型分型，并对9个耐旱相关性状开展表型鉴定。结合上述两组数据集，采用多位点随机SNP效应混合线性模型方法，对上述9个性状的数量性状核苷酸（Quantitative Trait Nucleotides，QTNs）进行定位分析。结果共检测到分布于16条染色体上的20个与6个耐旱相关性状显著关联的QTNs。在这20个QTNs侧翼区域的1326个基因中，有205个基因在干旱胁迫处理后被诱导表达，其中46个基因被注释到基因本体（Gene Ontology，GO）术语“胁迫响应”条目下。结合全基因组关联分析（Genome-Wide Association Study，GWAS）、RNA测序（RNA-seq）数据与实时定量荧光PCR（qRT-PCR）验证，最终筛选出4个与棉花耐旱性潜在相关的关键基因：编码响应干燥蛋白2的RD2基因、编码同源异型域-亮氨酸拉链蛋白的HAT22基因、编码质膜内在蛋白2的PIP2基因，以及编码蛋白磷酸酶2C的PP2C基因。本研究结果将加深我们对棉花耐旱胁迫遗传基础的理解，并可为耐旱棉花品种的培育提供候选分子标记。