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

Abstract

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.

Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.)

“…Using the genotypic data of 57,413 high-quality SNPs [18], a GWAS was conducted for the three traits in different environments and the BLUP values, using six methods ("mrMLM", "FASTmrMLM", "FASTmrEMMA", "pKWmE B", "ISIS EM-BLASSO" and "pLARmEB") of multi-loci mixed linear model (MLM) model in the R package "mrMLM" [19]. In total, 854 quantitative trait nucleotides (QTNs) on 26 chromosomes were identified as significantly associated with the three traits (Additional file 8: Table S6).…”

“…In total, 854 quantitative trait nucleotides (QTNs) on 26 chromosomes were identified as significantly associated with the three traits (Additional file 8: Table S6). We referenced the linkage disequilibrium (LD) in previous report [18] and calculated the average LD from each chromosome, further selected the lowest LD, about 200 kb, as the LD threshold, for merging QTNs into the same QTL. In total, 600 QTLs, including 151 of SBW, 417 of LP and 112 of BNPP, were detected 1446 times under different environments and BLUPs by six multi-loci MLM models (Table 1).…”

“…A CottonSNP80K array was used to genotype the 316 cotton accessions. The SNP genotyping and population structure were reported in our previous study [18]. A total of 57,413 SNPs (calling rate ≥ 0.9 and minor allele frequency (MAF) ≥ 0.05) were used for GWAS analysis.…”

“…We referenced the linkage disequilibrium (LD) published in a previous report [18] and calculated the average LD from each chromosome, and selected the lowest LD, about 200 kb, as the LD threshold, for merging QTNs into the same QTL. If the distance between two QTNs was less than 200 kb, these were merged into a single QTL.…”

Construction of a High Density Genetic Map and QTL Mapping of PEG-Induced Drought Tolerance at Seedling Stage in Sesame Using Whole Genome Re-Sequencing

“…Drought tolerance is a complex quantitative trait in plants. QTL mapping and genome-wide association study (GWAS) have been widely used for genetic analysis of drought tolerance related traits in many plants, such as rice [4,5], wheat [6][7][8], cotton [9,10] and Brassica napus [11]. These traits including root length, coleoptile length and shoot length for seedling stage, and yield-related traits for owering stage.…”