Genome-Wide Dissection of the Genetic Basis for Drought Tolerance in Gossypium hirsutum L. Races

Abstract

Drought seriously threats the growth and development of Gossypium hirsutum L. To dissect the genetic basis for drought tolerance in the G. hirsutum L. germplasm, a population, consisting of 188 accessions of G. hirsutum races and a cultivar (TM-1), was genotyped using the Cotton80KSNP biochip, and 51,268 high-quality single-nucleotide polymorphisms (SNPs) were obtained. Based on the phenotypic data of eight drought relative traits from four environments, we carried out association mapping with five models using GAPIT software. In total, thirty-six SNPs were detected significantly associated at least in two environments or two models. Among these SNPs, 8 and 28 (including 24 SNPs in 5 peak regions) were distributed in the A and D subgenome, respectively; eight SNPs were found to be distributed within separate genes. An SNP, TM73079, located on chromosome D10, was simultaneously associated with leaf fresh weight, leaf wilted weight, and leaf dry weight. Another nine SNPs, TM47696, TM33865, TM40383, TM10267, TM59672, TM59675, TM59677, TM72359, and TM72361, on chromosomes A13, A10, A12, A5, D6, and D9, were localized within or near previously reported quantitative trait loci for drought tolerance. Moreover, 520 genes located 200 kb up- and down-stream of 36 SNPs were obtained and analyzed based on gene annotation and transcriptome sequencing. The results showed that three candidate genes, Gh_D08G2462, Gh_A03G0043, and Gh_A12G0369, may play important roles in drought tolerance. The current GWAS represents the first investigation into mapping QTL for drought tolerance in G. hirsutum races and provides important information for improving cotton cultivars.

Genome-Wide Association Study of Lint Percentage in Gossypium hirsutum L. Races

“…Detailed descriptions of the SNP genotyping processes were published previously [ 30 ]. In brief, high-quality genomic DNA of each accession was extracted from the young leaf tissue and was diluted to 50 ng/μL.…”

“…One-hundred-and eighty-eight accessions consisted of all the seven G. hirsutum races, and the other was a representative of the cultivars, the upland cotton genetic standard G. hirsutum L. acc. Texas Marker-1 (TM-1) [30]. All the G. hirsutum races were originally introduced from the USDA-ARS Southern Agricultural Research Center in College Station, Texas, USA, were perennially purified and preserved in the National Wild Cotton Nursery, Sanya, Hainan, China At the open-boll bloom stage, we randomly collected 30 naturally full open bolls from the middle of each row and weighted the seed-cotton yield of each sample.…”

“…In the past years, with G. hirsutum races, several researchers executed linkage mapping, committing to broadening the genetic base for improving yield [ 23 , 24 , 25 , 26 ], fiber quality [ 22 , 27 ], and fiber color [ 25 , 28 ]. In our previous reports, SSR and SNP markers were selected to implement genome-wide association mapping for abiotic stress resistance, including glyphosate resistance [ 29 ] and drought resistance [ 30 ]. Furthermore, we performed a transcriptome analysis of G. hirsutum race accessions under alkali-salt stress and excavated the related candidate genes and signaling pathways [ 31 ].…”

Rapidly mining candidate cotton drought resistance genes based on key indicators of drought resistance

“…Abdelraheem et al [ 10 ] used a multiparent high-generation hybrid population composed of 550 recombinant inbred lines and 11 upland cotton parents based on the two indicators of plant height and dry weight to correlate the drought tolerance of cotton seedlings, and 13 and 7 QTLs were detected, respectively. Guo et al [ 11 ] investigated 189 upland cotton resource materials to obtain phenotypic data for 8 drought-related traits in four environments and used genomic data to carry out association analyses of 5 models. Li et al [ 12 ] used 517 natural populations of upland cotton plants as materials to conduct generalized heritability and coefficient of variation analyses of 18 traits and identified 33 QTLs related to the water limitation response by using the drought resistance coefficient.…”