Genetic diversity, linkage disequilibrium, and association mapping analyses of Gossypium barbadense L. germplasm

Abstract

Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers. Analyses revealed structured population characteristics and a high level of intra-variability (67.2%) and moderate interpopulation differentiation (32.8%). Eight percent and 4.3% of markers revealed LD in the genome of the G. barbadense at critical values of r2 ≥ 0.1 and r2 ≥ 0.2, respectively. The LD decay was on average 24.8 cM at the threshold of r2 ≥ 0.05. LD retained on average distance of 3.36 cM at the threshold of r2 ≥ 0.1. Based on the phenotypic evaluations in the two diverse environments, 100 marker loci revealed a strong association with major fiber quality traits using mixed linear model (MLM) based association mapping approach. Fourteen marker loci were found to be consistent with previously identified quantitative trait loci (QTLs), and 86 were found to be new unreported marker loci. Our results provide insights into the breeding history and genetic relationship of G. barbadense germplasm and should be helpful for the improvement of cotton cultivars using molecular breeding and omics-based technologies.

Fig 1. The UPGMA dendrogram of 288 G. barbadense accessions, constructed using the genotype of 301 polymorphic SSR alleles.

Horizontal lines denote thresholds of genetic distances. Groups A and B are obtained on the basis of differences in > 50%, whereas subgroups G1, G2 and G3 obtained based on the upper boundary distinctions in 40%, and the subgroups G5 and G4—the upper bound of 20%.

Fig 2. Principal component analysis, of 288 G. barbadense cultivars in the space of two main coordinate jointly by SSR genotypes.

PC—the main components; (A) and (B)—subgroups represented in the majority of varieties of Uzbekistan (UZ) and Turkmenistan (TM), respectively. (Mix)—represented by the most genetically differentiated samples from several geographic regions i.e., from Turkmenistan (8), Africa (3), Uzbekistan (3), and American (1). UZ—Uzbekistan, TM—Turkmenistan, TJ—Tajikistan, AF—Africa, US—US, SA—South America AZ—Azerbaijan and ME—Middle East.

Fig 3. Summary plots of Q-matrix for the G. barbadense germplasm inferred from STRUCTURE analysis.

K2—the division into two subpopulations:a small (green) and large (red). K3—further expansion of subpopulations on ecotypes (consistent with the results shown in Fig 2). Mix- represented by the most genetically differentiated samples from several geographic regions. UZ—Uzbek, and TK—Turkmen cotton accessions.

Fig 4. Scatter plot of significant r² values and genetic distance (cM) (p<0.001) of locus pairs on whole genome of G. barbadense germplasm.

Fig 5. Result of association mapping of fiber quality traits in a particular region.

Markers showed signisicant association (MLM; p ≤0.05) both in Uzbekistan (Uzb.), and the United States (US) environments.: FL-fiber length, FM- micronaire, FS- fiber strength, FU- uniformity.