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

PLoS One. 2017 Nov 14;12(11):e0188125. doi: 10.1371/journal.pone.0188125. eCollection 2017.

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.

MeSH terms

  • California
  • Genetic Markers
  • Genetic Variation*
  • Gossypium / genetics*
  • Linkage Disequilibrium*
  • Microsatellite Repeats
  • Phylogeny
  • Uzbekistan

Substances

  • Genetic Markers

Grants and funding

This work was supported by the Academy of Sciences of Uzbekistan, and Committee for Coordination Science and Technology Development of Uzbekistan have provided research grant fund under the project No.FA-F5-T030 to IYA and the Office of International Research Programs (OIRP) of the United States Department of Agriculture (USDA)—Agricultural Research Service (ARS) and U.S. Civilian Research and Development Foundation (CRDF) provided an international cooperative grant No. UZB-TA-31017 to IYA and MU. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.