Assessing genetic diversity and population structure analysis in upland cotton germplasm through microsatellites

Genetic diversity analyses were performed on 96 genotypes using 20 SSR markers to determine the genetic diversity and population structure of the genotypes of Gossypium hirsutum L. cotton at the molecular level. As a result of the bioinformatic analysis, 126 alleles ranging from 3 to 12 were produced for 20 SSR markers, with an average of 6.3 alleles per locus. In gene diversity analysis, the highest value was 0.4478 and the lowest value was 08.13, the mean GD was 0.2419. The PIC value ranged between 0.08 and 0.28, with a mean of 0.20. The genetic distance between the Upland cotton genotypes was calculated as the highest 0.973 and the lowest 0.156. According to the UPGMA method, the dendrogram obtained and the genotypes were divided into six main clusters. The optimum K number was K = 3 according to the analysis performed in the STRUCTURE v2.3.4 program examining the population structure. Accordingly, the genotypes used in the analysis were divided into three different groups. This information can be used in the development of mapping populations, in the selection of parents to be used in cultivar development breeding programs through crossbreeding, and in determining the polymorphic levels of SSR markers.