Genetic Diversity and Population Structure of Uzbek Upland Cotton (Gossypium hirsutum L.) Germplasm Revealed by SSR Markers

Genetic diversity is a fundamental resource for the conservation, improvement, and sustainable utilization of upland cotton (Gossypium hirsutum L.) germplasm. Assessing genetic variation and population structure using simple sequence repeat (SSR) markers provides valuable information for parent selection and marker-assisted breeding. In this study, the genetic diversity and population structure of 17 Uzbek upland cotton genotypes were evaluated using 20 SSR markers. A total of 53 alleles were detected, with an average of 2.65 alleles per locus. The polymorphism information content (PIC) ranged from 0.00 to 0.76, with a mean value of 0.38, indicating moderate genetic polymorphism. Among the markers analyzed, NAU2277, MUCS223, BNL3545, JESPR65, and NAU6315 were the most informative for distinguishing the studied germplasm. Population structure, principal component analysis, cluster analysis, and neighbor-joining analysis consistently classified the genotypes into three major genetic groups, demonstrating substantial genetic diversity. The first two principal components explained 34.7% of the total molecular variation. Analysis of molecular variance (AMOVA) revealed that 58% of the genetic variation occurred among groups, whereas 42% occurred within groups. High genetic differentiation (ΦST = 0.42) and low gene flow (Nm = 0.35) indicated limited genetic exchange among the identified groups. Genotypes T-2000, T-1003, T-1005, and T-1080 exhibited high genetic differentiation and represent valuable parental materials for breeding programs. Likewise, T-1002, Mehnat, Yulduz-2, and T-1004 were identified as highly divergent genotypes that could be exploited to broaden the genetic base of future breeding populations and germplasm collections. Overall, the results demonstrate that Uzbek upland cotton germplasm represents a valuable genetic resource for germplasm conservation, parent selection, and marker-assisted breeding aimed at developing genetically diverse and improved cotton cultivars. Keywords: Gossypium hirsutum; SSR markers; genetic diversity; population structure; molecular characterization; germplasm characterization; cotton breeding.

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