Abstract
<title>Abstract</title> <p> Soil salinity is a major abiotic constraint limiting cotton ( <italic>Gossypium hirsutum</italic> L.) productivity and fiber quality, particularly in arid and semi-arid regions. The identification of genetically diverse germplasm with superior salinity adaptation is essential for developing resilient cotton cultivars through marker-assisted breeding. In this study, the genetic diversity, population structure, and salinity adaptation potential of 17 upland cotton genotypes were investigated using 20 genome-wide simple sequence repeat (SSR) markers. A total of 53 alleles were detected, with an average of 2.65 alleles per locus. The SSR markers revealed substantial genetic polymorphism, with polymorphism information content (PIC) values ranging from 0.00 to 0.76 (mean = 0.38). Among them, NAU2277, MUCS223, BNL3545, JESPR65, and NAU6315 were the most informative markers for differentiating the studied germplasm. Cluster analysis, neighbor-joining analysis, and principal component analysis consistently classified the genotypes into three major groups, indicating considerable genetic diversity. The first two principal components accounted for 34.7% of the total genetic variation. Analysis of molecular variance (AMOVA) showed that 58% of the genetic variation occurred within populations and 42% among populations. High genetic differentiation (ΦST = 0.42) and low gene flow (Nm = 0.35) indicated restricted genetic exchange among the identified groups. The genotypes T-2000, T-1003, T-1005, and T-1080 were identified as promising parental lines for salinity-tolerance breeding, whereas T-1002, Mehnat, Yulduz-2, and T-1004 represented genetically divergent accessions with high breeding value. These findings demonstrate that Uzbek upland cotton germplasm constitutes a valuable genetic resource for developing salt-tolerant cultivars with improved fiber quality through marker-assisted breeding. </p>