Molecular analysis of genetic diversity and population structure of 288 Gossypium barbadense L. worldwide cotton varieties from Uzbek cotton germplasm collection was done by using 750 SSR primer pairs. Among the utilized SSRs 108 (14.4%) were informative and produced 302 polymorphic loci. PIC values of SSR markers varied from 0.02 to 0.65 with an average of 0.27 (SD=0.17) and could discriminate between all Pima cotton varieties. The minimum number of loci was 2 and maximum – 5 with an average 2, 8 loci per marker. Presence of minor alleles (MAF) was detected in 21% (41) of loci. Average heterozygosity (H) of SSRs was H=0,31 (SD=0,2) with maximum and minimum value of Н=0,02 and Н=0,72 respectively. Phylogenetic tree were generated by UPGMA and revealed genetic distances (GD) among 288 Pima cotton varieties which varied from GD=0.01 to GD=0.65 with an average of GD=0.2. The lowest genetic similarity (0,76±0,13) was observed in African cotton varieties whereas the highest genetic similarity observed in Uzbek and US varieties (0,81±0,11 and 0,81±0,10 respectively). Analysis of population structure identified two distinct subpopulations according to Q-matrix generated by STRUCTURE software. A highest genetic diversity (0,35) was identified inside the first subpopulation, consisting of 16 Pima varieties. In the second subpopulation, presented by 272 Pima varieties, genetic diversity was 0,15. Genetic variation in the first and the second subpopulation was 32,8% and 23,6% respectively. The Fst value from AMOVA between two subpopulations was 0,58 (р≤0,0001). Our further studies aimed to investigate genome wide linkage disequilibrium and association mapping of cotton fiber traits among germplasm collection of Pima cotton varieties.
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