Genome –wide Allelic Variations and Population Structure Analysis of Cotton Genotypes using SSR Markers

Abstract

The limited genetic base of modern cotton genotypes makes it difficult to improve cotton fibre yield and quality, emphasizing the necessity to study existing cotton germplasm resources. Therefore, this study was conducted to assess the genetic diversity and population structure of different cotton genotypes at DNA level. A total of 105 cotton genotypes were analyzed using 208 polymorphic SSR markers which were distributed on both A and D genomes. The total number of alleles in all genomes are 1382 Out of which 665 and 717 alleles were recorded in A and D genomes, respectively. In A genome, the maximum PIC values; 0.89 was observed for markers M92, M82 and M76 with the 10-total number of alleles exhibiting 100% polymorphism. These markers (M92, M82 and M76) located at the chromosomes 12A, 11A and 10A respectively with the estimation of 0.84 gene diversity. The highest PIC value 0.89 of D genome was detected for M191, M128 and M117 markers on 24D, 16D and 15D chromosomes with the 10 total numbers of alleles having the 0.84 values of gene diversity with 100% polymorphism. The UPGMA cluster DARWIN tree and Model-based Bayesian analysis clustered the studied cotton germplasm into four subpopulations, and the highest molecular variation revealed among subpopulations. Phylogenetic tree constructed for the whole germplasm population identified four major groups including; Group 1, Group 2, Group 3 and Group 4 consisting of 12, 21, 39 and 69 genotypes, respectively. Genetic distances among clusters clearly showed the variations among one another. SSR markers appear to be useful and reliable assets for future genetic and genomic analyses of cotton, such as genetic map construction, comparative genomic analyses, genetic diversity, and molecular marker-assisted breeding to select promising cotton genotypes, according to the current experiment.