Genetic Diversity and Population Structure Analysis in Upland Cotton Germplasm

Elite plant breeding programs could likely benefit from the unexploited standing genetic variation of obsolete genotypes without the yield drag typically associated with wild accessions. Twenty-eight upland cotton genotypes were characterized using 100 SSR (simple sequence repeat) markers. However, only 22 (out of 100) SSR markers were polymorphic and justified further analysis. Major allele frequency ranged from 0.29 (MGHES-20) to 0.93 (MGHES-15) with an average of 0.54. The average gene diversity was 0.57 varying from 0.13 (MGHES-15) to 0.78 (MGHES-20). Polymorphism information content (PIC) values ranged from 0.12 (MGHES-15) to 0.75 (BNL-3280) with an average of 0.53. Phylogenetic analysis supported the subgroups identified by STRUCTURE. Average genetic distance between genotypes was 0.57 indicating low levels of genetic diversity in upland cotton germplasm pool. Results from both phylogenetic tree and population structure analyses were in agreement with pedigree information; however, there were few exceptions like NIBGE-115, NN-3 and NIBGE-2472 which showed a little admixture in structural analysis and not in the phylogenetic tree. Further, core sets of different sizes representing different levels of allelic richness in upland cotton were identified. Establishment of genetic diversity and population structure from this study could be useful for genetic and genomic analysis and systematic utilization of the standing genetic variation in upland cotton. (C) 2019 Friends Science Publishers