Elucidating the genetic diversity and population structure of international Cotton germplasm using iPBS Retrotransposon Marker System

Abstract Cotton (Gossypium hirsutum L.) is an important crop throughout the world and is one of the most important industrial raw materials. It is very important to characterize the available cotton germplasm aiming to identify novel genetic and genomic resources that can be used for future cotton breeding. Keeping this in view, a total of 179 cotton genotypes were characterized with the interPrimer Binding Site (iPBS). Seven iPBS-retrotransposons primers yielded a total of 134 scoreable bands and among these totals of 134, 128 bands were polymorphic. The mean polymorphic bands per primer were 18.28, with values between 16 and 21. The mean polymorphism rate of 7 iPBS retrotransposon primers was calculated as 96.28%. The polymorphism information content (PIC) value varies between 0.31 and 0.46 with an average of 0.395. Genetic similarity was calculated using the POPGENE software and values ranged between 0.320 and 0.955. Population structure and neighbor-joining analysis divided the evaluated germplasm into two populations. The analysis of molecular variance revealed that maximum variations (96%) are due to differences within the populations. The information presented here has comprehensively demonstrated the potential of iPBS-retrotransposon markers in detecting genetic diversity and phylogenetic association analyses of cotton and resulted information will be helpful for future cotton breeding.