Evaluation of Genetic Diversity among CLCuD-Resistant Upland Cotton Varieties Using SSR Markers

Cotton leaf curl disease (CLCuD) is a dangerous viral disease that affects the productivity of cotton crops. Since early detection, this disease has spread worldwide and has caused serious damage to the production of cotton around the world particularly in Pakistan. In this study, we evaluated the genetic diversity of CLCuD-resistant upland cotton germplasm by using microsatellite markers. For this purpose, 25 pairs of microsatellite primers were screened and 9 were found to be polymorphic. These 9 primers were used for assessing the genetic diversity of 75 upland cotton varieties. Using these markers, a total of 46 loci were amplified with an average of 5.11 loci per primer. BNL0409 and BNL2835 produced the highest number of bands, 8 bands by each primer. Mean gene diversity was 0.651 with 0.91 (BNL2835) being the highest and 0.38 (JESPR0013) being the lowest. Polymorphism information content (PIC) and major allele frequency ranged between 0.91 to 0.36 (for BNL2835 and BNL0341) and 0.77 to 0.32 (for JESPR0013 and BNL0409) respectively. Mean PIC and major allele frequency were 0.62 and 0.49 respectively. BNL2835 showed the highest allele number of 23 and the mean allele number was 11. Principal component analysis (PCA) was performed and the PCA graph was plotted. These results showed that the 75 varieties studied, using 9 microsatellite markers have an average level of genetic diversity. The findings of this study could be utilized for genetic analysis and the outcomes might be useful for cotton breeding programs.