Exploring Genetic Diversity in Cotton Genotypes Using EST-SSR and ISSR Markers: A Comparative Study

Abstract

| Cotton (Gossypium hirsutum L.) is a significant global crop and a vital raw material for industries. Studying existing cotton germplasm is crucial for discovering new genetic resources for future breeding. In this study, the effectiveness of EST-SSRs and ISSRs markers were compared for assessing genetic variation among 45 Pakistani Bt and non-Bt cotton varieties. ISSR and EST-SSR primers yielded 108 and 28 loci, respectively. The polymorphism was found 32.40% for ISSR, while 89.28% was recorded for SSR primers. Cluster analysis revealed a high level of genetic similarity for ISSR (average 0.92) and EST-SSR (average 0.85) among cotton genotypes. The mean polymorphic information content (PIC) value was 0.25 for ISSR, whereas it was recorded 0.48 for EST-SSRs. Confusion probability (Cj) exhibited a negative association with discriminating power (Dj), while Dj displayed a positive association with PIC. Marker discriminating statistics showed that EST-SSRs have a high expected heterozygosity of polymorphic loci (Hep) as compared to ISSR, along with a higher marker index value (MI). The effective multiplex ratio for ISSRs (1.40) was greater than EST-SSRs (1.12). The structural analysis revealed 6 sub-clusters for EST-SSRs and 4 sub-clusters for ISSRs. This phylogenetic study is crucial for identifying promising genotypes for breeding programs, especially given the limited genetic diversity in cotton breeding. The study showed that Bt cotton genotypes share a high genetic similarity, emphasizing the need for introducing diverse or exotic genotypes into breeding programs to enrich genetic diversity. Additionally, marker-discriminating indices can aid in selecting effective markers to assess genetic variation, facilitating the development of improved cotton varieties with desired traits.