DNA Fingerprinting and Genetic Diversity Assessment of GM Cotton Genotypes for Protection of Plant Breeder Rights

Abstract

DNA fingerprinting is rapid, easy, and efficient method for discrimination, identification and characterization of various genotypes for protection of plant breeder’s rights (PBRs). Present study was designed for DNA fingerprinting and genetic diversity assessment of 25 GM cotton genotypes (possessing Cry1Ac gene) using 297 SSR markers through conventional PCR and Polyacrylamide gel electrophoresis. Out of 297 SSR markers, 25 markers were not amplified, 28 were monomorphic and 244 were polymorphic. A total of 1537 alleles were amplified among which 1294 (84.18%) were polymorphic. PIC value in our study ranged from 0.08 to 0.93 with an average of 0.73. Unique allelic pattern was observed for nineteen genotypes whereas six genotypes were identified using two-step identification methods. The UPGMA dendrogram divided the genotypes into two distinct clusters. Cluster I was comprised of 20 genotypes whereas cluster II was comprised of four genotypes. MNH-1020 did not obey any clustering and remained separated. The results of the structure analysis were complementary to cluster analysis and the population was divided into two subgroups. Our results evidenced narrow genetic base of the cotton genotypes cultivated in Punjab Pakistan due to use of common parents in the pedigree/parentage. Further, we proposed a core set of markers for future DNA fingerprinting and genetic diversity studies. The information generated in this study will be helpful in variety registration and subsequent protection under PBRs. Further our findings will be useful in selection of SSR markers for future studies which are focused on DNA fingerprinting and genetic diversity assessment.