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. © 2021 Friends Science Publishers

Genome –wide Allelic Variations and Population Structure Analysis of Cotton Genotypes using SSR Markers

“…Genome-wide allelic variation Among 300 SSR markers, 30 markers were not amplified whereas 32 were monomorphic and the remaining 208 were polymorphic in this experiment. We found only 69% of the markers revealing polymorphism among studied genotypes which is comparable to previous reports [3,5]. A total 208 polymorphic SSR markers were selected for genomewide allelic variation, among which 104 were present at the A and D, genomes, respectively.…”

“…The mean values and SE values propose that there is great genetic diversity at SSR loci among studied germplasm. In current study of private alleles were found in this study (number of alleles unique to a single population), which is similar to the previous study [5,22].The maximum mean values of gene diversity was identified in the D genome followed by A-genome, suggesting that the D-genome showed more variation and the existence of genetic diversity in cotton germplasm. Further the mean values of total number of alleles per marker in the Bgenome exhibited the maximum genetic diversity as compared to the Dgenome followed by A-genome which showed the minimum genetic diversity.…”

“…According to the cotton researchers, the number of alleles amplified per marker is determined by the markers utilized, the genotypes being studied, and the procedures used to resolve amplified products. [5,11]. The mean allele number obtained in this study was comparable to that obtained by other researchers.…”

“…However, average PIC value (0.89) reported in our study is highest among all the previously published reports. High number of alleles in our study and high PIC value corresponds to a large set of SSR markers used in recent research [5]. Current study on genetic diversity and genome-wide allelic variation in cotton genotypes may be favorable for planning the future strategies on cotton genetic resources and cotton breeding scheme for development of novel cotton genotypes.…”

“…However, because of environmental interactions, uncertain genetic control of characteristics, and insufficient genome sampling for phenotypic characterization, morphological markers do not accurately explore genetic relationships among genotypes [3]. Available germplasm of cotton crop have several useful allelic variations that can be used to develop cultivars adapted to emerging environmental condition using traditional and genomic breeding methods also for fingerprinting genotypes because they are unaffected by the environment [5]. Genotype characterization through molecular markers (DNA Fingerprinting) is the rapid, easy, and most common method to discriminate, identify and characterize various cultivars to protect plant breeder's right and promote marker-assisted breeding [6].…”