Molecular characterization and genetic relationships among cotton genotypes 1RAPD, ISSR and SSR analysis

ABSTRACT

Cotton is the world's leading fiber crop and the second important oil seed crop. Recent advances in genomics research have provided new tools, such as molecular markers, that will assist breeders in the improvement of this important crop. Use of molecular markers in genome analysis, mapping of agriculturally important traits and marker-assisted selection have been greatly advanced by the development of PCR-based markers. The present study is a part of a cotton genomics project that addresses the use of different PCR-based molecular markers [RAPD, ISSRI and SSR] for germplasm characterization, fingerprinting and assessing the genetic diversity among some of the accessions available at the Cotton Research Institute, ARC, and Egypt. Twenty one cotton accessions were assayed using 28 RAPD and 12 ISSR primers, in addition to 24 SSR specific primer pairs. The total number of amplicons detected by RAPD, ISSR and SSR was 323, 125 and 62, respectively. While, the number of polymorphic amplicons was 191, 62 and 39 respectively. Thus, the level of polymorphism among the 21 accessions as revealed by RAPD, ISSR and SSR was 59.1%, 49.6 and 62.9 respectively. The genetic relationships among the 21 accessions were estimated in terms of similarity using the Dice coefficient. The topology of the dendrograms derived from the different marker types was unique, however, with evident similarities. All dendrograms clearly clustered the accessions belonging to G. hirsutum in one group and those of G. barbadense, expect Pima Early American, in another group. One out of the 28 RAPD primers produced 21 different banding patterns, thus, identifying each of the 21 accessions by a unique banding profile. Two ISSR primers [SI and S2] revealed 18 banding patterns each and together made it possible the identification of all the genotypes. Moreover, accession-specific DNA markers characterized different genotypes and therefore were used to generate unique fingerprint for each genotype. The RAPD, ISSR and SSR detected 4, 8 and 5 unique positive and/or negative markers characterizing 3, 4 and 4 accessions, respectively. Furthermore, five SSR alleles [M8 280, M8 290, C11 250, C11 260 and M13 150] could the discriminate between accessions belonging to the species G. barbadense and those of G. hirsutum. Thus, they were considered as species-specific markers