Microsatellite marker based DNA fingerprinting of cotton (Gossypium spp.) hybrids and their parents

DOI: 10.37992/2022.1303.136

  • H. B. Santosh,
  • Ashwini Bargat,
  • V. Santhy,
  • K. P. Raghavendra,
  • K. R. Kranthi and V. N. Waghmare


Cotton production in India by the vast majority comes from cotton hybrids whose genetic purity is of great significance in the seed production chain and trade. Therefore, there is a need to develop a rapid, reliable and reproducible technique to assess the genetic purity of cotton hybrids as the traditional, morphological traits-based ‘Grow-Out Test’ is resource intensive, time consuming, tedious and not an infallible procedure. In this regard, a study was planned to understand the genetic diversity among the hybrids and their parents and also to identify SSR markers for confirmation of genetic purity or hybridity. One intra-arboreum hybrid, CICR2 (DS 5 GMS × LD 327 Sel.), four intra-hirsutum hybrids viz., CSHH198 (CSH 19 × CSH 8), CSHH238 (SH 2379 9Y × PIL 8 Sel.), CSHH243 (CSH 2013 × CSH 43), CSHH1862 (GMS 16A × CB 33) and one hirsutum × barbadense hybrid, Phule 388 (RHC-006 × RHCb-001) along with their respective parental lines were selected for molecular characterization. Of the total 215 SSR markers surveyed, 60 markers conveyed polymorphism. The information conveyed by the polymorphic SSR markers was utilized to assess the molecular divergence among the study material. Maximum genetic dissimilarity of 0.66 was noted between Phule 388 and LD 327 (Sel.), and between RHC-006 and DS 5 (GMS). Minimum genetic dissimilarity of 0.07 was observed between CSHH1862 and CB 33, followed by 0.11 between CICR2 and DS 5 (GMS). SSR markers were highly efficient in capturing both intra-species and inter-species level diversity. The clustering and factorial analysis were  in congruence with the species of Gossypium. The diploid species genotypes were clustered separately and distinctly from the rest of the genotypes. All the hirsutum hybrids and their respective parents were found closely clustered. The inter-specific hybrid, Phule 388 along with its parents was found grouped closely. The genetic purity of the hybrids was confirmed using identified SSR markers [GH486, BNL1421, BNL3594, JESPR151 for G. hirsutum hybrids, CSHH198; GH486, BNL2449, JESPR151, TMB0436 for G. hirsutum hybrids, CSHH238; BNL2449, JESPR151, JESPR152 for G. hirsutum hybrid, CSHH243 and GH527, BNL3812, TMB1484, TMB1645, NAU1190, BNL3816 for inter-specific G. hirsutum × G. barbadense hybrid Phule 388]. The SSR markers were efficient in the analysis of hybrid seed purity. The information generated in the present study about genetic diversity and genetic purity testing will greatly facilitate quality seed production of these cotton hybrids and thus, better cotton production.

Keywords: Cotton, DNA fingerprinting, Hybrids, Microsatellites, SSR markers, Diversity

How to Cite
Santosh, H. B., Bargat, A., Santhy, V., Raghavendra, K. P., & V. N. Waghmare, K. R. K. (2022). <p><strong>Microsatellite marker based DNA fingerprinting of cotton (<em>Gossypium spp.</em>) hybrids and their parents </strong></p&gt;. Electronic Journal of Plant Breeding, 13(3), 780-789. Retrieved from https://ejplantbreeding.org/index.php/EJPB/article/view/4408
Research Article