Molecular marker based genetic diversity analysis in cotton using RAPD and SSR markers SALONI TYAGI * , S.K. VERMA , KIRAN NEHRA AND D.R. BAJYA Central Institute for Cotton Research,Regional Station, Sirsa - 125 055 *E-mail : salonityagi10@gmail.com ABSTRACT : The relative efficiency of Randomly Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeats (SSR) markers was assessed for their suitability and reliability for estimating genetic diversity in cotton. The genetic variability and relationships among 23 cultivars of Gossypium hirsutum were investigated using 10 RAPD and 10 SSR primers, which produced 34 and 22 amplicons, respectively. The number of polymorphic amplicons was found to be 18 and 5, resulting into a polymorphism equivalent to 52.9 and 22.7, respectively. The genetic relationship was examined using the Numerical System Package (NTSYS-PC), UPGMA analysis was performed and dendrograms were constructed. Based on the RAPD and SSR combined data, the genetic similarities ranged from 54 to 96 per cent, respectively. All dendrograms clustered the 23 genotypes into 2 major clusters (A and B) showing affinity at genus level; most of the genotypes (20 out of 23) falling into cluster A. Maximum similarity (83%) was found in the cultivars RS 2013, H1098, LD694, LD327, H1117, LH1556, HD123, CISA310, RS921, HS6, F1861 and F846, followed by the cultivars H1226, RST9, H777, F505 and F1378 showing 78 per cent similarity; and RS875, LH900 and RS810 showing 76 per cent similarity. Keywords : Cotton, genetic diversity, molecular markers, RAPD, SSR Cotton, Gossypium spp., is an economically important crop that is grown throughout the world as a source of fibre, food and feed. The cotton belonging to the genus Gossypium (Malvaceae) comprises of approximately 50 species, distributed in various continents except Europe. It has 4 cultivated species: Gossypium hirsutum L., G. barbadense, G. arboreum L. and G. herbaceum L. G. hirsutum is the predominant cultivated cotton with high yield and wide adaptation, while its closely related species, G. barbadense is grown for its extra long, strong, and fine fibre. The diploid species, G. arboreum L. and G. herbaceum L. are cultivated only in very small acreage. Due to the narrow genetic base of cotton germplasm that cotton breeders have been utilizing low efficiency of traditional selection methods, cultivar improvement in cotton has slowed down in the past 10–15 years. Analysis of genetic diversity and relatedness between species and among genotypes is useful in plant breeding programs because it provides a tool for accurate organization of germplasm and efficient parental selection. During the past few decades, a number of molecular techniques have been recruited to complement traditional methods for the evaluation of biodiversity, estimation of relatedness and genotype identification ( Rana et al., 2005). DNA markers are, by far, the most powerful and the most widely used tool to uncover informative polymorphism and genome variability (Gostimsky et al ., 2005) With the development of the polymerase chain reaction (PCR) technology, the number of useful DNA based marker types has been expanded considerably. Different PCR based marker types are available now a days including Randomly Amplified Polymorphic DNA (RAPDs) Microsatellites (SSRs). Expressed Sequence Tags (ESTs) (Guo et al., 2007) and Amplified Fragment Length Polymorphisms (AFLPs) Keeping in view the above facts, the present investigation was conducted as an attempt to address the following objectives: (1) to estimate the genetic polymorphism among twenty three cotton genotypes using two types of PCR based DNA markers, i.e., RAPDs and EST- J. Cotton Res. Dev. 29 (2) 232-236 (July, 2015)