Indian Journal of Biotechnology Vol 13, October 2014, pp 486-495 Comparative efficiency of SRAP, SSR and AFLP-RGA markers in resolving genetic diversity in pigeon pea (Cajanus sp.) Ikechukwu O Agbagwa 1,2 *, Prakash Patil 2 , Subhojit Datta 2 and N Nadarajan 2 1 Department of Plant Science and Biotechnology, Faculty of Science, University of Port Harcourt, Nigeria 2 Indian Institute of Pulses Research, Kanpur 208 024, India Received 21 January 2013; revised 29 May 2013; accepted 17 July 2013 Three different marker systems, viz., sequence related amplified polymorphism (SRAP), simple sequence repeat (SSR) and resistance gene analogue anchored amplified fragment length polymorphism (AFLP-RGA) were employed to analyze genetic diversity among 29 pigeon pea genotypes. Furthermore, relative efficiencies of these marker systems were compared in relation to polymorphism information content (PIC), marker index (MI) and resolving power (RP). A total of 21 primers (4 SRAP, 15 SSR and 2 AFLP-RGA) screened on the genotypes that produced 258 fragments, of which 254 were polymorphic. High percentage polymorphism and average PIC were observed for SSR (97%, PIC 0.24), followed by SRAP (94%, PIC 0.21) and AFLP-RGA (93%, PIC 0.21). MI and RP values were observed to be the highest in SRAP (MI=7.30, RP=12.93), decreasing through AFLP-RGA (MI=6.05, RP=12.66) to as low as 0.71 and 1.04, respectively in SSR. Higher ranges of genetic distances were observed for AFLP-RGA (0.13-0.90), followed by SRAP (0.18-0.87) and SSR (0.28-0.97). Mantel test for matrix correspondence among the marker systems revealed SSR and SRAP matrices having good correlation (r=0.86) compared to SRAP and AFLP-RGA (r=0.68), and AFLP-RGA and SSR (0.62). UPGMA clustering based on individual and combined marker data clearly distinguished the 29 genotypes into two broad groups (cultivated and wild) mostly in relation to their pedigree. Overall ability to resolve diversity in pigeonpea as observed using these markers follows the sequence: SRAP > AFLP-RGA > SSR. Keywords: AFLP-RGA, genetic diversity, microsatellite, pigeon pea, polymorphism, SRAP, SSR Introduction Pigeonpea [Cajanus cajan (L.) Millsp.] is an important food legume crop of the semi-arid regions of the world. Being a drought tolerant crop, it is considered as one of the most nutritious 1 pulse crop forming the integral component of vegetarian diet of South Asia 2 . Globally this crop is cultivated in Asia, Africa, Latin America and Caribbean regions 3 . As the second most important pulse crop next to chickpea in India, it occupies an area of about 3.4 million ha with annual production of 2.89 million tons 4 . The relative yield advantage of pigeonpea is not witnessed so far due to non-availability of improved cultivars, poor crop husbandry and prevailing number of biotic and abiotic stresses. Narrow genetic diversity in cultivated pigeonpea germplasm further hampers the effective utilization of conventional breeding 5 . Recently, several studies regarding the application and/or use of different molecular marker techniques to reveal and understand genetic diversity among different plant species have been reported 6-8 . Similarly, in pigeonpea, genetic diversity studies have been pursued using different molecular markers techniques, viz., restriction fragment length polymorphism (RFLP), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR) and diversity array technology (DArT) etc., which revealed low level of polymorphism among pigeonpea cultivars compared to wild species 1,9-12 . Furthermore, two gene targeted marker techniques [resistance gene analogue anchored amplified fragment length polymorphism (AFLP-RGA) 13 and sequence related amplification polymorphism (SRAP) 14 ] have been reported as possessing the potential utility in revealing genetic diversity based on gene rich regions of the genome. SRAP technique aims at amplification of open reading frames (ORFs) 14 ; where the forward primers preferentially amplify exonic regions, the reverse primers preferentially amplify intronic regions and region with promoters 15 . The unique primer designed —————— *Author for correspondence: E-mail: ikechukwu.agbagwa@gmail.com †For Supplementry data, see www.nopr.niscair.res.in