<span style="font-size:11.0pt;font-family: "Times New Roman";mso-fareast-font-family:"Times New Roman";mso-bidi-font-family: Mangal;mso-ansi-language:EN-GB;mso-fareast-language:EN-US;mso-bidi-language: HI" lang="EN-GB">Comparative efficiency of SRAP, SSR and AFLP-RGA markers in resolving genetic diversity in pigeon pea (<i style="mso-bidi-font-style:normal">Cajanus</i> sp.)</span>

Abstract

Three different marker systems, <i style="mso-bidi-font-style: normal">viz</i>.<i>,</i> 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 &gt; AFLP-RGA &gt; SSR.