Genetic analysis of wild and cultivated germplasm of pigeonpea using random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) markers

Abstract

The reliability of the quantification of genetic diversity using only one type of marker has been questioned as compared to the combined use of different markers. To compare the efficiency of the use of single versus multiple markers, the genetic diversity was quantified among 12 diverse pigeonpea germplasm comprised of eight wild and four cultivated using both random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers, and how well these two types of markers discriminated the diverse pigeonpea germplasm was evaluated. The pigeonpea germplasm including eight wild species and four cultivated varieties was subjected to 40 RAPD and 40 microsatellite primers. The level of polymorphism as revealed by RAPD primers produced a total of 517 DNA fragments and all were found to be polymorphic that is, 100% and in SSR analysis 101 fragments were produced that too showed 100% polymorphism. The high similarity index value revealed by RAPD was 0.931 between GT-100 and ICPL-87 whereas through SSR, it was 1.00 between GTH-1 and GT-100 as well as Rhyncosia rothi and Rhyncosia minima. The least similarity index value revealed by RAPD (R. rothi and GTH-1) and SSR (Rhyncosia bracteata and ICPL-87) were 0.07 and 0.133, respectively. Using RAPD marker, the calculated arithmetic mean heterozygosity and the marker index were 0.90 and 22.47, respectively. The R. bracteata and ICPL-87 were found distinct from rest of other cultivars by showing only 13% similarity. Average PIC value shown by RAPD and SSR primers were found to be 0.90 and 0.18, respectively.

PineElm_SSRdb: a microsatellite marker database identified from genomic, chloroplast, mitochondrial and EST sequences of pineapple (Ananas comosus (L.) Merrill)

“…A high level of genetic variation is observed between and within species due to differences in the number of tandem repeating units at a locus which produces a highly polymorphic banding pattern [10] and is detected by the Polymerase Chain Reaction (PCR) using locus specific flanking primers [11]. Molecular markers are widely recognized as a tool in generating linkage maps [12] as they define specific locations in the genome unambiguously [13,14]. …”