Genetic differentiation of Vigna species by RAPD, URP and SSR markers

Abstract

Seventy genotypes belonging to 7 wild and cultivated Vigna species were genetically differentiated using randomly amplified polymorphic DNA (RAPD), universal rice primer (URP) and simple sequence repeat (SSR) markers. We identified RAPD marker, OPG13 which produced a species-specific fingerprint profile. This primer characterized all the Vigna species uniquely suggesting an insight for their co-evolution, domestication and interspecific relationship. The cluster analysis of combined data set of all the markers resulted in five major groups. Most of the genotypes belonging to cultivated species formed a specific group whereas all the wild species formed a separate cluster using unweighted paired group method with arithmetic averages and principle component analysis. The Mantel matrix correspondence test resulted in a high matrix correlation with best fit (r = 0.95) from combined marker data. Comparison of three-marker systems showed that SSR marker was more efficient in detecting genetic variability among all the Vigna species. The narrow genetic base of the V. radiata cultivars obtained in the present study emphasized that large germplasm collection should be used in Vigna improvement programme.

Efficiency of RAPD and ISSR markers system in accessing genetic variation of rice bean (Vigna umbellata) landraces

“…In RAPD analysis, the rice bean genotypes were grouped into three subclusters revealing sufficient amount of diversity within the cluster. Similar results have been found by Dikshit et al (2007) for V. umbellata accessions and estimated 53 per cent of genetic similarity based on RAPD, URP (universal rice primer) and SSR markers data. In our study, ISSR markers grouped nine rice bean genotypes in two subclusters.…”

“…DNA fingerprinting is a routine method employed to study the extent of genetic diversity across a set of germplasm or cultivars and group them into specific categories. Comparative studies in Vigna species involving RAPD, AFLP, ISSR and SSR marker systems were successfully used by very limited researchers (Souframanien and Gopalakrisna, 2004;Gillaspie et al 2005;Dikshit et al 2007). But, it has been carried out in many crops like rice (Ravi et al 2003), capsicum (Ruanet et al 2005) and common bean (Marotti et al 2006).…”

“…The most commonly used marker systems are restriction fragment length polymorphism (RFLP) (Soller and Beckmann, 1983), random amplified polymorphic DNA (RAPD) (Williams et al 1990), amplified fragment length polymorphism (AFLP) (Vos et al 1995), inter simple sequence repeats (ISSRs) (Zietkiewicz et al 1994) and microsatellites or simple sequence repeats (SSRs) (Becker and Heun, 1994). Among them to characterize DNA variation patterns within species and among closely related taxa in Vigna species have been RAPD (Ba et al 2004;Dikshit et al 2007), AFLP (Sivaprakash et al 2004;Seehalak et al 2006;Yoon et al 2007;Fang et al 2007), RFLP (Kaga et al 2000), ISSR (Ajibade et al 2000), SSRs (Li et al 2001;Dikshit et al 2007) and sequence tagged microsatellite site (STMS) (Phansak et al 2005).…”

Morphological and molecular diversity within Algerian cowpea (Vigna unguiculata (L.) Walp.) landraces

“…On the other hand, molecular markers are highly heritable, available in large numbers, and often polymorphic enough to enable discrimination of closely related genotypes. In recent years, various classes of molecular markers, including random amplified polymorphic DNA (RAPD) (Nkongolo 2003;Ba et al 2004;Badiane et al 2004;Sarutayophat et al 2007;Dikshit et al 2007), AFLP (Menendez et al 1997;Ouédraogo et al 2002), SSR (Gillaspie et al 2005;Li et al 2001;Diouf and Hilu 2005) and inter-simple sequence repeat (ISSR) (Ajibade et al 2000), have been used to detect genetic diversity in cowpea.…”

Assessment of Genetic Diversity by Using RAPD Markers of Vigna unguiculata cultivars in Telangana State, India

“…To characterize DNA variation patterns among closely related taxa and within species in Vigna, RAPD (Dikshit et al, 2007) and SSRs (Dikshit et al, 2007) have been adopted.…”