Pair-wise combinations of RAPD primers for diversity analysis with reference to protein and single primer RAPD in soybean

Abstract

Cultivated soybean, Glycine max (L.) Merr. belongs to family Leguminosae, subfamily Papilionoideae is grown primarily for protein and oil [1]. It is an important crop in world food trade containing 40% protein and 20% oil. The importance of the conservation and utilization of diversity is well understood as the function and sustainability of ecosystems are dependent on their biological diversity [2,3]. In order to keep cultivation of crop at economically viable level and realize full potential of crop's productivity regular varietals improvements are prerequisite. Hence, the studies on diversity are essential to determine the genetic distance among genotypes and to identify groups with similar genetic backgrounds for conserving, evaluating and utilizing germplasm for hybridization [4]. The extent of genetic diversity in can be assessed through protein and genetic markers. Genetic diversity and the pattern of variation in soybean have been evaluated with seed protein by various researchers [5,6]. However, a few studies indicated that cultivar identification is less reliable with the SDS-PAGE method [6] Evaluation of genetic diversity with molecular markers can distinguish the individual accessions' rapidly virtually with no environmental influence. One of the methods based on polymerase chain reaction (PCR) is a rapid DNA amplification technique, called RAPD (Random Amplified Polymorphic DNA). RAPD markers have been used for numerous applications in plant molecular genetics research despite having disadvantages of poor reproducibility and not generally being associated with gene regions [7,8]. RAPD, being a multi locus marker with the simplest [9] and fastest detection technology, have been successfully employed for determination of intra-species genetic diversity in several grain legumes [10]. RAPD markers have been used for genetic diversity analysis in soybean [[11], [12], [13]]. Recently, the pattern of genetic diversity among 92 genotypes of soybean from 5 different origins/sources was analyzed using 10 polymorphic RAPD markers [14]. The reports of various researchers in RAPD based study in soybean indicated the use of single primer (single primer act as both forward and reverse). However, scanty information is available regarding the performance of different primers used for primer combinations in RAPD reaction. Therefore in present study along with single primers pair-wise combinations of primers were also used to produce new markers by combining two primers in single RAPD reactions [7,15].