title: Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean.
abstract: Increase in food production viz-a-viz quality of food is important to feed the growing human population to attain food as well as nutritional security. The availability of diverse germplasm of any crop is an important genetic resource to mine the genes that may assist in attaining food as well as nutritional security. Here we used 15 RAPD and 23 SSR markers to elucidate diversity among 51 common bean genotypes mostly landraces collected from the Himalayan region of Jammu and Kashmir, India. We observed that both the markers are highly polymorphic. The discriminatory power of these markers was determined using various parameters like; percent polymorphism, PIC, resolving power and marker index. 15 RAPDs produced 171 polymorphic bands, while 23 SSRs produced 268 polymorphic bands. SSRs showed a higher PIC value (0.300) compared to RAPDs (0.243). Further the resolving power of SSRs was 5.241 compared to 3.86 for RAPDs. However, RAPDs showed a higher marker index (2.69) compared to SSRs (1.279) that may be attributed to their higher multiplex ratio. The dendrograms generated with hierarchical UPGMA cluster analysis grouped genotypes into two main clusters with various degrees of sub clustering within the cluster. Here we observed that both the marker systems showed comparable accuracy in grouping genotypes of common bean according to their area of cultivation. The model based STRUCTURE analysis using 15 RAPD and 23 SSR markers identified a population with 3 sub-populations which corresponds to distance based groupings. High level of genetic diversity was observed within the population. These findings have further implications in common bean breeding as well as conservation programs.
authors: School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu & Kashmir 180009, India.
authors: Sajad Majeed
authors: SM
authors: Zargar
authors: School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu & Kashmir 180009, India.
authors: Sufia
authors: S
authors: Farhat
authors: School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu & Kashmir 180009, India.
authors: Reetika
authors: R
authors: Mahajan
authors: School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu & Kashmir 180009, India.
authors: Ayushi
authors: A
authors: Bhakhri
authors: School of Biotechnology, S K University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu, Jammu & Kashmir 180009, India.
authors: Arjun
authors: A
authors: Sharma
keywords: Common bean; Dendrogram; MI, marker index; PAGE, polyacrylamide gel electrophoresis; PCA; PCA, principle component analysis; PIC, polymorphic information content; Population structure; QTL, quantitative trait loci; RAPD; RAPD, random amplified polymorphic DNA; RFLP, restriction fragment length polymorphism; Rp, resolving power; SSR; SSR, simple sequence repeat; UPGMA, unweighted pair group method with arithmetic averages