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.

Genetic diversity among mulberry genotypes from seven countries

“…Among 17 primers, 11 of them had the polymorphic percentages of 100%. The PIC was between 0.2921 (ISSR 15) and 0.3746 (ISSR 12) with an average of 0.3494, close to the results in common bean and chrysanthemum (Table 2; Kumar et al 2015;Zargar et al 2016). Five genetic parameters were measured (Table 3).…”

“…ISSRs are based on microsatellite DNAs, which have high levels of mutations in non-coding regions due to replication slippage, and, therefore, these mutations can accumulate and differ between varieties in different populations (Zietkiewicz et al 1994). Other than applications to genetic stability and gene variation (Qian et al 2001;Naz et al 2016), ISSRs have higher efficiencies in polymorphism analyses in plants (Nagaoka and Ogihara 1997;Devarumath et al 2002;Zargar et al 2016). However, AFLPs require known flanking sequence and advanced digestion, respectively.…”

Comparative assessment of genetic diversity in Sesamum indicum L. using RAPD and SSR markers

“…Mean PIC value, however, was found to be larger for SSR (0.194) than RAPD (0.186). The higher PIC value for SSR has been reported earlier in common bean (Zargar et al 2016) and walnut (Ahmed et al 2012). The PIC values ranging from 0.03 to 0.96 were reported in the previous studies also (Li-Bin et al 2008; Cho et al 2011; Spandana et al 2012; Park et al 2013).…”

Candidate gene based characterization of common bean genotypes

“…This was comparable to the mean PIC value of 0.28 obtained in another candidate gene based SSRs study in rice (Molla et al 2015). The values for marker index ranged from 0.391 to 1.28 with an average 0.80 which was less compared to 1.279 reported by Zargar et al (2016). Average resolving power was 1.12 detected in present study, less value have been observed for Bmd38 and BM172 and that of high for BM184 followed by BM142, BM141, BM98, BM170 and BM161.…”