Assessment of the congruity of genetic relationships and variation revealed by individual- and bulked-samples-based approaches using RAPD and ISSR markers in Japanese turnip (Brassica rapa ssp. rapa) cultivars

Abstract

NoteAssessment of the congruity of genetic relationships and variation revealed by individual-and bulked-samples-based approaches using RAPD and ISSR markers in Japanese turnip (Brassica rapa ssp. rapa) cultivars Kenji Wakui* 1) , Hiroyoshi Iwata 2) , Yu Takahashi To find out an efficient and accurate way to estimate the genetic relationship among cultivars having withinvariety genetic variation by using different types of approaches, we compared among-varieties genetic similarity estimated based on individual samples and also on bulked population samples of six Japanese turnip (Brassica rapa ssp. rapa) cultivars using RAPD and ISSR markers. In both individual-and bulked-samplesbased approaches, 37 individuals were sampled from each cultivar, amplified individually and also as bulked DNA, respectively. Genetic similarity matrices among six cultivars were estimated based on four similarity measures estimated with 125 or 124 polymorphic bands scored in the individual-or bulked-samples-based approach, respectively, and the correlations between the similarity matrices were calculated to evaluate the degree of agreement between matrices. Correlations between similarity matrices calculated based on individuals on the one hand and those calculated based on bulked samples on the other were also high and significant in all combinations of the four similarity measures. Use of computational analysis indicated that 6 to 8 individuals per cultivar were enough to accurately estimate similarity with the individual-based approach.Key Words: Brassica rapa ssp. rapa, Random amplified polymorphic DNA (RAPD), Inter-simple sequence repeat (ISSR), Individual-based approach, Bulked-samples-based approach.

Comparison of Individual- and Bulked-Samples-Based Approaches Using RAPD and ISSR Markers for Identifying Genetic Relationships in <i>Brassica</i> Cultivars

“…These comparative findings indicate that each cultivar could be profiled by RAPD and ISSR markers and classified similarly in the individual-and bulkedsamples-based approaches. This favors high correlation coefficients between the similarity measures for individual-and bulked-samples data, as shown in our previous study (Wakui et al 2009). Especially, eight individuals within a cultivar, which were determined based on the results of a previous study (Wakui et al 2009), appear to be appropriate and include the variation within a cultivar, because the expected heterozygosity value within each cultivar was low (Table 1).…”

“…This shows the importance of evaluating the number of individuals, which includes the variance of the variety used for analysis (Yu and Pauls 1993). Our previous study (Wakui et al 2009) with local varieties of turnip indicated that six to eight individuals per cultivar were enough to calculate an accurate estimate of similarity with the individual-based approach.…”

“…DNA amplification and data analysis RAPD and ISSR primers used in this study were the same as those reported by Wakui et al (2009). RAPD and ISSR analyses were performed using ten 10-mer random oligonucleotides (Eurofins Genomics) and ten selected ISSR primers from primer set No.…”

“…Among the Brassica species, B. rapa and B. oleracea are allogamous species, owing to their self-incompatible nature, and are expected to be genetically heterogeneous, especially in the indigenous varieties. In a previous study, we reported the congruity between genetic similarities among cultivars, calculated from the data based on individual and bulked population samples, to assess genetic relationships between Brassica cultivars, including heterogeneous species (Wakui et al 2009). In the above-mentioned study, we also determined that the number of plantlets that should be analyzed per cultivar using RAPD and ISSR analysis is 37, for each of the six cultivars of Japanese turnip (B. rapa ssp.…”

Elucidation of thermotolerance diversity in cotton (Gossypium hirsutum L.) using physio-molecular approaches

“…RAPD analysis has been demonstrated in many applications and in various organisms espe-R.M. Rana et al cially in the plant sciences (Sharma and Mohapatra, 1996) and was used successfully in field crops such as Iranian melon (Soltani et al, 2010), Brassica rapa (Wakui et al, 2009), cotton (Multani and Lyon, 1995;Chaudhary et al, 2010), etc.…”