Geographical Variations and Genetic Distances of Three Saxidomus purpuratus Populations ascertained by PCR Analysis

Abstract

Genomic DNA samples isolated from geographical purplish Washington clam (Saxidomus purpuratus) were obtained from three different regions in the Korean Peninsula: Geoje (Geoje population; GJP), Gunsan (Gunsan population; GSP) and a site of North Korea (North Korea population; NKP). The seven primers generated the total 369 loci that can be scored from the GSP clam population. 356 fragments were generated from the NKP clam population. The complexity of the banding patterns varies dramatically between the primers and three localities. In this study, 319 loci were identified in the purplish Washington clam from Geoje and 369 in the clam population from Gunsan: 221 specific loci (69.3%) in the GJP clam population and 300 (81.3%) in the GSP population. These results demonstrate that the primer detected a large quantity of specific fragments, suggesting that the genetic variation in the GSP is higher than in the GJP population. In particular, the BION-28 primer gave DNA profiles with more fragments than the other six primers in the NKP population. The oligonucleotides primer BION-75 produced 21 unique loci to each population, which were ascertaining each population, approximately 250 bp, 300 bp and 400 bp, in the GJP population. Outstandingly, the primer BION-50 detected 21 shared loci by the three populations, major and/or minor fragments of sizes 150 bp, which were matching in all samples. With regard to average bandsharing value (BS) results, individuals from GJP population (0.743) displayed higher bandsharing values than did individuals from GSP population (0.606). In the present study, the dendrogram gained by the seven oligonucleotides primers indicates three genetic clusters: cluster 1 (GEOJE 01 ~ GEOJE 07), cluster 2 (GUNSAN 08 ~ GUNSAN 14), cluster 3 (N.KOREA 15 ~ N.KOREA 21). Among the twenty one clams, the shortest genetic distance that revealed significant molecular differences was between individuals 08 and 09 from the NKP population (genetic distance = 0.073), while the longest genetic distance among the twenty-one individuals that demonstrated significant molecular differences was between individuals GEOJE no. 03 and GUNSAN no. 09 (genetic distance = 0.669). Comparatively, individuals of GJP population were properly closely related to that of NKP population, as revealed in the hierarchical dendrogram of genetic distances. In due course, PCR analysis has revealed the significant genetic distance among three purplish Washington clam populations. PCR fragments discovered in this study could be valuable as a DNA marker of the three geographical clam populations to distinguish.

Genetic Distances in Two Gracilaria Species (Gracilariaceae, Rhodophyta) Identified by PCR Technique

“…Particularly, 66 number of shared loci by the two species generated by the primer OPD-07 were identified commonly in two Gracilaria species, which identified populations and/or species. The specific primer was found to be useful in the identification of individuals and/or population, resulting from the different DNA polymorphism among individuals/species/population (Yoon & Park, 2002; Yoon & Kim, 2003a; Song & Yoon, 2013; Oh & Yoon, 2014; Yoon, 2015). Although the main disadvantage of this PCR method is its reproducibility, the method was considered suitable for the identification of a species.…”

“…The DNA band approximately 1.5kb was specificity to Lophopyrum elongatum . Generally, polymorphic loci generated by PCR using oligonucleotides primers were suitable to detect genetic similarity/diversity/ polymorphism among various organisms (Bommineni et al, 1997; Tassanakajon et al, 1998; McCormack et al, 2000; Nicolosi et al, 2000; Yoon & Kim, 2003a; Kim et al, 2004; Oh & Yoon, 2014; Yoon, 2015).…”

“…Till now, polymorphic bands generated by this PCR tehnique using arbitrary primers had good merits for detecting DNA similarity and diversity between life organisms (Jaiswal et al, 1998; Adams, 2000; Bartish et al, 2000; Nebauer et al, 2000; Kim et al, 2004; Yoon & Kim, 2004; Song & Yoon, 2013; Yoon, 2015). Generally, this PCR technique is one of fast and simple research methods to identify genetic difference and the polymorphism in various organisms that does not require the prior knowledge of the genomic DNA (Iyengar et al, 2000; Nicolosi et al, 2000).…”

Genetic Distances of Crucian Carp Populations analyzed by PCR Approach

“…As mentioned above, this method can also be applied to other habitat of crucian carp and make technicallyconvenient the analysis of many samples. Using diverse oligonucleotides primers, this PCR analysis has been applied to identify polymorphic/specific markers particular to line, species, genus and geographical population, as well as genetic diversity/polymorphism in various species of organisms ( Tassanakajon et al, 1998 ; McCormack et al, 2000 ; Yoon& Kim 2004 ; Oh & Yoon 2014 ; Yoon 2015 ). Preferentially, the habitat classification of genus Carassius is based on morphological variations in fin shape, body color, length and weight besides PCR analysis.…”

“…Only a few of information is known about the genetics of crucian carp in Korea ( Yoon & Park, 2001 ; Hong et al, 2007 ). In general, there are marked differences of the size, color and body structure in common carp along with the environmental surroundings of habitat such as water temperature, feed, stress and nutrition, etc ( Oh & Yoon 2014 ; Yoon 2015 ). We perform a clustering analysis to elucidate the genetic distances among four crucian carp populations from Hangang river, Geumgang river, Nakdonggang river and Yeongsangang river of the Korean Peninsula.…”