Development of new Microsatellite DNA Markers Using Next-generation Sequencing in pacific oyster Crassostrea gigas
Chun Mae Dong, Hye Min Lee, Mi Nan Lee, Eun Soo Noh, Bo Hye Nam, Young-Ok Kim1 and Eun-Mi Kim
Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Korea Aquaculture Management Division, National Institute of Fisheries Science, Busan 46083, Korea
This study was conducted to develop microsatellite markers in Crassostrea gigas using next-generation sequencing. A total of 46,335,655,445 bp reads were generated on an Illumina Hiseq x ten system, yielding 600,863,377 bp sequences. The de novo assembly resulted in 30.636 contigs. A total of 261 contigs, including 56 microsatellite loci, were derived from 30,636 contigs longer than 518 bp. A total of 22 polymorphic nuclear microsatellite markers were chosen to evaluate population genetic parameters in the farm. The mean number of effective alleles was 9, ranging from 3 to 25. The observed heterozygosity (HO) and expected heterozygosity (HE) ranged between 0.104 and 0.896 with an average of 0.469 and from 0.214 to 0.947 with an average of 0.579, respectively. No significant linkage disequilibrium was observed after Bonferroni revision in any loci. The results show that the 22 polymorphic nuclear microsatellite markers can be used to study the population and conservation genetics of Crassostrea gigas in Korea. The analysis of polymorphic SSR could provide an important experimental tool for examining a range of issues in Crassostrea gigas genetics
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