Development of SNP markers in Crassostrea hongkongensis based on the next-generation sequencing and high resolution melting analysis

Abstract

Novel single nucleotide polymorphisms (SNPs) were screened using next generation sequencing in Hong Kong oyster, Crassostrea hongkongensis. A total of 91,980 putative SNPs were identified through de novo assembly of the 454 transcriptome database, and 83 of these were selected to validate polymorphism. Using high resolution melting analysis, 17 SNP markers were developed successfully with 48 individuals from two wild populations from Shantou and Zhuhai, China. The observed heterozygosities ranged from 0.125 to 0.667 and 0 to 0.708 in the two populations, respectively, while the expected ones ranged from 0.311 to 0.511 and 0.120 to 0.511 in the two samples, respectively. Fifteen SNPs have been confirmed to fit Hardy-Weinberg Equilibrium after Bonferroni correction (p < 0.003) in both populations. To our knowledge, this is the first set of SNP markers developed in C. hongkongensis, which would provide valuable information in facilitating genetics and breeding studies in the future.