Development of polymorphic microsatellites for genetic studies of white scar oyster (Crassostrea belcheri) using paired-end shotgun sequencing

Abstract

White scar oyster Crassostrea belcheri is a commercially important bivalve species in Thailand. Appropriate genetic markers are needed for effective management to elevate its production efficiency. Type II microsatellites of C. belcheri were identified and characterized using an Illumina paired-end shotgun sequencing. A total of 14,743,710 reads were generated for which 198,849 reads containing microsatellites and 217,998 microsatellite loci were found. Twenty out of 60 microsatellite loci (33.33%) were polymorphic and these microsatellites were further tested against DNA bulks (N = 10 each) originating from 7 different geographic locations in Thai waters. Results indicated that newly developed microsatellites can be used for genetic diversity analysis of C. belcheri. Genotyping of C. belcheri collected from Surat Thani (Gulf of Thailand; N = 50) were performed. The number of alleles per locus ranged from 2 to 12 (average = 4.95). Observed and expected heterozygosities ranged from 0.0000 to 0.9400 (average = 0.3419) and 0.1139 to 0.8190 (average = 0.5844), respectively. Genome information and 20 newly isolated microsatellites will facilitate further studies in population genetics, stock management, and genetic improvement of C. belcheri in Thailand.