Abstract:Atrina pectinata is a large deep-water mollusk species that has high economic values. It is distributed in the coastal areas of China, from the Liaodong Peninsula in the north to the Qiongzhou Strait in the south. Its habitat is adjacent to China’s provinces such as Fujian, Guangdong, Liaoning and Shandong. In recent decades, the natural resource of A. pectinata has declined due to the environment destruction and overfishing. To better protect the resource of A. pectinata, we need to understand its population genetic structure. Microsatellites is a widely used method to assess the genetic diversity in farmed aquatic species and construct QTL due to its characteristics such as the abundant polymorphism, the rich information, the co-dominance and conservation. The EST-SSR marker is inexpensive and is probably associated with functional regions of the genome. Therefore, in this research, we developed a series of EST-SSR markers using a transcriptome-based platform to study the genetic diversity of A. pectinata. We identified 10550 EST-SSR (8.2%) using MISA software, and the corresponding frequency was 1 EST-SSR per 9.01 kb of the sequence. Dinucleotide repeats were dominant among all EST-SSRs, counting for 77.08%. We designed 120 primers for PCR, and 36 out of 120 resulted in successful amplification. Fragments amplified with 12 primers were polymorphic. Next we used these SSR primers to explore the genetic variation of 30 A. pectinata samples collected from the Qingdao Bay. The number of alleles for the 12 SSR makers varied from 2 to 5 in these samples with an average of 3.5 alleles per locus. The observed heterozygosity ranged from 0.1667 to 0.6667, and the expected heterozygosity varied from 0.4316 to 0.7938. Polymorphic information content ranged from 0.3679 to 0.7459. These indicated high genetic diversity of the A. pectinata population in the Qingdao Bay. Moreover, we verified that the polymorphic EST-SSR markers could be a useful tool in comparative mapping, gene tagging and QTL mapping.
