Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam Ruditapes philippinarum Based on High-Resolution Melting (HRM) Analysis
2024
Sichen Zheng | Yancui Chen | Biao Wu | Liqing Zhou | Zhihong Liu | Tianshi Zhang | Xiujun Sun
Single-nucleotide polymorphisms (SNPs) are the most commonly used DNA markers in population genetic studies. We used the Illumina HiSeq4000 platform to develop single-nucleotide polymorphism (SNP) markers for Manila clam Ruditapes philippinarum using restriction site-associated DNA sequencing (RAD-seq) genotyping. Eighty-eight SNP markers were successfully developed by using high-resolution melting (HRM) analysis, with a success rate of 44%. SNP markers were analyzed for genetic diversity in two clam populations. The observed heterozygosity per locus ranged from 0 to 0.9515, while the expected heterozygosity per locus ranged from 0.0629 to 0.4997. The value of FIS was estimated to be from &minus:0.9643 to 1.0000. The global Fst value was 0.1248 (p <: 0.001). After Bonferroni correction, 15 loci deviated significantly from the Hardy&ndash:Weinberg equilibrium (p <: 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species.
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