1. Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam Ruditapes philippinarum Based on High-Resolution Melting (HRM) Analysis.
- Author
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Zheng, Sichen, Chen, Yancui, Wu, Biao, Zhou, Liqing, Liu, Zhihong, Zhang, Tianshi, and Sun, Xiujun
- Subjects
MANILA clam ,SINGLE nucleotide polymorphisms ,CONSERVATION genetics ,GENETIC variation ,POPULATION genetics ,GENETIC markers - Abstract
Simple Summary: In this study, we performed a simplified genome sequencing of 301 individuals from 10 populations of Ruditapes philippinarum in coastal China using restriction site-associated DNA sequencing (RAD-seq) technology, and obtained a large number of single-nucleotide polymorphism (SNP) markers of Manila clam. Eighty-eight SNP markers were successfully developed using high-resolution melting (HRM) analysis, and the genetic structure and genetic diversity of two populations were analyzed. SNP markers provide a valuable resource for population and conservation genetics studies of this commercially important species. 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 F
IS was estimated to be from −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–Weinberg equilibrium (p < 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species. [ABSTRACT FROM AUTHOR]- Published
- 2024
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