Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam Ruditapes philippinarum Based on High-Resolution Melting (HRM) Analysis
文献类型： 外文期刊
作者： Zheng, Sichen 1 ; Chen, Yancui 4 ; Wu, Biao 1 ; Zhou, Liqing 1 ; Liu, Zhihong 1 ; Zhang, Tianshi 1 ; Sun, Xiujun 1 ;
作者机构： 1.Chinese Acad Fishery Sci, Yellow Sea Fisheries Res Inst, State Key Lab Mariculture Biobreeding & Sustainabl, Qingdao 266071, Peoples R China
2.Laoshan Lab, Lab Marine Fisheries Sci & Food Prod Proc, Qingdao 266237, Peoples R China
3.Shanghai Ocean Univ, Coll Fisheries & Life Sci, Shanghai 201306, Peoples R China
4.Zhangzhou Aquat Technol Promot Stn, Zhangzhou 363000, Peoples R China
关键词： Ruditapes philippinarum; RAD-seq; SNP; high-resolution melting
期刊名称：ANIMALS （ 影响因子：3.0； 五年影响因子：3.2 ）
ISSN： 2076-2615
年卷期： 2024 年 14 卷 4 期
页码：
收录情况： SCI
摘要： 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 -0.9643 to 1.0000. The global F-st 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.
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