Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam <i>Ruditapes philippinarum</i> Based on High-Resolution Melting (HRM) Analysis
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 <i>Ruditapes philippinarum</i> using restriction site-associated DN...
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MDPI AG
2024-02-01
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| Online Access: | https://www.mdpi.com/2076-2615/14/4/542 |
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| author | Sichen Zheng Yancui Chen Biao Wu Liqing Zhou Zhihong Liu Tianshi Zhang Xiujun Sun |
| author_facet | Sichen Zheng Yancui Chen Biao Wu Liqing Zhou Zhihong Liu Tianshi Zhang Xiujun Sun |
| author_sort | Sichen Zheng |
| collection | DOAJ |
| description | 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 <i>Ruditapes philippinarum</i> 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<sub>IS</sub> was estimated to be from −0.9643 to 1.0000. The global F<sub>st</sub> value was 0.1248 (<i>p</i> < 0.001). After Bonferroni correction, 15 loci deviated significantly from the Hardy–Weinberg equilibrium (<i>p</i> < 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species. |
| first_indexed | 2024-03-07T22:45:39Z |
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| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-07T22:45:39Z |
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| spelling | doaj.art-70714fd263034ade971a968173b34aae2024-02-23T15:04:35ZengMDPI AGAnimals2076-26152024-02-0114454210.3390/ani14040542Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam <i>Ruditapes philippinarum</i> Based on High-Resolution Melting (HRM) AnalysisSichen Zheng0Yancui Chen1Biao Wu2Liqing Zhou3Zhihong Liu4Tianshi Zhang5Xiujun Sun6State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaZhangzhou Aquatic Technology Promotion Station, Zhangzhou 363000, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaState Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaSingle-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 <i>Ruditapes philippinarum</i> 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<sub>IS</sub> was estimated to be from −0.9643 to 1.0000. The global F<sub>st</sub> value was 0.1248 (<i>p</i> < 0.001). After Bonferroni correction, 15 loci deviated significantly from the Hardy–Weinberg equilibrium (<i>p</i> < 0.0006). These SNP markers provide a valuable resource for population and conservation genetics studies in this commercially important species.https://www.mdpi.com/2076-2615/14/4/542<i>Ruditapes philippinarum</i>RAD-seqSNPhigh-resolution melting |
| spellingShingle | Sichen Zheng Yancui Chen Biao Wu Liqing Zhou Zhihong Liu Tianshi Zhang Xiujun Sun Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam <i>Ruditapes philippinarum</i> Based on High-Resolution Melting (HRM) Analysis Animals <i>Ruditapes philippinarum</i> RAD-seq SNP high-resolution melting |
| title | Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam <i>Ruditapes philippinarum</i> Based on High-Resolution Melting (HRM) Analysis |
| title_full | Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam <i>Ruditapes philippinarum</i> Based on High-Resolution Melting (HRM) Analysis |
| title_fullStr | Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam <i>Ruditapes philippinarum</i> Based on High-Resolution Melting (HRM) Analysis |
| title_full_unstemmed | Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam <i>Ruditapes philippinarum</i> Based on High-Resolution Melting (HRM) Analysis |
| title_short | Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam <i>Ruditapes philippinarum</i> Based on High-Resolution Melting (HRM) Analysis |
| title_sort | characterization of eighty eight single nucleotide polymorphism markers in the manila clam i ruditapes philippinarum i based on high resolution melting hrm analysis |
| topic | <i>Ruditapes philippinarum</i> RAD-seq SNP high-resolution melting |
| url | https://www.mdpi.com/2076-2615/14/4/542 |
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