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Zheng S, Chen Y, Wu B, Zhou L, Liu Z, Zhang T, Sun X. Characterization of Eighty-Eight Single-Nucleotide Polymorphism Markers in the Manila Clam Ruditapes philippinarum Based on High-Resolution Melting (HRM) Analysis. Animals (Basel) 2024; 14:542. [PMID: 38396510 PMCID: PMC10886362 DOI: 10.3390/ani14040542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 01/26/2024] [Accepted: 02/04/2024] [Indexed: 02/25/2024] Open
Abstract
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 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.
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Affiliation(s)
- Sichen Zheng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (S.Z.); (B.W.); (L.Z.); (Z.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
- College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
| | - Yancui Chen
- Zhangzhou Aquatic Technology Promotion Station, Zhangzhou 363000, China;
| | - Biao Wu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (S.Z.); (B.W.); (L.Z.); (Z.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Liqing Zhou
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (S.Z.); (B.W.); (L.Z.); (Z.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Zhihong Liu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (S.Z.); (B.W.); (L.Z.); (Z.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Tianshi Zhang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (S.Z.); (B.W.); (L.Z.); (Z.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Xiujun Sun
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (S.Z.); (B.W.); (L.Z.); (Z.L.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
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Silliman K, Spencer LH, White SJ, Roberts SB. Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate. Genome Biol Evol 2023; 15:evad013. [PMID: 36740242 PMCID: PMC10468963 DOI: 10.1093/gbe/evad013] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 01/10/2023] [Accepted: 01/24/2023] [Indexed: 02/07/2023] Open
Abstract
Delineating the relative influence of genotype and the environment on DNA methylation is critical for characterizing the spectrum of organism fitness as driven by adaptation and phenotypic plasticity. In this study, we integrated genomic and DNA methylation data for two distinct Olympia oyster (Ostrea lurida) populations while controlling for within-generation environmental influences. In addition to providing the first characterization of genome-wide DNA methylation patterns in the oyster genus Ostrea, we identified 3,963 differentially methylated loci between populations. Our results show a clear coupling between genetic and epigenetic patterns of variation, with 27% of variation in interindividual methylation differences explained by genotype. Underlying this association are both direct genetic changes in CpGs (CpG-SNPs) and genetic variation with indirect influence on methylation (mQTLs). When comparing measures of genetic and epigenetic population divergence at specific genomic regions this relationship surprisingly breaks down, which has implications for the methods commonly used to study epigenetic and genetic coupling in marine invertebrates.
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Affiliation(s)
- Katherine Silliman
- South Carolina Department of Natural Resources, Marine Resources Research
Institute, Charleston, South Carolina
| | - Laura H Spencer
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Samuel J White
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
| | - Steven B Roberts
- School of Aquatic and Fishery Sciences, University of
Washington, Seattle
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