Skip to main content

Development of SNP Panels as a New Tool to Assess the Genetic Diversity, Population Structure, and Parentage Analysis of the Eastern Oyster (Crassostrea virginica)

Abstract

Culture of the eastern oyster (Crassostrea virginica) is rapidly expanding. Combined with their continuing role as an environmental sentinel species and ecological model, this trend necessitates improved molecular tools for breeding and selection, as well as population assessment and genetic conservation. Here, we describe the development and validation of two panels of 58 single nucleotide polymorphism markers (SNPs) for the species. Population analyses revealed three distinct populations, based on FST values and STRUCTURE, among wild oysters sampled from Delaware Bay (1), northwest Florida (2), Alabama (2), Louisiana (2), and the Texas Gulf Coast (3), consistent with previous microsatellite and mtDNA analyses. In addition, utilizing the developed panels for parentage assignment in cultured oysters (Rutgers, New Jersey) resulted in a highly accurate identification of parent pairs (99.37%). The SNP markers could, furthermore, clearly discriminate between hatchery stocks and wild-sourced individuals. The developed SNP panels may serve as an important tool for more rapid and affordable genetic analyses in eastern oyster.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

References

  • Anderson EC (2010) Computational algorithms and user-friendly software for parentage-based tagging of Pacific salmonids. Final report submitted to the Pacific Salmon Commission’s Chinook Technical Committee (US Section)

  • Anderson JD, Karel WJ, Mace CE, Bartram BL, Hare MP (2014) Spatial genetic features of eastern oysters (Crassostrea virginica Gmelin) in the Gulf of Mexico: northward movement of a secondary contact zone. Ecol Evol 4:1671–1685

    Article  PubMed  PubMed Central  Google Scholar 

  • Baird D, Christian RR, Peterson CH, Johnson GA (2004) Consequences of hypoxia on estuarine ecosystem function: energy diversion from consumers to microbes. Ecol Appl 14:805–822

    Article  Google Scholar 

  • Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA (2008) Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One 3:e3376

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Boudry P, Collet B, Cornette F, Hervouet V, Bonhomme F (2002) High variance in reproductive success of the Pacific oyster (Crassostrea gigas, Thunberg) revealed by microsatellite-based parentage analysis of multifactorial crosses. Aquaculture 204:283–296

    Article  Google Scholar 

  • Breitburg DL, Coen LD, Luckenbach MW, Mann R, Posey MH, Wesson JA (2000) Oyster reef restoration: convergence of harvest and conservation strategies. J Shellfish Res 19:371–377

    Google Scholar 

  • Buroker NE (1983) Population genetics of the American oyster Crassostrea virginica along the Atlantic coast and the Gulf of Mexico. Mar Biol 75:99–112

    Article  Google Scholar 

  • Coen LD, Brumbaugh RD, Bushek D, Grizzle R, Luckenbach MW, Posey MH, Powers SP, Tolley SG (2007) Ecosystem services related to oyster restoration. Mar Ecol Prog Ser 341:303–307

    Article  Google Scholar 

  • Cressman K, Posey MH, Mallin MA, Leonard LA, Alphin T (2003) Effects of oyster reefs on water quality in a tidal creek estuary. J Shellfish Res 22:753–762

    Google Scholar 

  • Cunningham CW, Collins TM (1994) Developing model systems for molecular biogeography: vicariance and interchange in marine invertebrates. In: Schierwater B, Streit B, Wagner GP, DeSalle R (eds) Molecular ecology and evolution: approaches and applications. Experientia Supplementum, vol 69. Birkhäuser, Basel

    Google Scholar 

  • Dharmarajan G, Beatty WS, Rhodes OE (2013) Heterozygote deficiencies caused by a Wahlund effect: dispelling unfounded expectations. J Wildl Manag 77:226–234

    Article  Google Scholar 

  • Eierman LE, Hare MP (2014) Transcriptomic analysis of candidate osmoregulatory genes in the eastern oyster Crassostrea virginica. BMC Genomics 15:503

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Eierman LE, Hare MP (2016) Reef-specific patterns of gene expression plasticity in eastern oysters (Crassostrea virginica). J Hered 107:90–100

    Article  PubMed  CAS  Google Scholar 

  • Ellegren H, Galtier N (2016) Determinants of genetic diversity. Nat Rev Genet 17:422–433

    Article  PubMed  CAS  Google Scholar 

  • Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6:e19379

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • EOBRT (2007) Eastern Oyster Biological Review Team, Status review of the eastern oyster (Crassostrea virginica). Report to the National Marine Fisheries Service, Northeast Regional Office. 16 February 2007. NOAA Tech. Memo. NMFS F/SPO-88

  • FAO (2017) Food and Agriculture Organization of the United Nations, FishStatJ - Software for fishery statistical time series. http://www.fao.org/fishery/statistics/en. Accessed 10 Mar 2017

  • Fischer MC, Rellstab C, Leuzinger M, Roumet M, Gugerli F, Shimizu KK, Holderegger R, Widmer A (2017) Estimating genomic diversity and population differentiation—an empirical comparison of microsatellite and SNP variation in Arabidopsis halleri. BMC Genomics 18:69

    Article  PubMed  PubMed Central  Google Scholar 

  • Gaffney PM (2006) The role of genetics in shellfish restoration. Aquat Living Resour 19:277–282

    Article  Google Scholar 

  • Galindo-Sánchez CE, Gaffney PM, Pérez-Rostro CI, La Rosa-Vélez JD, Candela J, Cruz P (2008) Assessment of genetic diversity of the eastern oyster Crassostrea virginica in Veracruz, Mexico using microsatellite markers. J Shellfish Res 27:721–727

    Article  Google Scholar 

  • Glaubitz JC, Rhodes OE, DeWoody JA (2003) Prospects for inferring pairwise relationships with single nucleotide polymorphisms. Mol Ecol 12:1039–1047

    Article  PubMed  CAS  Google Scholar 

  • Graffelman J, Camarena JM (2008) Graphical tests for Hardy-Weinberg equilibrium based on the ternary plot. Hum Hered 65:77–84

    Article  PubMed  Google Scholar 

  • Gu XH, Jiang DL, Huang Y, Li BJ, Chen CH, Lin HR, Xia JH (2018) Identifying a major QTL associated with salinity tolerance in Nile tilapia using QTL-seq. Mar Biotechnol 20:98–107

    Article  PubMed  CAS  Google Scholar 

  • Guo X, DeBrosse G, Allen SK (1996) All-triploid Pacific oysters (Crassostrea gigas Thunberg) produced by mating tetraploids and diploids. Aquaculture 142:149–161

    Article  Google Scholar 

  • Hare MP, Avise JC (1996) Molecular genetic analysis of a stepped multilocus cline in the American oyster (Crassostrea virginica). Evolution 50:2305–2315

    PubMed  Google Scholar 

  • Hare MP, Avise JC (1998) Population structure in the American oyster as inferred by nuclear gene genealogies. Mol Biol Evol 15:119–128

    Article  PubMed  CAS  Google Scholar 

  • Harrang E, Lapègue S, Morga B, Bierne N (2013) A high load of non-neutral amino-acid polymorphisms explains high protein diversity despite moderate effective population size in a marine bivalve with sweepstakes reproduction. G3 (Bethesda) 3:333–341

    Article  CAS  Google Scholar 

  • He Y, Ford SE, Bushek D, Powell EN, Bao Z, Guo X (2012) Effective population sizes of eastern oyster Crassostrea virginica (Gmelin) populations in Delaware Bay, USA. J Shellfish Res 70:357–379

    Google Scholar 

  • Hedgecock D, Gaffney PM, Goulletquer P, Guo X, Reece K, Warr G (2005) A case for sequencing the Pacific oyster genome. J Shellfish Res 24:429–441

    Article  Google Scholar 

  • Hoover CA, Gaffney PM (2005) Geographic variation in nuclear genes of the eastern oyster, Crassostrea virginica Gmelin. J Shellfish Res 24:103–112

    Article  Google Scholar 

  • Jehan T, Lakhanpaul S (2006) Single nucleotide polymorphism (SNP)–methods and applications in plant genetics: a review. Indian J Biotechnol 5:435–459

    CAS  Google Scholar 

  • Jin YL, Kong LF, Yu H, Li Q (2014) Development, inheritance and evaluation of 55 novel single nucleotide polymorphism markers for parentage assignment in the Pacific oyster (Crassostrea gigas). Genes Genomes 36:129–141

    Article  CAS  Google Scholar 

  • Jung H, Lyons RE, Li Y, Thanh NM, Dinh H, Hurwood DA, Salin KR, Mather PB (2014) A candidate gene association study for growth performance in an improved giant freshwater prawn (Macrobrachium rosenbergii) culture line. Mar Biotechnol 16:161–180

    Article  PubMed  CAS  Google Scholar 

  • Kalinowski ST, Taper ML, Marshall TC (2007) Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16:1099–1106

    Article  PubMed  Google Scholar 

  • Karl SA, Avise JC (1992) Balancing selection at allozyme loci in oysters: implications from nuclear RFLPs. Science 256:100–102

    Article  PubMed  CAS  Google Scholar 

  • King TL, Ward R, Zimmerman EG (1994) Population structure of eastern oysters (Crassostrea virginica) inhabiting the Laguna Madre, Texas, and adjacent bay systems. Can J Fish Aquat Sci 51:215–222

    Article  Google Scholar 

  • La Peyre MK, Humphries AT, Casas SM, La Peyre JF (2014) Temporal variation in development of ecosystem services from oyster reef restoration. Ecol Eng 63:34–44

    Article  Google Scholar 

  • Lapègue S, Harrang E, Heurtebise S, Flahauw E, Donnadieu C, Gayral P, Ballenghien M, Genestout L, Barbotte L, Mahla R, Haffray P, Klopp C (2014) Development of SNP-genotyping arrays in two shellfish species. Mol Ecol Resour 14:820–830

    Article  PubMed  CAS  Google Scholar 

  • Li C, Gowan S, Anil A, Beck BH, Thongda W, Kucuktas H, Kaltenboeck L, Peatman E (2015) Discovery and validation of gene-linked diagnostic SNP markers for assessing hybridization between Largemouth bass (Micropterus salmoides) and Florida bass (M. floridanus). Mol Ecol Resour 15:395–404

    Article  PubMed  CAS  Google Scholar 

  • Li C, Waldbieser G, Bosworth B, Beck BH, Thongda W, Peatman E (2014) SNP discovery in wild and domesticated populations of blue catfish, Ictalurus furcatus, using genotyping-by-sequencing and subsequent SNP validation. Mol Ecol Resour 14:1261–1270

    Article  PubMed  CAS  Google Scholar 

  • McDonald JH, Verrelli BC, Geyer LB (1996) Lack of geographic variation in anonymous nuclear polymorphisms in the American oyster, Crassostrea virginica. Mol Biol Evol 13:1114–1118

    Article  PubMed  CAS  Google Scholar 

  • Milbury CA, Meritt DW, Newell RIE, Gaffney PM (2004) Mitochondrial DNA markers allow monitoring of oyster stock enhancement in the Chesapeake Bay. Mar Biol 145:351–359

    Article  CAS  Google Scholar 

  • Morin PA, Luikart G, Wayne RK, the SNP workshop group (2004) SNPs in ecology, evolution and conservation. Trends Ecol Evol 19:208–216

    Article  Google Scholar 

  • O’Neill R, Snowdon R, Köhler W (2003) Population genetics: aspects of biodiversity. In: Esser K, Lüttge U, Beyschlag W, Hellwig F (eds) Progress in botany. Progress in Botany, vol 64. Springer, Heidelberg

  • Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Article  Google Scholar 

  • Peakall R, Smouse PE (2012) GENALEX 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Peterson BK, Weber JN, Kay EH, Fisher HS, Hoekstra HE (2012) Double digest RADseq: an inexpensive method for de novo SNP discovery and genotyping in model and non-model species. PLoS One 7:e37135

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Peterson CH, Grabowski JH, Powers SP (2003) Estimated enhancement of fish production resulting from restoring oyster reef habitat: quantitative valuation. Mar Ecol Prog Ser 264:249–264

    Article  Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    PubMed  PubMed Central  CAS  Google Scholar 

  • Quilang J, Wang S, Li P, Abernathy J, Peatman E, Wang Y, Wang L, Shi Y, Wallace R, Guo X, Liu Z (2007) Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers. BMC Genomics 8:157

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Reeb CA, Avise JC (1990) A genetic discontinuity in a continuously distributed species: mitochondrial DNA in the American oyster, Crassostrea virginica. Genetics 124:397–406

    PubMed  PubMed Central  CAS  Google Scholar 

  • Rodney WS, Paynter KT (2006) Comparisons of macrofaunal assemblages on restored and non-restored oyster reefs in mesohaline regions of Chesapeake Bay in Maryland. J Exp Mar Biol Ecol 335:39–51

    Article  Google Scholar 

  • Rousset F (2008) genepop’007: a complete re-implementation of the genepop software for Windows and Linux. Mol Ecol Resour 8:103–106

    Article  PubMed  Google Scholar 

  • Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson J, Gilman B, Schaffner S, van Etten W, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D, International SNP Map Working Group (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409:928–933

    Article  PubMed  CAS  Google Scholar 

  • Sauvage C, Bierne N, Lapègue S, Boudry P (2007) Single nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas. Gene 406:13–22

    Article  PubMed  CAS  Google Scholar 

  • Sellars MJ, Dierens L, McWilliam S, Little B, Murphy B, Coman GJ, Barendse W, Henshall J (2014) Comparison of microsatellite and SNP DNA markers for pedigree assignment in Black Tiger shrimp, Penaeus monodon. Aquac Res 45:417–426

    Article  CAS  Google Scholar 

  • Slate J, Gratten J, Beraldi D, Stapley J, Hale M, Pemberton JM (2009) Gene mapping in the wild with SNPs: guidelines and future directions. Genetica 136:97–107

    Article  PubMed  CAS  Google Scholar 

  • Small MP, Chapman RW (1997) Intraspecific variation in the 16S ribosomal gene of Crassostrea virginica. Mol Mar Biol Biotechnol 6:189–196

    CAS  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vandeputte M, Haffray P (2014) Parentage assignment with genomic markers: a major advance for understanding and exploiting genetic variation of quantitative traits in farmed aquatic animals. Front Genet 5:432

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Varney RL, Galindo-Sanchez CE, Cruz P, Gaffney PM (2009) Population genetics of the eastern oyster Crassostrea virginica (Gmelin, 1791) in the Gulf of Mexico. J Shellfish Res 28:855–864

    Article  Google Scholar 

  • Wang L, Bai B, Huang S, Liu P, Wan ZY, Ye B, Wu J, Yue GH (2017) QTL mapping for resistance to iridovirus in Asian seabass using genotyping-by-sequencing. Mar Biotechnol 19:517–527

    Article  PubMed  CAS  Google Scholar 

  • Wang Y, Wang X, Wang A, Guo X (2010) A 16-microsatellite multiplex assay for parentage assignment in the eastern oyster (Crassostrea virginica Gmelin). Aquaculture 308:S28–S33

    Article  CAS  Google Scholar 

  • Xu L, Li Q, Yu H, Kong L (2017) Estimates of heritability for growth and shell color traits and their genetic correlations in the black shell strain of Pacific Oyster Crassostrea gigas. Mar Biotechnol 19:421–429

    Article  PubMed  CAS  Google Scholar 

  • Zhang L, Guo X (2010) Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing. Aquaculture 302:124–129

    Article  CAS  Google Scholar 

Download references

Acknowledgements

This research was carried out with a part of a grant from The Gulf of Mexico Research Initiative through the Alabama Center for Ecological Resilience Consortium administered by the Dauphin Island Sea Lab. The authors are grateful to Perry R. Bass Marine Fisheries Research Station, Texas Parks and Wildlife, especially Joel D. Anderson for supplying Texas oyster DNA samples. Wilawan Thongda personally thanks the Royal Thai Government for their support of her study at Auburn University.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Eric Peatman.

Electronic Supplementary Material

Table S1

(XLSX 24 kb)

Table S2-S5

(DOCX 96 kb)

Table S6

(XLSX 132 kb)

Table S7

(XLSX 18 kb)

Fig. S1

(DOCX 210 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Thongda, W., Zhao, H., Zhang, D. et al. Development of SNP Panels as a New Tool to Assess the Genetic Diversity, Population Structure, and Parentage Analysis of the Eastern Oyster (Crassostrea virginica). Mar Biotechnol 20, 385–395 (2018). https://doi.org/10.1007/s10126-018-9803-y

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10126-018-9803-y

Keywords

  • Crassostrea virginica
  • SNP panels
  • Microsatellites
  • Population genetics