Evidence map›Paper›PMID 36622459›Full record

ArticleMarine biotechnology (New York, N.Y.)2023

Development and Evaluation of High-Density SNP Arrays for the Eastern Oyster Crassostrea virginica.

Ximing Guo, Jonathan B Puritz, Zhenwei Wang, Dina Proestou, Standish Allen, Jessica Small, Klara Verbyla, Honggang Zhao, Jaime Haggard, Noah Chriss and 17 more

Open access · greenAbstract read
PubMed Publisher
In one paragraph

Article in Marine biotechnology (New York, N.Y.), 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed
5.8field-weighted citation impact, top 3% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

17 citing papers in PubMed, 36 citations in OpenAlex.

  1. Article
  2. Reefense: Living shoreline mosaics can achieve ecological and engineering outcomes with interdisciplinary design.Proceedings of the National Academy of Sciences of the United States of America · 2026
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  3. Genome-Wide Development and Validation of KASP-Based SNP Markers inAnimals : an open access journal from MDPI · 2026
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  4. Article
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  8. Genome of Kumamoto OysterEvolutionary applications · 2025
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

27 authors at 16 institutions in 3 countries.

Ximing GuoHaskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA. xguo@rutgers.edu.ORCID http://orcid.org/0000-0002-6758-2709
Jonathan B PuritzDepartment of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA.
Zhenwei WangHaskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
Dina ProestouUSDA ARS NCWMAC Shellfish Genetics Lab, 120 Flagg Rd., Kingston, RI, 02881, USA.
Standish AllenVirginia Institute of Marine Science, 1375 Greate Rd., Gloucester Pt., VA, 23062, USA.
Jessica SmallVirginia Institute of Marine Science, 1375 Greate Rd., Gloucester Pt., VA, 23062, USA.
Klara VerbylaCSIRO, Canberra, ACT, 2601, Australia.
Honggang ZhaoDepartment of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA.
Jaime HaggardHaskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
Noah ChrissHaskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
Dan ZengHaskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
Kathryn LundgrenUSDA ARS NCWMAC Shellfish Genetics Lab, 120 Flagg Rd., Kingston, RI, 02881, USA.
Bassem AllamSchool of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA.
David BushekHaskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA.
Marta Gomez-ChiarriDepartment of Fisheries, Animal and Veterinary Science, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA.
Matthew HareDepartment of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA.
Christopher HollenbeckTexas A&M University - Corpus Christi, Texas A&M AgriLife Research, 6300 Ocean Drive Unit 5892, Corpus Christi, TX, 78412, USA.
Jerome La PeyreSchool of Animal Sciences, Louisiana State University Agricultural Center, 201 Animal and Food Sciences Laboratory Building, Forestry Lane, Baton Rouge, LA, 70803, USA.
Ming LiuPatuxent Environmental and Aquatic Research Laboratory, Morgan State University, 10545 Mackall Road, Saint Leonard, MD, 20685, USA.
Katie E LotterhosNortheastern Marine Science Center, 430 Nahant Rd, Nahant, MA, 01908, USA.ORCID http://orcid.org/0000-0001-7529-2771
Louis PloughHorn Point Lab, University of Maryland, 5745 Lovers Lane, Cambridge, MD, 21613, USA.
Paul RawsonSchool of Marine Sciences, University of Maine, 5751 Murray Hall, , Orono, ME, 04469, USA.ORCID http://orcid.org/0000-0003-0875-1493
Scott RikardSchool of Fisheries Aquaculture and Aquatic Sciences, Auburn University Shellfish Laboratory, Auburn University, 150 Agassiz St., Dauphin Island, AL, 36528, USA.
Eric SaillantSchool of Ocean Science and Engineering, The University of Southern Mississippi, 103 McIlwain Drive, Ocean Springs, MS, 39564, USA.
Robin VarneyShellfish Research Hatchery, University of North Carolina Wilmington, 5600 Marvin K. Moss Ln., Wilmington, NC, 28409, USA.
Gary WikforsMilford CT Laboratory, NOAA Fisheries, 212 Rogers Avenue, Milford, CT, 06460, USA.
Ami WilburShellfish Research Hatchery, University of North Carolina Wilmington, 5600 Marvin K. Moss Ln., Wilmington, NC, 28409, USA.
Rutgers, The State University of New Jersey · USAgricultural Research Service · USCornell University · USUniversity of North Carolina Wilmington · USUniversity of Rhode Island · USAuburn University · USCommonwealth Scientific and Industrial Research Organisation · AULouisiana State University Agricultural Center · USMorgan State University · USNOAA National Marine Fisheries Service · USNOAA National Marine Fisheries Service Northeast Fisheries Science Center · USStony Brook University · USTexas A&M University – Corpus Christi · USUniversity of Maine · USUniversity of Maryland, College Park · USUniversity of Southern Mississippi · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The eastern oyster Crassostrea virginica is a major aquaculture species for the USA. The sustainable development of eastern oyster aquaculture depends upon the continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance the genetics and breeding of the eastern oyster. To facilitate efficient genotyping needed for genomic studies and selection, the consortium developed two single-nucleotide polymorphism (SNP) arrays for the eastern oyster: one screening array with 566K SNPs and one breeders' array with 66K SNPs. The 566K screening array was developed based on whole-genome resequencing data from 292 oysters from Atlantic and Gulf of Mexico populations; it contains 566,262 SNPs including 47K from protein-coding genes with a marker conversion rate of 48.34%. The 66K array was developed using best-performing SNPs from the screening array, which contained 65,893 oyster SNPs including 22,984 genic markers with a calling rate of 99.34%, a concordance rate of 99.81%, and a much-improved marker conversion rate of 92.04%. Null alleles attributable to large indels were found in 13.1% of the SNPs, suggesting that copy number variation is pervasive. Both arrays provided easy identification and separation of selected stocks from wild progenitor populations. The arrays contain 31 mitochondrial SNPs that allowed unambiguous identification of Gulf mitochondrial genotypes in some Atlantic populations. The arrays also contain 756 probes from 13 oyster and human pathogens for possible detection. Our results show that marker conversion rate is low in high polymorphism species and that the two-step process of array development can greatly improve array performance. The two arrays will advance genomic research and accelerate genetic improvement of the eastern oyster by delineating genetic architecture of production traits and enabling genomic selection. The arrays also may be used to monitor pedigree and inbreeding, identify selected stocks and their introgression into wild populations, and assess the success of oyster restoration.

Indexed as

CrassostreaAnimalsDNA Copy Number VariationsGenomeGenomicsGenotypePolymorphism, Single NucleotideCopy number variationGenome-wide association studyGenomic selectionOyster aquacultureSingle-nucleotide polymorphismSNP array

Identifiers

PMID36622459
OpenAlexW4313880060

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.