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

Autor: Guo X; Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA. xguo@rutgers.edu., Puritz JB; Department of Biological Sciences, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA., Wang Z; Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA., Proestou D; USDA ARS NCWMAC Shellfish Genetics Lab, 120 Flagg Rd., Kingston, RI, 02881, USA., Allen S Jr; Virginia Institute of Marine Science, 1375 Greate Rd., Gloucester Pt., VA, 23062, USA., Small J; Virginia Institute of Marine Science, 1375 Greate Rd., Gloucester Pt., VA, 23062, USA., Verbyla K; CSIRO, Canberra, ACT, 2601, Australia., Zhao H; Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA., Haggard J; Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA., Chriss N; Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA., Zeng D; Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA., Lundgren K; USDA ARS NCWMAC Shellfish Genetics Lab, 120 Flagg Rd., Kingston, RI, 02881, USA., Allam B; School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, 11794, USA., Bushek D; Haskin Shellfish Research Laboratory, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA., Gomez-Chiarri M; Department of Fisheries, Animal and Veterinary Science, University of Rhode Island, 120 Flagg Road, Kingston, RI, 02881, USA., Hare M; Department of Natural Resources and the Environment, Cornell University, Ithaca, NY, 14853, USA., Hollenbeck C; Texas A&M University - Corpus Christi, Texas A&M AgriLife Research, 6300 Ocean Drive Unit 5892, Corpus Christi, TX, 78412, USA., La Peyre J; School of Animal Sciences, Louisiana State University Agricultural Center, 201 Animal and Food Sciences Laboratory Building, Forestry Lane, Baton Rouge, LA, 70803, USA., Liu M; Patuxent Environmental and Aquatic Research Laboratory, Morgan State University, 10545 Mackall Road, Saint Leonard, MD, 20685, USA., Lotterhos KE; Northeastern Marine Science Center, 430 Nahant Rd, Nahant, MA, 01908, USA., Plough L; Horn Point Lab, University of Maryland, 5745 Lovers Lane, Cambridge, MD, 21613, USA., Rawson P; School of Marine Sciences, University of Maine, 5751 Murray Hall, , Orono, ME, 04469, USA., Rikard S; School of Fisheries Aquaculture and Aquatic Sciences, Auburn University Shellfish Laboratory, Auburn University, 150 Agassiz St., Dauphin Island, AL, 36528, USA., Saillant E; School of Ocean Science and Engineering, The University of Southern Mississippi, 103 McIlwain Drive, Ocean Springs, MS, 39564, USA., Varney R; Shellfish Research Hatchery, University of North Carolina Wilmington, 5600 Marvin K. Moss Ln., Wilmington, NC, 28409, USA., Wikfors G; Milford CT Laboratory, NOAA Fisheries, 212 Rogers Avenue, Milford, CT, 06460, USA., Wilbur A; Shellfish Research Hatchery, University of North Carolina Wilmington, 5600 Marvin K. Moss Ln., Wilmington, NC, 28409, USA.
Jazyk: angličtina
Zdroj: Marine biotechnology (New York, N.Y.) [Mar Biotechnol (NY)] 2023 Feb; Vol. 25 (1), pp. 174-191. Date of Electronic Publication: 2023 Jan 09.
DOI: 10.1007/s10126-022-10191-3
Abstrakt: 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.
(© 2023. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)
Databáze: MEDLINE
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