Development and evaluation of high-density SNP arrays for the eastern oyster Crassostrea virginica

Authors: GUO, XIMING - Rutgers University; PURITZ, JONATHAN - University Of Rhode Island; ZHENWEI, WANG - Rutgers University; Proestou, Dina; ALLEN, STANDISH - Virginia Institute Of Marine Science; SMALL, JESSICA - Virginia Institute Of Marine Science; VERBYLA, KLARA - Commonwealth Scientific And Industrial Research Organisation (CSIRO); ZHAO, HONGGANG - Cornell University; HAGGARD, JAIME - Rutgers University; CHRISS, NOAH - Rutgers University; ZENG, DAN - Rutgers University; Markey Lundgren, Kathryn; ALLAM, BASSEM - Stony Brook University; BUSHEK, DAVE - Rutgers University; GOMEZ-CHIARRI, MARTA - University Of Rhode Island; HARE, MATTHEW - Cornell University; HOLLENBECK, CHRISTOPER - Texas A&M University; LAPEYRE, JEROME - Louisiana State University; LIU, MING - Morgan State University; LOTTERHOS, KATIE - Northeastern University; PLOUGH, LOUIS - University Of Maryland; RAWSON, PAUL - University Of Maine; RIKARD, SCOTT - Auburn University; SALLIENT, ERIC - University Of Southern Mississippi; VARNEY, ROBIN - University Of North Carolina-Wilmington; WIKFORS, GARY - National Oceanic & Atmospheric Administration (NOAA); WILBUR, AMI - University Of North Carolina-Wilmington

Submitted to: Marine Biotechnology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/7/2022
Publication Date: 1/9/2023
Citation: Guo, X., Puritz, J., Zhenwei, W., Proestou, D.A., Allen, S., Small, J., Verbyla, K., Zhao, H., Haggard, J., Chriss, N., Zeng, D., Markey Lundgren, K.R., Allam, B., Bushek, D., Gomez-Chiarri, M., Hare, M., Hollenbeck, C., Lapeyre, J., Liu, M., Lotterhos, K., Plough, L., Rawson, P., Rikard, S., Sallient, E., Varney, R., Wikfors, G., Wilbur, A. 2023. Development and evaluation of high-density SNP arrays for the eastern oyster Crassostrea virginica. Marine Biotechnology. https://doi.org/10.1007/s10126-022-10191-3.
DOI: https://doi.org/10.1007/s10126-022-10191-3

Interpretive Summary: The eastern oyster aquaculture industry will benefit greatly from advanced selective breeding technologies. One such technology incorporates genotype information during the selection process. To facilitate cost-effective, efficient, genotyping of oysters for genomic selection, two single-nucleotide polymorphism (SNP) arrays were developed. The first array, containing 566K single nucleotide polymorphism (SNP) markers, was created from whole genome sequences of 292 oysters collected throughout the species US range. The purpose of this array was to capture representative variation for the species as a whole and address complications in genotyping assays that arise in species with highly polymorphic genomes. Less than 50% of the SNPs on the first array produced accurate, scoreable genotypes. A second, 66K 'breeder's' array was developed using best-performing SNPs from the 566K array, and the call rate (99.34%) and marker conversion rate (92.04%) were much improved. Both arrays provide easy identification and separation of selected stocks from wild progenitor populations. 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.

Technical Abstract: The eastern oyster Crassostrea virginica is a major aquaculture species for the United States. 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 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.