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ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Publications at this Location » Publication #389186

Research Project: Genetic Improvement of North American Atlantic Salmon and the Eastern Oyster for Aquaculture Production

Location: National Cold Water Marine Aquaculture Center

Title: DEVELOPMENT AND EVALUATION OF HIGH-DENSITY SNP ARRAYS FOR THE EASTERN OYSTER CRASSOSTREA VIRGINICA

Author
item GUO, XIMING - Rutgers University
item PURITZ, JON - University Of Rhode Island
item Proestou, Dina
item ALLEN, STAN - Virginia Institute Of Marine Science
item SMALL, JESSICA - Virginia Institute Of Marine Science
item Markey Lundgren, Kathryn
item GOMEZ-CHIARRI, MARTA - University Of Rhode Island
item LOTTERHOS, KATIE - Northeastern University
item HARE, MATT - Cornell University - New York
item PLOUGH, LOUIS - University Of Maryland
item WILBER, AMI - University Of North Carolina-Wilmington
item WIKFORS, GARY - National Oceanic & Atmospheric Administration (NOAA)

Submitted to: World Aquaculture Society Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 10/15/2021
Publication Date: N/A
Citation: N/A

Interpretive Summary: N/A

Technical Abstract: The Eastern Oyster Breeding Consortium (EOBC) was formed to advance genetics and breeding of the Eastern oyster. To facilitate efficient genotyping needed for genome-based analyses and breeding, we developed two single-nucleotide polymorphism (SNP) arrays: one with 566k SNPs and the other with 66k SNPs. The 566k array was developed based on resequencing data from 293 oysters from diverse populations. It consists of 566,262 SNPs with an average marker interval across 10 chromosomes of 1207 bp. The 566k array was evaluated with 960 oysters yielding a sample passing rate of 87.89%, SNP calling rate of 98.89% and sample reproducibility of 99.24%. 299,899 or 52.96% of SNPs were called at high resolution and recommended for genotyping. The 66k array was developed using the best-performing SNPs from the 566k array and consisted of 65,893 SNPs. Evaluation of 66k with 384 oysters yielded a sample passing rate of 94.00%, SNP calling rate of 99.34% and concordance rate of 99.81%. 60,673 or 92.08% were called at high resolution and recommended for genotyping, a big improvement over the 566k array. The 56k array provides efficient and cost-effective genotyping needed for GWAS and genomic selection. The development and implementation of these tools are expected to advance genomic research and accelerate genetic improvement of the Eastern oyster, by streamlining the breeding process, increasing selection precision, lowering long-term costs and enabling advanced breeding across the region.