Aquaculture 2022

February 28 - March 4, 2022

San Diego, California

DEVELOPMENT AND EVALUATION OF HIGH-DENSITY SNP ARRAYS FOR THE EASTERN OYSTER Crassostrea virginica

Ximing Guo*, Jonathan Puritz, Dina Proestou, Zhenwei Wang, Standish Allen, Jr., Jessica Small, Klara Verbyla, Noah Chriss, Jaime Haggard, Kathryn Lundgren, Bassem Allam, Marta Gomez-Chiarri, Matthew Hare, Christopher Hollenbeck, Ming Liu, Katie Lotterhos, Louis Plough, Paul Rawson, Eric Saillant, Robin Varney, Gary Wikfors, and Ami Wilbur

 

Haskin Shellfish Research Laboratory

Department of Marine and Coastal Sciences

Rutgers University

Port Norris, NJ 08349

xguo@hsrl.rutgers.edu

 



 The Eastern oyster  Crassostrea virginica  is a major aquaculture species for the United States.  The sustainable development of  Eastern oyster aquaculture  depends on continued improvement of cultured stocks through advanced breeding technologies. The Eastern Oyster Breeding Consortium (EOBC) was formed to advance genetics and breeding of the E astern oyster. Members of  EOBC  have developed oyster strains with improved disease resistance through selective breeding and sequenced the Eastern oyster genome . T o  facilitate efficient genotyping needed for genome-based analyses and breeding , the consortium  developed two single-nucleotide polymorphism (SNP) arrays for  the Eastern oyster: one with 566K SNPs and the other with 66K SNPs. The 566K array was developed based on resequencing data from 293 o ysters from Atlantic and Gulf populations . It contains 566 ,262  SNPs including 47K from protein coding genes and 33 SNPs from the mitochondrial genome .  The 566K  array  was evaluated with 960 oysters yielding a sample passing rate of 87.89%, cluster calling rate of 98.89% and sample reproducibility of 99.24%. Of all SNPs on the array, 299,899 or 52.99 % were called at high  resolution and recommended for downstream applications . The 66K array was developed using the best-performing  65,893  SNPs from the 566K array. Evaluation of  the 66K  array with 384 oysters yielded a sample passing rate of 94.00%, cluster calling rate of 99.34% and concordance of  99.81%. Of all SNPs on the array, 60,673 or 92.08%  were  called at high resolution and recommended for downstream applications , a big improvement  in efficiency  over the 566K array. Both arrays contained 756 probes from 13  oyster and human pathogens for their detection in genotyped oysters . The  high-density 566K array is designed for  marker screening and high-resolution genome-wide associ ation studies (GWAS),  and  the 66K array  can  provide efficient and cost-effective genotyping needed for  routine 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  delineating genetic architecture of production traits,  enabling genomic selection,  increasing selection precision and l owering long-term  breeding costs .