An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster

Abstract

Maintaining genetic diversity in cultured shellfish can be challenging due to high variance in individual reproductive output, founder effects, and rapid genetic drift. However, it is important to consider for retaining adaptive potential and avoiding inbreeding depression, particularly in species with high mutational load. To support management of genetic diversity and selective breeding efforts in cultured Pacific oyster (Crassostrea gigas; a.k.a.Magallana gigas), we developed an amplicon panel comprising 592 amplicons positioned throughout the genome with an average of 50 markers per chromosome. Markers were selected based on high heterozygosity or high differentiation in Pacific oyster populations from the eastern Pacific Ocean. The developed panel was tested in a pilot study on 371 unique individuals, including those from hatcheries and farms (n = 72) and from three generations of the Vancouver Island University (VIU) breeding program (n = 181), as well as from naturalized or wild populations in the Northern Hemisphere (n = 118). High repeatability was observed in technical replicate samples; on average, 97.5% of typed markers were concordant between samples (n = 68 replicate sample pairs). In the pilot dataset, following quality filters, 463 markers were retained for analysis (average observed heterozygosity = 0.29 ± 0.19; andFST= 0.040 ± 0.046). Principal components analysis showed separate clustering of the Japan translocation lineage, China, and a commercial aquaculture population. Parentage analysis of the VIU breeding program identified 84% and 66% of the possible parent-offspring assignments in two spawning events involving 98 and 40 offspring each, respectively. Results were strongest in individuals with the highest genotyping rates, highlighting the value of sample and target SNP quality. The analysis identified pedigree errors that were then corrected. All code required to analyze the data is provided, includingamplitools, a repository to move the panel target SNP output through parentage analysis. Collectively, these advances will enable rapid, consistent, and cost-effective genotyping of Pacific oyster.