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

Authors: SUTHERLAND, BEN - Thermo Fisher Scientific; Thompson, Neil; SURRY, LIAM - Vancouver Island University; GUJJULA, KRISHNA REDDY - Thermo Fisher Scientific; CARRASCO, CLAUDIO - Thermo Fisher Scientific; CHADARAM, SRINIVAS - Thermo Fisher Scientific; LUNDA, SPENCER - Oregon State University; LANGDON, CHRISTOPHER - Oregon State University; CHAN, AMY - University Of British Columbia; SUTTLE, CURTIS - University Of British Columbia; GREEN, TIMOTHY - Thermo Fisher Scientific

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/27/2024
Publication Date: 6/13/2024
Citation: Sutherland, B.J., Thompson, N., Surry, L.B., Gujjula, K., Carrasco, C.D., Chadaram, S., Lunda, S.L., Langdon, C.J., Chan, A.M., Suttle, C.A., Green, T.J. 2024. An amplicon panel for high-throughput and low-cost genotyping of Pacific oyster. G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkae125.
DOI: https://doi.org/10.1093/g3journal/jkae125

Interpretive Summary: Pacific oysters are cultured worldwide and the subject of multiple genetic selection programs. To date, the implementation of modern genomic selection methods has been impeded by a high cost of genotyping. This research project describes a novel genotyping panel, that may be used to lower the cost of genotyping Pacific oyster individuals, thereby increasing the potential for genomic selection methods to be implemented where appropriate. Additionally, the panel enables lower cost genetic parentage analysis and population genetic data production. Using samples from naturalized populations of Pacific oysters in North America, and their progenitor stocks, a set of markers was chosen to enable population identification via genetic stock identification analyses and genetic parentage analysis. The uses for this panel are numerous, including monitoring of genetic diversity in aquaculture stocks, verification of pedigree in breeding programs, and as a part of imputation based genomic selection workflows. Importantly, the panel developed here is malleable, with the ability to add or remove markers relatively easily compared to other genotyping technologies. This allows specific markers of interest (e.g. those used for Marker Assisted Selection) to be added as needed, and underperforming markers to be dropped from future iterations of the panel. The adaptable nature of this genetic marker panel is likely to facilitate adoption by user groups and make the panel a useful long-term tool for oyster breeders and geneticists.

Technical 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; and FST = 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, including amplitools, 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.