A free lunch: Microhaplotype discovery in an existing amplicon panel improves parentage assignment for the highly polymorphic Pacific oyster

Authors: Thompson, Neil; SUTHERLAND, BEN - Vancouver Island University; GREEN, TIMOTHY - Vancouver Island University; Delomas, Thomas

Submitted to: G3: Genes, genomics, genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/12/2024
Publication Date: 12/19/2024
Citation: Thompson, N., Sutherland, B.J., Green, T.J., Delomas, T.A. 2024. A free lunch: Microhaplotype discovery in an existing amplicon panel improves parentage assignment for the highly polymorphic Pacific oyster. G3, Genes/Genomes/Genetics. https://doi.org/10.1093/g3journal/jkae280.
DOI: https://doi.org/10.1093/g3journal/jkae280

Interpretive Summary: Aquaculture programs are in need of high-throughput and inexpensive genotyping tools to facilitate genome-enabled selection strategies. Recently a panel of Single Nucleotide Polymorphisms (SNPs) was developed using Pacific oysters that utilizes a cost-effective genotyping-by-sequencing approach. In this study we utilized this new SNP panel to sequence animals from the Pacific Shellfish Research Unit’s Pacific Oyster Genomic Selection (POGS) project, a new breeding program on the United States Pacific Coast. We investigated how harvesting multi-SNP markers (microhaplotypes) from the existing panel data could increase relationship assignment power for the POGS population, and using publicly available data from a Vancouver Island University breeding program population. Microhaplotypes increased statistical power for relationship assignment in both the POGS and VIU populations, however a substantial number of markers indicated non-mendelian inheritance patterns, likely owing to null alleles (a polymorphism in the parent that prevents successful allele amplification). Overall, the discovery of microhaplotypes was highly successful with 89% of panel loci harboring such variation. Additional panel development could provide an inexpensive, high throughput genotyping tool to use in myriad applications, ranging from parentage analysis to imputation-based genomic selection.

Technical Abstract: Amplicon panels using genotyping-by-sequencing are now common, but have focused on characterizing SNP markers. We investigate how microhaplotype discovery within a recently developed Pacific oyster (Crassostrea (Magallana) gigas) amplicon panel could increase the statistical power for relationship assignment. Trios (offspring and two parents) from three populations in a newly established breeding program were genotyped on a 592 locus panel. After processing, 89% of retained amplicons contained microhaplotype variants. The increased allelic richness resulted in substantially improved power for relationship assignment with much lower estimated false positive rates. No substantive differences in assignment accuracy occurred between SNP and microhaplotype datasets, but using microhaplotypes increased the separation in log-likelihood values between true parents and highly-related potential parents (aunts and uncles). A high number of Mendelian incompatibilies among trios were observed, likely due to null alleles. Further development of a microhaplotype panel, including removing loci with high rates of null alleles, would enable high-throughput genotyping by reducing panel size and therefore cost for Pacific oyster research and breeding programs.