Skip to main content
ARS Home » Pacific West Area » Newport, Oregon » Pacific Shellfish Research Unit » Research » Publications at this Location » Publication #411265
Research Project: Improving the Sustainability and Productivity of Shellfish Culture in Pacific Estuaries

Location: Pacific Shellfish Research Unit

Title: Microhaplotpes boost power for relatedness analysis from SNP-based amplicon sequence panels in Pacific oyster

Author
item Thompson, Neil
item SUTHERLAND, BEN - Vancouver Island University
item GREEN, TIMOTHY - Vancouver Island University
item Delomas, Thomas

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract Only
Publication Acceptance Date: 11/13/2023
Publication Date: 1/13/2024
Citation: Thompson, N., Sutherland, B., Green, T., Delomas, T.A. 2024. Microhaplotpes boost power for relatedness analysis from SNP-based amplicon sequence panels in Pacific oyster. Plant and Animal Genome Conference.

Interpretive Summary: The development of modern sequencing based tools for Pacific oyster breeding has lagged other major aquaculuture species. Recently a panel of genetic markers (loci) was developed using Next-Generation sequencing methodology that reports one variant per locus (SNP). Newer methods that capture multiple variants within a locus (microhaplotypes) are becoming more widely used and can provide increased statistical power from the same original panel. In this project we evaluated three populations of Pacific oyster (Crassostrea gigas) on the existing SNP panel to assess the panels utility for the USDA ARS Pacific Oyster Genomic Selection project (breeding program). We also evaluated if using microhaplotype data instead of SNP data would be beneficial for the USDA breeding program. After processing the genetic data it was evident that microhaplotypes provide higher statistical power than the original SNP variants. Using microhaplotypes from this panel would provide robust relationship assignments which are vital for many scientific studies within the Pacific Oyster Genomic Selection Project. The current panel is reliable for relationship assignment and with some development could become a valuable tool to perform imputation based genomic selection for the USDA breeding program.

Technical Abstract: The development of modern sequencing based tools for Pacific oyster breeding has lagged other major aquaculuture species. Recently a panel of genetic markers (loci) was developed using Next-Generation sequencing methodology that reports one variant per locus (SNP). Newer methods that capture multiple variants within a locus (microhaplotypes) are becoming more widely used and can provide increased statistical power from the same original panel. In this project we evaluated three populations of Pacific oyster (Crassostrea gigas) on the existing SNP panel to assess the panels utility for the USDA ARS Pacific Oyster Genomic Selection project (breeding program). We also evaluated if using microhaplotype data instead of SNP data would be beneficial for the USDA breeding program. After processing the genetic data it was evident that microhaplotypes provide higher statistical power than the original SNP variants. Using microhaplotypes from this panel would provide robust relationship assignments which are vital for many scientific studies within the Pacific Oyster Genomic Selection Project. The current panel is reliable for relationship assignment and with some development could become a valuable tool to perform imputation based genomic selection for the USDA breeding program.