A SNP parentage assignment panel for the silver lipped pearl oyster (Pinctada maxima)

The silver-lipped pearl oyster, Pinctada maxima, is an important aquaculture species extensively farmed in tropical Australia and Southeast Asia to produce South Sea pearls. The pearling industry in Australia is in the process of implementing breeding programs targeting improved disease resistance, growth and pearl quality, and as a result genetic tools that can be readily implemented into breeding programs have been developed. However, to date there is no routine single nucleotide polymorphism (SNP) pedigree reconstruction tool publicly available. In this study, we isolated and assessed a panel of 934 genome-wide DArTcapTM SNPs for their utility and discriminatory power in resolving pedigree relationships in P. maxima. The panel was assessed for its power to assign parentage through in silico simulations of 1,000 progeny in a mass-spawning scenario, based on genotypes of 100 broodstock (1:1 sex ratio) and allowing for random missing genotypes in individuals (0-40%). Assignment success was then assessed across various pedigree panel sizes (25-934 SNPs ranked from the highest minor allele frequency). Simulations showed that a SNP panel comprising 50 or more SNPs had high pedigree resolution and the power to correctly assign progeny to a parent-progeny trio with 95 % confidence. In the simulation exam-ining the effect of missing genotypes on assignment success, even where 40 % of alleles were missing in in-dividuals only 150 SNPs were required in the panel to accurately assign parentage. Progeny from a commercial hatchery mass spawn involving 184 candidate parents were also assigned to their parents using the SNP panel and identified 79 full-sib families and genetic contributions from 33 sires and 11 dams. A highly skewed rep-resentation of family distributions in the cohort was observed which highlights the challenge of using a mass-spawning approach to the capture and identification of genetic diversity in P. maxima breeding programs.

Automated summary

A genetic tool for resolving pedigree relationships in the silver-lipped pearl oyster, Pinctada maxima, has been developed and shown to accurately assign progeny to parents with a 95% confidence using a panel of 50 or more SNPs.