Development of SNP parentage assignment in the Portuguese oyster Crassostrea angulata

Abstract

In recent decades, developing countries with traditionally strong links with aquaculture have adopted genetic improvement programs for newly domesticated and captively bred aquaculture species. Accurate genealogical and pedigree information is an essential tool for efficient and successful genetic improvement programs and traditionally this type of information was obtained by separate rearing of families and physical tagging of the animals. More recently, molecular based pedigrees (e.g. using SNPs) is becoming a potential option, which also may permit the communal rearing of families at a stage earlier than usual, prior to physical tagging. Here we consider the utility of molecular based pedigrees in a multi-generation breeding and selection program for the Portuguese oyster (Crassostrea angulata) and assess parameters for parentage assignment. Using 18,849 SNP markers obtained from 489 sequenced oysters including parents and their progeny, our results indicated that approximately 400 SNPs with minor allele frequency ≥ 0.3 were capable of assigning offspring to their 33 parents (18 sires and 15 dams).