Genetic relationships among founders of a silver carp (Hypophthalmichthys molitrix) genetic improvement program in Bangladesh

Abstract

Silver carp (Hypophthalmichthys molitrix) is an important aquaculture species in Bangladesh and globally. Multiple introductions have been made of this exotic species to Bangladesh since 1969. Accordingly, the genetic composition of the species in the country is complex and imperfectly understood. In 2015–16, WorldFish sourced silver carp individuals from 21 Bangladeshi hatcheries as ‘candidate founders’ of a family-based genetic improvement program. In total, 544 candidate founders were sampled, of which 220 from 17 hatcheries were ultimately spawned as the ‘actual founders’ of the WorldFish Silver Carp Genetic Improvement Program (WSCGIP) population. The extent of relatedness among candidate founders was unknown when they were sourced from hatcheries. Candidate founders were genotyped using the DArTseq platform – with a total of 15,102 single nucleotide polymorphisms (SNPs) and 13,504 silicoDArT markers obtained – and genetic affinities among hatcheries examined. Based on unsupervised k-means clustering and hatchery-identified origins, each hatchery was assigned to one of six genetic groups to enable the adoption of genetic group models in pedigree-based analyses. Within genetic groups, sibship was assigned using COLONY software, and a pedigree constructed and validated against genomic relationships generated from 2007 SNPs retained after quality control. The mean pedigree-derived additive genetic relationship between actual founders was small (0.0093), indicating that relationships between actual founders are unlikely to have a meaningful impact on future parent selection, mating decisions or rates of inbreeding.