217 Capturing genetic diversity – an assessment of the nation’s gene bank in securing Duroc pigs

Abstract

Abstract Benchmarking the completeness of gene bank collections (GBC) vs in-situ populations is an indicator of how well collections can represent a breed. To that end, we compared Durocs in the gene bank (69 animals) vs in-situ population (175 animals) using molecular markers. The in-situ pigs were from 10 states and 42 breeders (provided by National Swine Registry and USMARC) while the GBC pigs were from 14 states and 39 breeders. In-situ and GBC pigs were genotyped using the Illumina PorcineSNP60v1 and GGP-HD SNP arrays, respectively. Using both arrays, the SNP mapped to autosomal chromosomes were imputed using AlphaImpute software resulting in a combination of 71,515 SNP. Analyses were done using SNP & Variation Suite v8.8.1. After quality control deletions for call rate, sample rate, and monomorphic markers, 32,215 SNP remained and 4 in-situ animals were excluded. In-situ and GBC estimates of heterozygosity were similar (HO ~ 0.32 and HE ~ 0.32). The in-situ and GBC populations had 459 and 1,228 monomorphic markers, respectively, that were polymorphic in the other population. The in-situ pigs had more rare alleles, defined as an allele frequency < 0.01, than the GBC pigs (1,790 vs 1,154). Both populations had a similar number of highly polymorphic markers, defined as an allele frequency 0.3 to 0.5, with 12,703 for the in-situ and 12,603 for the GBC pigs. Wright’s FST between the two populations was 0.0065, suggesting no difference between the two populations. Principle components 1 and 2 explained 22 and 12% of the variation, respectively, with no distinction between the in-situ and GBC populations. Benchmarking the in-situ and GBC populations indicated 98.1% of sampled in-situ alleles were captured in the collection. This evaluation indicates that gene banks can capture a breed’s genetic diversity and have the germplasm available for utilization by industry and research communities.