The use of alternative genomic metrics in swine nucleus herds to manage the diversity of purebred and crossbred animals

Abstract Text: In livestock breeding populations regions of the genome with a high frequency of runs of homozygosity (ROH) have reduced diversity. Metrics that reduce ROH frequency may provide an attractive way to manage the diversity and ensure long-term gains while avoiding inbreeding accumulation. The two objectives of the current work were to characterize the frequency of ROH in Landrace (LR) Large White (LW) and their cross (LR x LW) through a combination of real and simulated genotypes and to determine the impact of optimizing different inbreeding metrics for nucleus and crossbred populations. A ROH statistic (ROH5Mb; ‘1’ if SNP was in ROH of 5 Mb, ‘0’ otherwise) was calculated across the genome for genotyped LR (n=1206) and LW (n=1349) dams and simulated crossbred genotypes derived from mating 81 LR sires to 100 LW dams. High ROH5Mb frequencies were declared for a contiguous set of SNP within the top 5%. In addition to random mating, pedigree, genomic or shared ROH based relationship matrices were utilized to minimize relationships between mating pairs within-breed and the latter two were in crossings. Mating plans with 25 sires available with a restriction on the maximum number of mating were devised for within-breed and across-breed mating populations of 625 and 1250 dams, respectively. Each plan was replicated 25 times. Regions of shared high ROH5Mb frequency were found on SS1, SS3 and SS14 and regions with a high ROH5Mb frequency within a breed were found to persist in the crossbreds. ROH and genomic-based relationship matrices decreased the proportion of the overall genome in a ROH by 2.45 and 2.19 fold when compared to pedigree-based relationships. Furthermore, the use of pedigree-based relationships was not able to decrease regions with high ROH5Mb frequency more heavily than ROH or G based relationships. The use of alternative genomic relatedness metrics such as ROH allow for relationships to be minimized for targeted regions of low diversity.

Keywords: Swine, Inbreeding, Mating Designs