Genomic measures of inbreeding in the Norwegian–Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits

BACKGROUND: Since the 1950s, the Norwegian–Swedish Coldblooded trotter (NSCT) has been intensively selected for harness racing performance. As a result, the racing performance of the NSCT has improved remarkably; however, this improved racing performance has also been accompanied by a gradual increase in inbreeding level. Inbreeding in NSCT has historically been monitored by using traditional methods that are based on pedigree analysis, but with recent advancements in genomics, the NSCT industry has shown interest in adopting molecular approaches for the selection and maintenance of this breed. Consequently, the aims of the current study were to estimate genomic-based inbreeding coefficients, i.e. the proportion of runs of homozygosity (ROH), for a sample of NSCT individuals using high-density genotyping array data, and subsequently to compare the resulting rate of genomic-based F (F(ROH)) to that of pedigree-based F (F(PED)) coefficients within the breed. RESULTS: A total of 566 raced NSCT were available for analyses. Average F(ROH) ranged from 1.78 to 13.95%. Correlations between F(ROH) and F(PED) were significant (P < 0.001) and ranged from 0.27 to 0.56, with F(PED) and F(ROH) from 2000 to 2009 increasing by 1.48 and 3.15%, respectively. Comparisons of ROH between individuals yielded 1403 regions that were present in at least 95% of the sampled horses. The average percentage of a single chromosome covered in ROH ranged from 9.84 to 18.82% with chromosome 31 and 18 showing, respectively, the largest and smallest amount of homozygosity. CONCLUSIONS: Genomic inbreeding coefficients were higher than pedigree inbreeding coefficients with both methods showing a gradual increase in inbreeding level in the NSCT breed between 2000 and 2009. Opportunities exist for the NSCT industry to develop programs that provide breeders with easily interpretable feedback on regions of the genome that are suboptimal from the perspective of genetic merit or that are sensitive to inbreeding within the population. The use of molecular data to identify genomic regions that may contribute to inbreeding depression in the NSCT will likely prove to be a valuable tool for the preservation of its genetic diversity in the long term. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12711-019-0465-7) contains supplementary material, which is available to authorized users.