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, 10 (1), 466

Genomic Inbreeding Trends, Influential Sire Lines and Selection in the Global Thoroughbred Horse Population

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Genomic Inbreeding Trends, Influential Sire Lines and Selection in the Global Thoroughbred Horse Population

Beatrice A McGivney et al. Sci Rep.

Abstract

The Thoroughbred horse is a highly valued domestic animal population under strong selection for athletic phenotypes. Here we present a high resolution genomics-based analysis of inbreeding in the population that may form the basis for evidence-based discussion amid concerns in the breeding industry over the increasing use of small numbers of popular sire lines, which may accelerate a loss of genetic diversity. In the most comprehensive globally representative sample of Thoroughbreds to-date (n = 10,118), including prominent stallions (n = 305) from the major bloodstock regions of the world, we show using pan-genomic SNP genotypes that there has been a highly significant decline in global genetic diversity during the last five decades (FIS R2 = 0.942, P = 2.19 × 10-13; FROH R2 = 0.88, P = 1.81 × 10-10) that has likely been influenced by the use of popular sire lines. Estimates of effective population size in the global and regional populations indicate that there is some level of regional variation that may be exploited to improve global genetic diversity. Inbreeding is often a consequence of selection, which in managed animal populations tends to be driven by preferences for cultural, aesthetic or economically advantageous phenotypes. Using a composite selection signals approach, we show that centuries of selection for favourable athletic traits among Thoroughbreds acts on genes with functions in behaviour, musculoskeletal conformation and metabolism. As well as classical selective sweeps at core loci, polygenic adaptation for functional modalities in cardiovascular signalling, organismal growth and development, cellular stress and injury, metabolic pathways and neurotransmitters and other nervous system signalling has shaped the Thoroughbred athletic phenotype. Our results demonstrate that genomics-based approaches to identify genetic outcrosses will add valuable objectivity to augment traditional methods of stallion selection and that genomics-based methods will be beneficial to actively monitor the population to address the marked inbreeding trend.

Conflict of interest statement

This research was conducted with the financial support of Plusvital Ltd. (www.plusvital.com) and a grant to EWH from Science Foundation Ireland (www.sfi.ie) (SFI/11/PI/1166). EWH is Chief Science Officer for Plusvital Ltd. BAM, HH and LRC are employees of Plusvital Ltd. EWH and DEM are shareholders in Plusvital Ltd. LMK and DEM are consultants of Plusvital Ltd. Other than the authors, the funders played no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. Plusvital Ltd. has been engaged by the American Jockey Club (The Jockey Club) to provide expert advice and services, which may relate to data/results included in the manuscript.

Figures

Figure 1
Figure 1
Principal component analysis plot of the genetic relatedness matrix based on genotype data for prominent global Thoroughbred stallions (n = 305). Individuals are colour coded based on region of birth: Australia/New Zealand (ANZ), red; Europe (EUR), green; Japan (JAP), blue; North America (NAM), light green; South Africa (SAF), purple.
Figure 2
Figure 2
The regression of the mean annual FIS [top] and FROH [bottom] on year of birth for n = 10,118 Thoroughbred horses born between 1996 and 2017.

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