Genomics in the Horse Industry: Discovering New Questions at Every Turn

Genomic tools for early selection among Thoroughbreds and Polo Argentino horses for practicing polo

The Polo Argentino (PA) horse is a recognized breed, developed originally by mixing crossbred and Thoroughbred (TB) horses to play polo. Early PA selection is difficult due to unreliable performance estimations. This study investigated the usefulness of genomic markers previously linked to morphological and functional traits as a tool for the early selection of PA. To this, we genotyped 520 PA and 30 TB horses using the Equine GGPArray (Illumina, n = 71,778 SNPs). Analyses included a genetic characterization of six genetic markers associated with behavioral (DRD4), muscular development (MSTN), and body size (LCORL, HMGA6, ZFAT, and LASP1) genes. Genetic differences in the DRD4, MSTN, and LCORL SNP were found between the two breeds, in the last two FST index between breeds was 0.13 and 0.6, respectively (p < 0.01). In DRD4, G allele was the more prevalent in PA (0.56 vs 0.45 in TB, p < 0.05), but no differences were observed between the genotypes associated with phenotypes. In MSTN, heterozygous genotypes were the most common in PA (48 %), with a significant decrease in AA (Hardy-Weinberg p < 0.05), suggesting a negative selection against it in polo horses. In body size, HMGA2 was monomorphic in all horses, while ZFAT and LASP1 SNP showed higher variability. Interestingly, 99 % of PA showed a TT genotype in LCORL (only 66 % in TB), demonstrating selection for smaller horses. Our results suggest that empirical selection in PA has generated an incipient genomic differentiation in discrete traits which could be used as a marker-assisted selection tool for early selection of polo horses.

Congenital heart defects in Arabian horses and the prospects of genetic testing: A review

Congenital heart defects (CHDs) can have profound and potentially life-threatening consequences on horses' health and performance capability. While CHDs are rare in the general horse population, the Arabian breed is disproportionately overrepresented and thus is widely suspected to be genetically predisposed. This review discusses the most common CHDs in Arabian horses, including ventricular septal defect (VSD), tetralogy of Fallot (TOF), patent duct arteriosus (PDA), tricuspid valve atresia (TVA) and atrial septal defect (ASD). This review also explores how future research into the genetic factors that likely underpin many CHDs can revolutionise the way these disorders are managed in Arabian horses.

Geometric morphometrics of face profile across horse breeds and within Arabian horses

Horse traits under selection are largely quantitative and affected by multiple genes. Horse face shape is an example of a continuous trait, which due to the reliance on observational assessments, is classified into; "dished", "straight", and "roman-nosed". This categorization is often inadequate to convey the full spectrum of the face shape variation especially for genetic studies. The first objective of the current study was to use geometric morphometric methods to quantitatively phenotype face shapes and examine its variation across horse breeds. The second objective was to analyze the face shape variation within Arabian horses since face shape is (1) favored, valued, and genetically selected in certain lineages (e.g. Egyptian), (2) is evaluated by registries and scored in shows, and (3) in its extreme forms pose health concerns. We digitized landmarks on lateral profile photos, particularly on the dorsal curvature of the rostrum, and subjected these landmarks to Generalized Procrustes Analysis to generate independent shape and size variables which were statistically compared across breeds and within Arabians. Horse breeds varied in nasal curvature, ranging from extremely concave to extremely convex, with over 70 % of horse breeds exhibiting intermediate concavity (i.e., straight profile). Interestingly, Arabian horses possessed the highest diversity in face profile and individuals clustered into three distinct shape sub-groups (one dished and two straight profile clusters). Our quantitative phenotyping method can be the basis of future genetic studies of facial profile within Arabian lineages as a favored traits and potentially manage its extreme forms as a likely genetic disease.

Unlocking Horse Y Chromosome Diversity

The present equine genetic variation mirrors the deep influence of intensive breeding programs during the last 200 years. Here, we provide a comprehensive current state of knowledge on the trends and prospects on the variation in the equine male-specific region of the Y chromosome (MSY), which was assembled for the first time in 2018. In comparison with the other 12 mammalian species, horses are now the most represented, with 56 documented MSY genes. However, in contrast to the high variability in mitochondrial DNA observed in many horse breeds from different geographic areas, modern horse populations demonstrate extremely low genetic Y-chromosome diversity. The selective pressures employed by breeders using pedigree data (which are not always error-free) as a predictive tool represent the main cause of this lack of variation in the Y-chromosome. Nevertheless, the detailed phylogenies obtained by recent fine-scaled Y-chromosomal genotyping in many horse breeds worldwide have contributed to addressing the genealogical, forensic, and population questions leading to the reappraisal of the Y-chromosome as a powerful genetic marker to avoid the loss of biodiversity as a result of selective breeding practices, and to better understand the historical development of horse breeds.