Genome-Wide Association Studies Based on Equine Joint Angle Measurements Reveal New QTL Affecting the Conformation of 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.

Genomic association using principal components of morphometric traits in horses: identification of genes related to bone growth

The measurement of morphometric traits in horses is important for determining breed qualification and is one of the main selection criteria for the species. The development of an index (HPC) that consists of principal components weighted by additive genetic values allows to explore the most relevant relationships using a reduced number of variables that explain the greatest amount of variation in the data. Genome-wide association studies (GWAS) using HPC are a relatively new approach that permits to identify regions related to a set of traits. The aim of this study was to perform GWAS using HPC for 15 linear measurements as the explanatory variable in order to identify associated genomic regions and to elucidate the biological mechanisms linked to this index in Campolina horses. For GWAS, weighted single-step GBLUP was applied to HPC. The eight genomic windows that explained the highest proportion of additive genetic variance were identified. The sum of the additive variance explained by the eight windows was 95.89%. Genes involved in bone and cartilage development were identified (SPRY2, COL9A2, MIR30C, HEYL, BMP8B, LTBP1, FAM98A, and CRIM1). They represent potential positional candidates for the HPC of the linear measurements evaluated. The HPC is an efficient alternative to reduce the 15 usually measured traits in Campolina horses. Moreover, candidate genes inserted in region that explained high additive variance of the HPC were identified and might be fine-mapped for searching putative mutation/markers.

Genetic analysis of geometric morphometric 3D visuals of French jumping horses

BACKGROUND

For centuries, morphology has been the most commonly selected trait in horses. A 3D video recording enabled us to obtain the coordinates of 43 anatomical landmarks of 2089 jumping horses. Generalized Procrustes analysis provided centered and scaled coordinates that were independent of volume, i.e., centroid size. Genetic analysis of these coordinates (mixed model; 17,994 horses in the pedigree) allowed us to estimate a variance-covariance matrix. New phenotypes were then defined: the "summarized shapes". They were obtained by linear combinations of Procrustes coordinates with, as coefficients, the eigenvectors of the genetic variance-covariance matrix. These new phenotypes were used in genome-wide association analyses (GWAS) and multitrait genetic analysis that included judges' scores and competition results of the horses.

RESULTS

We defined ten shapes that represented 86% of the variance, with heritabilities ranging from 0.14 to 0.42. Only one of the shapes was found to be genetically correlated with competition success (rg = - 0.12, standard error = 0.07). Positive and negative genetic correlations between judges' scores and shapes were found. This means that the breeding objective defined by judges involves improvement of anatomical parts of the body that are negatively correlated with each other. Known single nucleotide polymorphisms (SNPs) on chromosomes 1 and 3 for height at withers were significant for centroid size but not for any of the shapes. As these SNPs were not associated with the shape that distinguished rectangular horses from square horses (with height at withers greater than body length), we hypothesize that these SNPs play a role in the overall development of horses, i.e. in height, width, and length but not in height at withers when standardized to unit centroid size. Several other SNPs were found significant for other shapes.

CONCLUSIONS

The main application of 3D morphometric analysis is the ability to define the estimated breeding value (EBV) of a sire based on the shape of its potential progeny, which is easier for breeders to visualize in a single synthetic image than a full description based on linear profiling. However, the acceptance of these new phenotypes by breeders and the complex nature of summarized shapes may be challenging. Due to the low genetic correlations of the summarized shapes with jumping performance, the methodology did not allow indirect performance selection criteria to be defined.

New genomic insights into the conformation of Lipizzan horses

Conformation traits are important selection criteria in equine breeding, as they describe the exterior aspects of the horse (height, joint angles, shape). However, the genetic architecture of conformation is not well understood, as data of these traits mainly consist of subjective evaluation scores. Here, we performed genome-wide association studies on two-dimensional shape data of Lipizzan horses. Based on this data, we identified significant quantitative trait loci (QTL) associated with cresty neck on equine chromosome (ECA)16 within the MAGI1 gene, and with type, hereby differentiating heavy from light horses on ECA5 within the POU2F1 gene. Both genes were previously described to affect growth, muscling and fatty deposits in sheep, cattle and pigs. Furthermore, we pin-pointed another suggestive QTL on ECA21, near the PTGER4 gene, associated with human ankylosing spondylitis, for shape differences in the back and pelvis (roach back vs sway back). Further differences in the shape of the back and abdomen were suggestively associated with the RYR1 gene, involved in core muscle weakness in humans. Therefore, we demonstrated that horse shape space data enhance the genomic investigations of horse conformation.

Estimates of Genetic Parameters for Shape Space Data in Franches-Montagnes Horses

Simple Summary

Equine breeding is often based on conformation traits, describing the proportions, shape and joint angles of a horse. These conformations traits are, however, mostly subjectively judged and not measured objectively, affecting the response of selection through lower heritabilities and precision. In this study, we measured joint angles, quantified the variation in shape of 608 Swiss Franches-Montagnes (FM) horses and estimated the heritability of these traits. We found that the poll angle had the highest heritability of all joint angles (h² = 0.37), and variation in shape describing the type (heavy–light) was also fairly heritable (h² = 0.36–0.37). Furthermore, the shape of the FM stallions has clearly evolved towards a lighter type from 1940 to 2018 without stabilisation in recent years, risking the loss of the light draught horse type. Phenotyping based on photographs allowed us to improve the accuracy of certain joint angle traits, and to monitor the conformational development of the FM breed.

Abstract

Conformation traits such as joint angles are important selection criteria in equine breeding, but mainly consist of subjective evaluation scores given by breeding judges, showing limited variation. The horse shape space model extracts shape data from 246 landmarks (LM) and objective joint angle measurements from triplets of LM on standardized horse photographs. The heritability was estimated for 10 joint angles (seven were measured twice with different LM placements), and relative warp components of the whole shape, in 608 Franches-Montagnes (FM) horses (480 stallions, 68 mares and 60 geldings born 1940–2018, 3–25 years old). The pedigree data comprised 6986 horses. Genetic variances and covariances were estimated by restricted maximum likelihood model (REML), including the fixed effects birth year, age (linear and quadratic), height at withers (linear and quadratic), as well as postural effects (head, neck, limb position and body alignment), together with a random additive genetic animal component and the residual effect. Estimated heritability varied from 0.08 (stifle joint) to 0.37 (poll). For the shape, the type was most heritable (0.36 to 0.37) and evolved from heavy to light over time. Image-based phenotyping can improve the selection of horses for conformation traits with moderate heritability (e.g., poll, shoulder and fetlock).

A Novel QTL and a Candidate Gene Are Associated with the Progressive Motility of Franches-Montagnes Stallion Spermatozoa after Thaw

The use of frozen-thawed semen is an important reproduction tool to preserve the biodiversity of small, native horse breeds such as the Franches-Montagnes (FM). However, not all stallions produce cryotolerant semen with a progressive motility after thaw ≥ 35%. To improve our understanding of the genetic background of male fertility traits in both fresh and frozen-thawed semen, we performed genome-wide association studies (GWAS) on gel-free volume, sperm cell concentration, total sperm count, and progressive motility in fresh and frozen-thawed semen from 109 FM stallions using 335,494 genome-wide single nucleotide polymorphisms (SNPs). We identified one significant (p < 1.69 × 10-7) quantitative trait locus (QTL) on ECA6 within the SCN8A gene for progressive motility after thaw, which was previously associated with progressive motility in boars. Homozygous stallions showed a substantial drop in progressive motility after thaw. This QTL could be used to identify cryointolerant stallions, avoiding the costly cryopreservation process. Further studies are needed to confirm whether this QTL is also present in other horse breeds.

A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses

BACKGROUND

The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soundness, gait ability, and performance of riding and racehorses. Conformation is commonly used to select horses for breeding and performance in multiple horse breeds, where the back and croup conformation plays a significant role. The conformation of back and croup plays an important role on riding ability in Icelandic horses. However, the genes behind this trait are still unknown. Therefore, the aim of this study was to identify genomic regions associated with conformation of back and croup in Icelandic horses and to investigate their effects on riding ability. One hundred seventy-seven assessed Icelandic horses were included in the study. A genome-wide association analysis was performed using the 670 K+ Axiom Equine Genotyping Array, and the effects of different haplotypes in the top associated region were estimated for riding ability and additional conformation traits assessed during breeding field tests.

RESULTS

A suggestive quantitative trait loci (QTL) for the score of back and croup was detected on Equus caballus (ECA) 22 (p-value = 2.67 × 10- 7). Haplotype analysis revealed two opposite haplotypes, which resulted in higher and lower scores of the back and croup, respectively (p-value < 0.001). Horses with the favorable haplotype were more inclined to have a well-balanced backline with an uphill conformation and had, on average, higher scores for the lateral gaits tölt (p-value = 0.02) and pace (p-value = 0.004). This genomic region harbors three genes: C20orf85, ANKRD60 and LOC100056167. ANKRD60 is associated with body height in humans. C20orf85 and ANKRD60 are potentially linked to adolescent idiopathic scoliosis in humans.

CONCLUSIONS

Our results show that the detected QTL for conformation of back and croup is of importance for quality of lateral gaits in Icelandic horses. These findings could result in a genetic test to aid in the selection of breeding horses, thus they are of major interest for horse breeders. The results may also offer a gateway to comparative functional genomics by potentially linking both motor laterality and back inclination in horses with scoliosis in humans.

Identification and Functional Annotation of Genes Related to Horses' Performance: From GWAS to Post-GWAS

Simple Summary

It is assumed that the athletic performance of horses is influenced by a large number of genes; however, to date, not many genomic studies have been performed to identify candidate genes. In this study we performed a systematic review of genome-wide association studies followed by functional analyses aiming to identify the most candidate genes for horse performance. We were successful in identifying 669 candidate genes, from which we built biological process networks. Regulatory elements (transcription factors, TFs) of these genes were identified and used to build a gene–TF network. Genes and TFs presented in this study are suggested to play a role in the studied traits through biological processes related with exercise performance, for example, positive regulation of glucose metabolism, regulation of vascular endothelial growth factor production, skeletal system development, cellular response to fatty acids and cellular response to lipids. In general, this study may provide insights into the genetic architecture underlying horse performance in different breeds around the world.

Abstract

Integration of genomic data with gene network analysis can be a relevant strategy for unraveling genetic mechanisms. It can be used to explore shared biological processes between genes, as well as highlighting transcription factors (TFs) related to phenotypes of interest. Unlike other species, gene–TF network analyses have not yet been well applied to horse traits. We aimed to (1) identify candidate genes associated with horse performance via systematic review, and (2) build biological processes and gene–TF networks from the identified genes aiming to highlight the most candidate genes for horse performance. Our systematic review considered peer-reviewed articles using 20 combinations of keywords. Nine articles were selected and placed into groups for functional analysis via gene networks. A total of 669 candidate genes were identified. From that, gene networks of biological processes from each group were constructed, highlighting processes associated with horse performance (e.g., regulation of systemic arterial blood pressure by vasopressin and regulation of actin polymerization and depolymerization). Transcription factors associated with candidate genes were also identified. Based on their biological processes and evidence from the literature, we identified the main TFs related to horse performance traits, which allowed us to construct a gene–TF network highlighting TFs and the most candidate genes for horse performance.

A Genome-Wide Association Analysis in Noriker Horses Identifies a SNP Associated With Roan Coat Color

The roan coat color in horses is characterized by dispersed white hair and dark points. This phenotype segregates in a broad range of horse breeds, while the underlying genetic background is still unknown. Previous studies mapped the roan locus to the KIT gene on equine chromosome 3 (ECA3). However, this association could not be validated across different horse breeds. Performing a genome-wide association analysis (GWAS) in Noriker horses, we identified a single nucleotide polymorphism (SNP) (ECA3:g.79,543.439 A > G) in the intron 17 of the KIT gene. The G -allele of the top associated SNP was present in other roan horses, namely Quarter Horse, Murgese, Slovenian, and Belgian draught horse, while it was absent in a panel of 15 breeds, including 657 non-roan horses. In further 379 gray Lipizzan horses, eight animals exhibited a heterozygous genotype (A/G). Comparative whole-genome sequence analysis of the KIT region revealed two deletions in the downstream region (ECA3:79,533,217_79,533,224delTCGTCTTC; ECA3:79,533,282_79,533,285delTTCT) and a 3 bp deletion combined with 17 bp insertion in intron 20 of KIT (ECA3:79,588,128_79,588,130delinsTTATCTCTATAGTAGTT). Within the Noriker sample, these loci were in complete linkage disequilibrium (LD) with the identified top SNP. Based upon pedigree information and historical records, we were able to trace back the genetic origin of roan coat color to a baroque gene pool. Furthermore, our data suggest allelic heterogeneity and the existence of additional roan alleles in ponies and breeds related to the English Thoroughbred. In order to study the roan phenotype segregating in those breeds, further association and verification studies are required.

Genomic inbreeding trends, influential sire lines and selection in the global Thoroughbred horse population

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.

Whole-Genome Signatures of Selection in Sport Horses Revealed Selection Footprints Related to Musculoskeletal System Development Processes

Selective breeding has led to gradual changes at the genome level of horses. Deciphering selective pressure patterns is progressive to understand how breeding strategies have shaped the sport horse genome; although, little is known about the genomic regions under selective pressures in sport horse breeds. The major goal of this study was to shed light on genomic regions and biological pathways under selective pressures in sport horses. In this study, whole-genome sequences of 16 modern sport and 35 non-sport horses were used to investigate the genomic selective signals of sport performance, by employing fixation index, nucleotide diversity, and Tajima's D approaches. A total number of 49 shared genes were identified using these approaches. The functional enrichment analysis for candidate genes revealed novel significant biological processes related to musculoskeletal system development, such as limb development and morphogenesis, having been targeted by selection in sport breeds.