A candidate gene approach identifies variants in SLC 45A2 that explain dilute phenotypes, pearl and sunshine, in compound heterozygote horses

Coloration in Equine: Overview of Candidate Genes Associated with Coat Color Phenotypes

Variation in coat color among equids has attracted significant interest in genetics and breeding research. The range of colors is primarily determined by the type, concentration, and distribution of melanin pigments, with the balance between eumelanin and pheomelanin influenced by numerous genetic factors. Advances in genomic and sequencing technologies have enabled the identification of several candidate genes that influence coat color, thereby clarifying the genetic basis of these diverse phenotypes. In this review, we concisely categorize coat coloration in horses and donkeys, focusing on the biosynthesis and types of melanin involved in pigmentation. Moreover, we highlight the regulatory roles of some key candidate genes, such as MC1R, TYR, MITF, ASIP, and KIT, in coat color variation. Moreover, the review explores how coat color relates to selective breeding and specific equine diseases, offering valuable insights for developing breeding strategies that enhance both the esthetic and health aspects of equine species.

Predicted genetic burden and frequency of phenotype-associated variants in the horse

Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.

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.

Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep

Wool color is controlled by a variety of genes. Although the gene regulation of some wool colors has been studied in relative depth, there may still be unknown genetic variants and control genes for some colors or different breeds of wool that need to be identified and recognized by whole genome resequencing. Therefore, we used whole genome resequencing data to compare and analyze sheep populations of different breeds by population differentiation index and nucleotide diversity ratios (Fst and θπ ratio) as well as extended haplotype purity between populations (XP-EHH) to reveal selection signals related to wool coloration in sheep. Screening in the non-white wool color group (G1 vs. G2) yielded 365 candidate genes, among which PDE4B, GMDS, GATA1, RCOR1, MAPK4, SLC36A1, and PPP3CA were associated with the formation of non-white wool; an enrichment analysis of the candidate genes yielded 21 significant GO terms and 49 significant KEGG pathways (p < 0.05), among which 17 GO terms and 21 KEGG pathways were associated with the formation of non-white wool. Screening in the white wool color group (G2 vs. G1) yielded 214 candidate genes, including ABCD4, VSX2, ITCH, NNT, POLA1, IGF1R, HOXA10, and DAO, which were associated with the formation of white wool; an enrichment analysis of the candidate genes revealed 9 significant GO-enriched pathways and 19 significant KEGG pathways (p < 0.05), including 5 GO terms and 12 KEGG pathways associated with the formation of white wool. In addition to furthering our understanding of wool color genetics, this research is important for breeding purposes.

Analysis of the genetic loci of pigment pattern evolution in vertebrates

Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.

Breed Distribution and Allele Frequencies of Base Coat Color, Dilution, and White Patterning Variants across 28 Horse Breeds

Since domestication, horses have been selectively bred for various coat colors and white spotting patterns. To investigate breed distribution, allele frequencies, and potential lethal variants for recommendations on genetic testing, 29 variants within 14 genes were investigated in 11,281 horses from 28 breeds. The recessive chestnut ea allele in melanocortin 1 receptor (MC1R) (p.D84N) was identified in four breeds: Knabstrupper, Paint Horse, Percheron, and Quarter Horse. After filtering for relatedness, ea allele frequency in Knabstruppers was estimated at 0.035, thus illustrating the importance of testing for mate selection for base coat color. The Rocky Mountain Horse breed had the highest allele frequency for two of the dilution variants under investigation (Za.f. = 0.32 and Cha.f. = 0.026); marker-assisted selection in this breed could aid in the production of horses with desirable dilute coats with less severe ocular anomalies caused by the silver (Z) allele. With regard to white patterning, nine horses homozygous for the paired box 3 (PAX3) splashed white 2 (SW2) allele (p.C70Y) and six horses homozygous for the KIT proto-oncogene, receptor tyrosine kinase (KIT) sabino 1 (SB1) allele (ECA3g.79544206A>T) were identified, thus determining they are rare and confirming that homozygosity for SW2 is not embryonic lethal. The KIT dominant white 20 (W20) allele (p.R682H) was identified in all but three breeds: Arabian (n = 151), Icelandic Horse (n = 66), and Norwegian Fjord Horse (n = 90). The role of W20 in pigmentation across breeds is not well understood; given the different selection regimes of the breeds investigated, these data provide justification for further evaluating the functional role of this allele in pigmentation. Here, we present the largest dataset reported for coat color variants in horses to date, and these data highlight the importance of breed-specific studies to inform on the proper use of marker-assisted selection and to develop hypotheses related to pigmentation for further testing in horses.

One Hundred Years of Coat Colour Influences on Genetic Diversity in the Process of Development of a Composite Horse Breed

Genetic diversity and demographic parameters were computed to evaluate the historic effects of coat colour segregation in the process of configuration of the Hispano-Arabian horse (Há). Pedigree records from 207,100 individuals born between 1884 and 2019 were used. Although coat colour is not a determinant for the admission of Hispano-Arabian individuals as apt for breeding, it may provide a representative visual insight into the gene contribution of Spanish Purebred horses (PRE), given many of the dilution genes described in Há are not present in the Arabian Purebred breed (PRá). The lack of consideration of coat colour inheritance patterns by the entities in charge of individual registration and the dodging behaviour of breeders towards the historic banning policies, may have acted as a buffer for diversity loss (lower than 8%). Inbreeding levels ranged from 1.81% in smokey cream horses to 8.80 for white horses. Contextually, crossbred breeding may increase the likelihood for double dilute combinations to occur as denoted by the increased number of Há horses displaying Pearl coats (53 Há against 3 PRE and 0 PRá). Bans against certain coat colours and patterns may have prevented an appropriate registration of genealogical information from the 4th generation onwards for decades. This may have brought about the elongation of generation intervals. Breeder tastes may have returned to the formerly officially-recognised coat colours (Grey and Bay) and Chestnut/Sorrel. However, coat colour conditioning effects must be evaluated timely for relatively short specific periods, as these may describe cyclic patterns already described in owners’ and breeders’ tastes over the centuries.

Genetic Testing in the Horse

Genetic testing in horses began in the 1960s, when parentage testing using blood group markers became the standard. In the 1990s, parentage testing shifted from evaluating blood groups to DNA testing. The development of genetics and genomics in both human and veterinarian medicine, along with continued technological advances in the last 2 decades, has helped unravel the causal variants for many horse traits. Genetic testing is also now possible for a variety of phenotypic and disease traits and is used to assist in breeding and clinical management decisions. This article describes the genetic tests that are currently available for horses.

Genome-wide association studies for iris pigmentation and heterochromia patterns in Large White pigs

Eye colour genetics have been extensively studied in humans since the rediscovery of Mendel's laws. This trait was first interpreted using simplistic genetic models but soon it was realised that it is more complex. In this study, we analysed eye colour variability in a Large White pig population (n = 897) and report the results of GWASs based on several comparisons including pigs having four main eye colour categories (three with both pigmented eyes of different brown grades: pale, 17.9%; medium, 14.8%; and dark, 54.3%; another one with both eyes completely depigmented, 3.8%) and heterochromia patterns (heterochromia iridis - depigmented iris sectors in pigmented irises, 3.2%; heterochromia iridum - one whole eye iris of depigmented phenotype and the other eye with the iris completely pigmented, 5.9%). Pigs were genotyped with the Illumina PorcineSNP60 BeadChip and GEMMA was used for the association analyses. The results indicated that SLC45A2 (on chromosome 16, SSC16), EDNRB (SSC11) and KITLG (SSC5) affect the different grades of brown pigmentation of the eyes, the bilateral eye depigmentation defect and the heterochromia iridis defect recorded in this white pig population respectively. These genes are involved in several mechanisms affecting pigmentation. Significant associations for the eye depigmented patterns were also identified for SNPs on two SSC4 regions (including two candidate genes: NOTCH2 and PREX2) and on SSC6, SSC8 and SSC14 (including COL17A1 as candidate gene). This study provided useful information to understand eye pigmentation mechanisms, further valuing the pig as animal model to study complex phenotypes in humans.

Frameshift Variant in MFSD12 Explains the Mushroom Coat Color Dilution in Shetland Ponies

Mushroom is a unique coat color phenotype in Shetland Ponies characterized by the dilution of the chestnut coat color to a sepia tone and is hypothesized to be a recessive trait. A genome wide association study (GWAS), utilizing the Affymetrix 670K array (MNEc670k) and a single locus mixed linear model analysis (EMMAX), identified a locus on ECA7 for further investigation (P_corrected = 2.08 × 10⁻¹⁰). This locus contained a 3 Mb run of homozygosity in the 12 mushroom ponies tested. Analysis of high throughput Illumina sequencing data from one mushroom Shetland pony compared to 87 genomes from horses of various breeds, uncovered a frameshift variant, p.Asp201fs, in the MFSD12 gene encoding the major facilitator superfamily domain containing 12 protein. This variant was perfectly concordant with phenotype in 96 Shetland Ponies (P = 1.15 × 10⁻²²), was identified in the closely related Miniature Horse for which the mushroom phenotype is suspected to occur (f_mu = 0.02), and was absent in 252 individuals from seven additional breeds not reported to have the mushroom phenotype. MFSD12 is highly expressed in melanocytes and variants in this gene in humans, mice, and dogs impact pigmentation. Given the role of MFSD12 in melanogenesis, we propose that p.Asp201fs is causal for the dilution observed in mushroom ponies.