The cream dilution gene, responsible for the palomino and buckskin coat colours, maps to horse chromosome 21

Genetics of swayback in American Saddlebred horses

Extreme lordosis, also called swayback, lowback or softback, can occur as a congenital trait or as a degenerative trait associated with ageing. In this study, the hereditary aspect of congenital swayback was investigated using whole genome association studies of 20 affected and 20 unaffected American Saddlebred (ASB) Horses for 48,165 single-nucleotide polymorphisms (SNPs). A statistically significant association was identified on ECA20 (corrected P=0.017) for SNP BIEC2-532523. Of the 20 affected horses, 17 were homozygous for this SNP when compared to seven homozygotes among the unaffected horses, suggesting a major gene with a recessive mode of inheritance. The result was confirmed by testing an additional 13 affected horses and 166 unaffected horses using 35 SNPs in this region of ECA20 (corrected P=0.036). Combined results for 33 affected horses and 287 non-affected horses allowed identification of a region of homozygosity defined by four SNPs in the region. Based on the haplotype defined by these SNPs, 80% of the 33 affected horses were homozygous, 21% heterozygous and 9% did not possess the haplotype. Among the non-affected horses, 15% were homozygous, 47% heterozygous and 38% did not possess the haplotype. The differences between the two groups were highly significant (P<0.00001). The region defined by this haplotype includes 53 known and predicted genes. Exons from three candidate genes, TRERF1, RUNX2 and CNPY3 were sequenced without finding distinguishing SNPs. The mutation responsible for swayback may lie in other genes or in regulatory regions outside exons. This information can be used by breeders to reduce the occurrence of swayback among their livestock. This condition may serve as a model for investigation of congenital skeletal deformities in other species.

Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses

Champagne coat color in horses is controlled by a single, autosomal-dominant gene (CH). The phenotype produced by this gene is valued by many horse breeders, but can be difficult to distinguish from the effect produced by the Cream coat color dilution gene (CR). Three sires and their families segregating for CH were tested by genome scanning with microsatellite markers. The CH gene was mapped within a 6 cM region on horse chromosome 14 (LOD = 11.74 for theta = 0.00). Four candidate genes were identified within the region, namely SPARC [Secreted protein, acidic, cysteine-rich (osteonectin)], SLC36A1 (Solute Carrier 36 family A1), SLC36A2 (Solute Carrier 36 family A2), and SLC36A3 (Solute Carrier 36 family A3). SLC36A3 was not expressed in skin tissue and therefore not considered further. The other three genes were sequenced in homozygotes for CH and homozygotes for the absence of the dilution allele (ch). SLC36A1 had a nucleotide substitution in exon 2 for horses with the champagne phenotype, which resulted in a transition from a threonine amino acid to an arginine amino acid (T63R). The association of the single nucleotide polymorphism (SNP) with the champagne dilution phenotype was complete, as determined by the presence of the nucleotide variant among all 85 horses with the champagne dilution phenotype and its absence among all 97 horses without the champagne phenotype. This is the first description of a phenotype associated with the SLC36A1 gene.

The horse genome derby: racing from map to whole genome sequence

The map of the horse genome has undergone unprecedented expansion during the past six years. Beginning from a modest collection of approximately 300 mapped markers scattered on the 31 pairs of autosomes and the X chromosome in 2001, today the horse genome is among the best-mapped in domestic animals. Presently, high-resolution linearly ordered gene maps are available for all autosomes as well as the X and the Y chromosome. The approximately 4350 mapped markers distributed over the approximately 2.68 Gbp long equine genome provide on average 1 marker every 620 kb. Among the most remarkable developments in equine genome analysis is the availability of the assembled sequence (EquCab2) of the female horse genome and the generation approximately 1.5 million single nucleotide polymorphisms (SNPs) from diverse breeds. This has triggered the creation of new tools and resources like the 60K SNP-chip and whole genome expression microarrays that hold promise to study the equine genome and transcriptome in ways not previously envisaged. As a result of these developments it is anticipated that, during coming years, the genetics underlying important monogenic traits will be analyzed with improved accuracy and speed. Of larger interest will be the prospects of dissecting the genetic component of various complex/multigenic traits that are of vital significance for equine health and welfare. The number of investigations recently initiated to study a multitude of such traits hold promise for improved diagnostics, prevention and therapeutic approaches for horses.

Homozygosity mapping approach identifies a missense mutation in equine cyclophilin B (PPIB) associated with HERDA in the American Quarter Horse

Hereditary equine regional dermal asthenia (HERDA), a degenerative skin disease that affects the Quarter Horse breed, was localized to ECA1 by homozygosity mapping. Comparative genomics allowed the development of equine gene-specific markers which were used with a set of affected horses to detect a homozygous, identical-by-descent block spanning approximately 2.5 Mb, suggesting a recent origin for the HERDA mutation. We report a mutation in cyclophilin B (PPIB) as a novel, causal candidate gene for HERDA. A c.115G>A missense mutation in PPIB alters a glycine residue that has been conserved across vertebrates. The mutation was homozygous in 64 affected horses and segregates concordant with inbreeding loops apparent in the genealogy of 11 affected horses. Screening of control Quarter Horses indicates a 3.5% carrier frequency. The development of a test that can detect affected horses prior to development of clinical signs and carriers of HERDA will allow Quarter Horse breeders to eliminate this debilitating disease.

The genetics of cream coat color in dogs

Cream dogs of several breeds require a genotype of e/e at MC1R based on 27 individuals in this study. All Akita, Caucasian Mountain Dogs, German Shepherd Dogs, Miniature Schnauzer, and Puli with this genotype are cream, suggesting they are fixed at a second locus which causes the phaeomelanin pigmentation caused by this genotype to be diluted or pale. Conversely, although all Chinese Shar-Pei and Poodles that were cream had an e/e genotype at MC1R, not all dogs with this genotype are cream. Today, many Golden Retrievers and Labrador Retrievers with an e/e genotype are cream instead of the traditional yellow to golden color seen in the past. The second gene in these breeds must have multiple alleles, only one of which causes phaeomelanin pigment to be diluted or pale. Tyrosinase (TYR) and solute carrier family 45, member 2 (SLC45A2) have been shown to cause cream coat color in other species and were therefore investigated in dogs as candidate genes for this second locus. Although polymorphisms were detected in cDNA sequence from TYR and SLC45A2, no polymorphism was consistently associated with cream dogs or cosegregated with cream coat color in any of the families used in this study. A microsatellite was detected in a published BAC sequence (GenBank no. AAEX01017083) in intron 2 and was used to map SLC45A2 to CFA4.

Whole-genome linkage disequilibrium screening for complex traits in horses

The identification of candidate genes for significant traits is crucial. In this study, we developed and tested effective and systematic methods based on linkage disequilibrium (LD) for the identification of candidate regions for genes with Mendelian inheritance and those associated with complex traits. Our approach entailed the combination of primary screening using pooled DNA samples based on DeltaTAC, secondary screening using an individual typing method and tertiary screening using a permutation test based on the differences in the haplotype frequency between two neighbouring microsatellites. This series of methods was evaluated using horse coat colour traits (chestnut/non-chestnut) as a simple Mendelian inheritance model. In addition, the methods were evaluated using a complex trait model constructed by mixing samples from chestnut and non-chestnut horses. Using both models, the methods could detect the expected regions for the horse coat colour trait. The results revealed that LD extends up to several centimorgans in horses, indicating that whole-genome LD screening in horses could be performed systematically and efficiently by combining the above-mentioned methods. Since genetic maps based on microsatellites have been constructed for many other species, the approaches present here could have wide applicability.

Equine genomics: galloping to new frontiers

Analysis of the horse genome is proceeding at a rapid pace. Within a short span of 6-7 years, approximately 1,500 markers have been mapped in horse, of which at least half are genes/ESTs. Health, performance and phenotypic characteristic are of major concern/interest to horse breeders and owners. Current efforts to analyze the equine genome are primarily aimed at developing critical resources (including an advanced gene map) that could readily be used in the near future to i) identify genes and mutations responsible for inherited equine diseases/disorders and to formulate approaches for accurate diagnostics, therapeutics and prevention, ii) discover genes associated with various other traits of significance, e.g. fertility, disease resistance, coat color and athletic performance etc., and iii) use functional genomic approaches to identify gene regulatory events involved in the manifestation of various diseases.

Assignment of the horse grey coat colour gene to ECA25 using whole genome scanning

The dominant grey coat colour gene of horses has been mapped using a whole genome scanning approach. Samples from a large half-sibling pedigree of Thoroughbred horses were utilized in order to map the grey coat colour locus, G. Multiplex groups of microsatellite markers were developed and used to efficiently screen the horse genome at a resolution of approximately 22 cM, based on an estimated map length for the horse genome of 2720 cM. The grey gene was assigned to chromosome 25 (ECA25), one of the smaller acrocentric horse chromosomes. Based on the current state of knowledge of conserved synteny and coat colour genetics in other mammalian species, there are no obvious candidate genes for the grey gene in the region.