Two Variants in SLC24A5 Are Associated with "Tiger-Eye" Iris Pigmentation in Puerto Rican Paso Fino Horses

Skin colour: A window into human phenotypic evolution and environmental adaptation

As modern humans ventured out of Africa and dispersed around the world, they faced novel environmental challenges that led to geographic adaptations including skin colour. Over the long history of human evolution, skin colour has changed dramatically, showing tremendous diversity across different geographical regions, for example, the majority of individuals from the expansive lands of Africa have darker skin, whereas the majority of people from Eurasia exhibit lighter skin. What adaptations did lighter skin confer upon modern humans as they migrated from Africa to Eurasia? What genetic mechanisms underlie the diversity of skin colour observed in different populations? In recent years, scientists have gradually gained a deeper understanding of the interactions between pigmentation gene and skin colour through population-based genomic studies of different groups around the world, particularly in East Asia and Africa. In this review, we summarize our current understanding of 26 skin colour-related pigmentation genes and 48 SNPs that influence skin colour. Important pigmentation genes across three major populations are described in detail: MFSD12, SLC24A5, PDPK1 and DDB1/CYB561A3/TMEM138 influence skin colour in African populations; OCA2, KITLG, SLC24A2, GNPAT and PAH are key to the evolution of skin pigmentation in East Asian populations; and SLC24A5, SLC45A2, TYR, TYRP1, ASIP, MC1R and IRF4 significantly contribute to the lightening of skin colour in European populations. We summarized recent findings in genomic studies of skin colour in populations that implicate diverse geographic environments, local adaptation among populations, gene flow and multi-gene interactions as factors influencing skin colour diversity.

Identification of Differentially Expressed Genes and microRNAs in the Gray and White Feather Follicles of Shitou Geese

The Shitou goose, a highly recognized indigenous breed with gray plumage originating from Chaozhou Raoping in Guangdong Province, China, is renowned for being the largest goose species in the country. Notably, during the pure breeding process of Shitou geese, approximately 2% of the offspring in each generation unexpectedly exhibited white plumage. To better understand the mechanisms underlying white plumage color formation in Shitou geese, we conducted a comparative transcriptome analysis between white and gray feather follicles, aiming to identify key genes and microRNAs that potentially regulate white plumage coloration in this unique goose breed. Our results revealed a number of pigmentation genes, encompassing TYR, TYRP1, EDNRB2, MLANA, SOX10, SLC45A2, GPR143, TRPM1, OCA2, ASIP, KIT, and SLC24A5, which were significantly down-regulated in the white feather follicles of Shitou geese. Among these genes, EDNRB2 and KIT emerged as the most promising candidate genes for white plumage coloration in Shitou geese. Additionally, our analysis also uncovered 46 differentially expressed miRNAs. Of these, miR-144-y may play crucial roles in the regulation of feather pigmentation. Furthermore, the expression of novel-m0086-5p, miR-489-y, miR-223-x, miR-7565-z, and miR-3535-z exhibits a significant negative correlation with the expression of pigmentation genes including TYRP1, EDNRB2, MLANA, SOX10, TRPM1, and KIT, suggesting these miRNAs may indirectly regulate the expression of these genes, thereby influencing feather color. Our findings provide valuable insights into the genetic mechanisms underlying white plumage coloration in Shitou geese and contribute to the broader understanding of avian genetics and coloration research.

A de novo 2.3 kb structural variant in MITF explains a novel splashed white phenotype in a Thoroughbred family

Splashed white in horses is characterized by extensive white patterning on the legs, face and abdomen and may be accompanied by deafness. To date, seven variants in microphthalmia-associated transcription factor (MITF) and two variants in Paired Box 3 (PAX3) have been identified to explain this phenotype. A splashed white Thoroughbred stallion, whose sire and dam were not patterned, was hypothesized to have a de novo variant leading to his white coat pattern. A whole-genome sequencing candidate gene approach identified two single nucleotide variants (SNVs) in SOX10, four SNVs in MITF and a 2.3 kb deletion in MITF with the alternative allele present in this stallion but absent in the other 18 horses analyzed. All six SNVs were annotated as modifiers and were not further considered. The deletion in MITF (NC_009159.3:g.21555811_21558139delinsAAAT) encompasses exon 9 encoding a part of the helix-loop-helix domain required for DNA binding. Sanger sequencing and parentage testing confirmed that this deletion was a de novo mutation of maternal origin. Consistent with the published nomenclature, we denote this likely causal variant as SW8. Genotyping three of this stallion's offspring identified SW8 only in the nearly all-white foal that was confirmed deaf by brainstem auditory evoked response testing. This foal was also a compound heterozygote for dominant white variants (W20/W22), but to date, W variants alone have not been connected to deafness. SW8 marks the fourth de novo MITF variant in horses reported to cause white patterning. The link between deafness and all MITF variants with and without other variants impacting melanocyte development and function needs to be further explored.

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.

A community-science approach identifies genetic variants associated with three color morphs in ball pythons (Python regius)

Color morphs in ball pythons (Python regius) provide a unique and largely untapped resource for understanding the genetics of coloration in reptiles. Here we use a community-science approach to investigate the genetics of three color morphs affecting production of the pigment melanin. These morphs-Albino, Lavender Albino, and Ultramel-show a loss of melanin in the skin and eyes, ranging from severe (Albino) to moderate (Lavender Albino) to mild (Ultramel). To identify genetic variants causing each morph, we recruited shed skins of pet ball pythons via social media, extracted DNA from the skins, and searched for putative loss-of-function variants in homologs of genes controlling melanin production in other vertebrates. We report that the Albino morph is associated with missense and non-coding variants in the gene TYR. The Lavender Albino morph is associated with a deletion in the gene OCA2. The Ultramel morph is associated with a missense variant and a putative deletion in the gene TYRP1. Our study is one of the first to identify genetic variants associated with color morphs in ball pythons and shows that pet samples recruited from the community can provide a resource for genetic studies in this species.

Population structure and genomic footprints of selection in five major Iranian horse breeds

The genetic structure and characteristics of Iranian native breeds are yet to be comprehensibly investigated and studied. Therefore, we employed genomic information of 364 Iranian native horses representing the Asil (n = 109), Caspian (n = 40), Dareshuri (n = 44), Kurdish (n = 95), and Turkoman (n = 76) breeds to reveal the genetic structure and characteristics. For these and 19 other horse breeds, principal component analysis, Bayesian model-based, Neighbor-Net, and bootstrap-based TreeMix approaches were applied to investigate and compare their genetic structure. Additionally, three haplotype-based methods including haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length were applied to trace genomic footprints of selection of Asil, Caspian, Dareshuri, Kurdish, and Turkoman groups. Then, the Mahalanobis distance based on the negative-log₁₀ rank-based P-values was estimated based on the haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length values. Asil, Caspian, Dareshuri, Kurdish, and Turkoman can be categorized into five different genetic clusters. Based on the top 1% of Mahalanobis distance based on the negative-log₁₀ rank-based P-values of SNPs, we identified 24 SNPs formerly reported to be associated with different traits and >100 genes undergoing selection pressures in Asil, Caspian, Dareshuri, Kurdish, and Turkoman. The detected QTL undergoing selection pressures were associated with withers height, equine metabolic syndrome, overall body size, insect bite hypersensitivity, guttural pouch tympany, white markings, Rhodococcus equi infection, jumping test score, alternate gaits, and body weight traits. Our findings will aid to have a better perspective of the genetic characteristics and population structure of Asil, Caspian, Dareshuri, Kurdish, and Turkoman horses as Iranian native horse breeds.

Genetic diversity and selection in Puerto Rican horses

Since the first Spanish settlers brought horses to America centuries ago, several local varieties and breeds have been established in the New World. These were generally a consequence of the admixture of the different breeds arriving from Europe. In some instances, local horses have been selectively bred for specific traits, such as appearance, endurance, strength, and gait. We looked at the genetics of two breeds, the Puerto Rican Non-Purebred (PRNPB) (also known as the "Criollo") horses and the Puerto Rican Paso Fino (PRPF), from the Caribbean Island of Puerto Rico. While it is reasonable to assume that there was a historic connection between the two, the genetic link between them has never been established. In our study, we started by looking at the genetic ancestry and diversity of current Puerto Rican horse populations using a 668 bp fragment of the mitochondrial DNA D-loop (HVR1) in 200 horses from 27 locations on the island. We then genotyped all 200 horses in our sample for the "gait-keeper" DMRT3 mutant allele previously associated with the paso gait especially cherished in this island breed. We also genotyped a subset of 24 samples with the Illumina Neogen Equine Community genome-wide array (65,000 SNPs). This data was further combined with the publicly available PRPF genomes from other studies. Our analysis show an undeniable genetic connection between the two varieties in Puerto Rico, consistent with the hypothesis that PRNPB horses represent the descendants of the original genetic pool, a mix of horses imported from the Iberian Peninsula and elsewhere in Europe. Some of the original founders of PRNRB population must have carried the "gait-keeper" DMRT3 allele upon arrival to the island. From this admixture, the desired traits were selected by the local people over the span of centuries. We propose that the frequency of the mutant "gait-keeper" allele originally increased in the local horses due to the selection for the smooth ride and other characters, long before the PRPF breed was established. To support this hypothesis, we demonstrate that PRNPB horses, and not the purebred PRPF, carry a signature of selection in the genomic region containing the DMRT3 locus to this day. The lack of the detectable signature of selection associated with the DMRT3 in the PRPF would be expected if this native breed was originally derived from the genetic pool of PRNPB horses established earlier and most of the founders already had the mutant allele. Consequently, selection specific to PRPF later focused on allels in other genes (including CHRM5, CYP2E1, MYH7, SRSF1, PAM, PRN and others) that have not been previously associated with the prized paso gait phenotype in Puerto Rico or anywhere else.

Identification of W13 in the American Miniature Horse and Shetland Pony Populations

Coat color is a trait of economic significance in horses. Variants in seven genes have been documented to cause white patterning in horses. Of the 34 variants that have been identified in KIT proto-oncogene, receptor tyrosine kinase (KIT), 27 have only been reported in a single individual or family and thus not all are routinely offered for genetic testing. Therefore, to enable proper use of marker-assisted selection, determining breed specificity for these alleles is warranted. Screening 19 unregistered all-white Shetland ponies for 16 white patterning markers identified 14 individuals whose phenotype could not be explained by testing results. In evaluating other known dominant white variants, 14 horses were heterozygous for W13. W13 was previously only reported in two quarter horses and a family of Australian miniature horses. Genotyping known white spotting variants in 30 owner-reported white animals (25 Miniature Horses and five Shetland ponies) identified two additional W13/N American Miniature Horses. The estimated allele frequency of W13 in the American Miniature Horse was 0.0063 (79 N/N, 1 W13/N) and the allele was not detected in a random sample (n = 59) of Shetland ponies. No homozygous W13 individuals were identified and W13/N ponies had a similar all-white coat with pink skin phenotype, regardless of the other white spotting variants present, demonstrating that W13 results in a Mendelian inherited dominant white phenotype and homozygosity is likely lethal. These findings document the presence of W13 in the American Miniature Horse and Shetland pony populations at a low frequency and illustrate the importance of testing for this variant in additional breeds.

Analysis of Genetic Diversity in the American Standardbred Horse Utilizing Short Tandem Repeats and Single Nucleotide Polymorphisms

American Standardbreds were developed as a harness racing horse breed. The United States Trotting Association closed the studbook in 1973 and implemented a book size cap in 2009. This study aimed to investigate genetic diversity in the American Standardbred after the studbook cap was introduced using short tandem repeats (STRs) and single-nucleotide polymorphisms (SNPs). Sixteen STRs from horses foaled from 2010 to 2015 and their sires and dams (n = 50 621) were utilized to examine allelic richness (A_r), expected heterozygosity (H_E), observed heterozygosity (H_O), unbiased heterozygosity (H_U), inbreeding coefficient (F_IS), and fixation index (F_ST). These analyses found that trotting and pacing sires were less genetically diverse than dams (H_EP_Bonferroni = 0.029 and 6.3 × 10⁻⁵, respectively) and their offspring (A_rP_Bonferroni = 0.034 and 6.9 × 10^-6, respectively), and pacing offspring were significantly less diverse than their dams (H_EP_Bonferroni = 2 × 10^-3). Inbreeding coefficients for trotters (F_IS = −0.014) and pacers (F_IS = −0.012) suggest that breeding practices have maintained diversity. Moderate levels of genetic differentiation (0.066 < F_ST < 0.11) were found between pacing and trotting groups. Additionally, 10 of the most prolific trotting sires and their male offspring (n = 84) were genotyped on the 670K Axiom Equine HD Array. H_O values higher than H_E (P < 0.001), low inbreeding coefficients (mean F = −0.064), and mean F_ROH = 21% indicate relatively high levels of diversity in this cohort, further supporting the STR data. However, in contrast, H_O values were higher for trotting sires (0.41) than their offspring (0.36). This observation warrants further monitoring of diversity over time. These data provide an updated foundation of diversity indices for further, long-term analysis in the breed.

Phylogenetic Analysis of Core Melanin Synthesis Genes Provides Novel Insights Into the Molecular Basis of Albinism in Fish

Melanin is the most prevalent pigment in animals. Its synthesis involves a series of functional genes. Particularly, teleosts have more copies of these genes related to the melanin synthesis than tetrapods. Despite the increasing number of available vertebrate genomes, a few systematically genomic studies were reported to identify and compare these core genes for the melanin synthesis. Here, we performed a comparative genomic analysis on several core genes, including tyrosinase genes (tyr, tyrp1, and tyrp2), premelanosome protein (pmel), microphthalmia-associated transcription factor (mitf), and solute carrier family 24 member 5 (slc24a5), based on 90 representative vertebrate genomes. Gene number and mutation identification suggest that loss-of-function mutations in these core genes may interact to generate an albinism phenotype. We found nonsense mutations in tyrp1a and pmelb of an albino golden-line barbel fish, in pmelb of an albino deep-sea snailfish (Pseudoliparis swirei), in slc24a5 of cave-restricted Mexican tetra (Astyanax mexicanus, cavefish population), and in mitf of a transparent icefish (Protosalanx hyalocranius). Convergent evolution may explain this phenomenon since nonsense mutations in these core genes for melanin synthesis have been identified across diverse albino fishes. These newly identified nonsense mutations and gene loss will provide molecular guidance for ornamental fish breeding, further enhancing our in-depth understanding of human skin coloration.

A De Novo MITF Deletion Explains a Novel Splashed White Phenotype in an American Paint Horse

Splashed white is a coat color pattern in horses characterized by extensive white patterning on the legs, belly, and face often accompanied by blue eyes and deafness. Three mutations in microphthalmia-associated transcription factor (MITF) and two mutations in Paired Box 3 (PAX3) have been identified that explain splashed white patterns (SW1-SW5). An American Paint Horse stallion with a splashed white phenotype and blue eyes, whose parents were not white patterned, was negative for the 5 known splashed white variants and other known white spotting alleles. This novel splashed white phenotype (SW6) was hypothesized to be caused by a de novo mutation in MITF or PAX3. Analysis of whole-genome sequencing using the EquCab3.0 reference genome for comparison identified an 8.7 kb deletion in MITF on ECA16 (NC_009159.3:g.21551060-21559770del). The deletion encompassed part of intron 7 through the 3' UTR of exon 9 of MITF, including the helix-loop-helix DNA-binding domain (ENSECAT00000006375.3). This variant is predicted to truncate protein and impair binding to DNA. Sanger sequencing confirmed the stallion was heterozygous for the MITF deletion. No single nucleotide polymorphisms (SNPs) or structural variants were identified in PAX3 or any of the other candidate genes that were unique to the stallion or predicted to affect protein function. Genotyping five of the stallion's splashed white offspring, including one all white foal, found that they were also heterozygous for the deletion. Given the role of MITF in producing white pattern phenotypes, and the predicted deleterious effect of this mutation, this 8.7 kb deletion is the likely causal variant for SW6.

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.

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.

Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era

The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.

Genome-Wide Homozygosity Patterns and Evidence for Selection in a Set of European and Near Eastern Horse Breeds

Intensive artificial and natural selection have shaped substantial variation among European horse breeds. Whereas most equine selection signature studies employ divergent genetic population structures in order to derive specific inter-breed targets of selection, we screened a total of 1476 horses originating from 12 breeds for the loss of genetic diversity by runs of homozygosity (ROH) utilizing a 670,000 single nucleotide polymorphism (SNP) genotyping array. Overlapping homozygous regions (ROH islands) indicating signatures of selection were identified by breed and similarities/dissimilarities between populations were evaluated. In the entire dataset, 180 ROH islands were identified, whilst 100 islands were breed specific, all other overlapped in 36 genomic regions with at least one ROH island of another breed. Furthermore, two ROH hot spots were determined at horse chromosome 3 (ECA3) and ECA11. Besides the confirmation of previously documented target genes involved in selection for coat color (MC1R, STX17, ASIP), body size (LCORL/NCAPG, ZFAT, LASP1, HMGA2), racing ability (PPARGC1A), behavioral traits (GRIN2B, NTM/OPCML) and gait patterns (DMRT3), several putative target genes related to embryonic morphogenesis (HOXB), energy metabolism (IGFBP-1, IGFBP-3), hair follicle morphogenesis (KRT25, KRT27, INTU) and autophagy (RALB) were highlighted. Furthermore, genes were pinpointed which might be involved in environmental adaptation of specific habitats (UVSSA, STXBP4, COX11, HLF, MMD).

Neurocristopathies: New insights 150 years after the neural crest discovery

The neural crest (NC) is a transient, multipotent and migratory cell population that generates an astonishingly diverse array of cell types during vertebrate development. These cells, which originate from the ectoderm in a region lateral to the neural plate in the neural fold, give rise to neurons, glia, melanocytes, chondrocytes, smooth muscle cells, odontoblasts and neuroendocrine cells, among others. Neurocristopathies (NCP) are a class of pathologies occurring in vertebrates, especially in humans that result from the abnormal specification, migration, differentiation or death of neural crest cells during embryonic development. Various pigment, skin, thyroid and hearing disorders, craniofacial and heart abnormalities, malfunctions of the digestive tract and tumors can also be considered as neurocristopathies. In this review we revisit the current classification and propose a new way to classify NCP based on the embryonic origin of the affected tissues, on recent findings regarding the molecular mechanisms that drive NC formation, and on the increased complexity of current molecular embryology techniques.

Genes related to the white face colour pattern in eight Russian cattle breeds

One of the major effects of domestication is change of animal coat colour to up to complete white colour of the whole body. It is possible that white colour of livestock animals had aesthetic significance for humans as well. The first step towards detection of genes and mutations controlling white colouring in animals is the genome-wide association studies. These studies, however, have not been done for the cattle breeds native to the Russian Federation. The aim of this study was therefore to identify genomic intervals and candidate genes that could be responsible for white face colouring in eight Russian cattle breeds. The data on genome-wide genotyping of 131,709 high-quality single nucleotide polymorphisms (SNPs) on 148 animas have been used in the program ­EMMAX. Association analysis has been performed using two related phenotypes: a) the white face with the rest of the body of any colour and b) white face with the rest of the body of different (non-white) colour. In the first case, the only statistically significant marker found was the SNP BovineHD0500019319 located on cattle chromosome (BTA) 5. The same SNP was the most significant within the cluster of three SNPs on BTA5: 68,803,879–69,365,854 associated also with the second phenotype. Five genes were found within this interval in the cattle genome, out of which the most likely functional candidate was SLC41A2, with the SNP BovineHD0500019319 found within its intronic sequence. SLC41A2 encodes a magnesium transporter protein. However, the function of this gene is not well established. Other members of this gene family are the key genes controlling differences in human skin and animal coat colour. Additional significant association signals with the second phenotype have been detected in BTA 1–4, 6–15, 18, 19, 24, 27, and 29. Overall, 37 genomic intervals have been detected associated with white face colouring in eight Russian native cattle breeds.