Close association between sequence polymorphism in the KIT gene and the roan coat color in horses

Population Analysis Identifies 15 Multi-Variant Dominant White Haplotypes in Horses

The influence of a horse's appearance on health, sentimental and monetary value has driven the desire to understand the etiology of coat color. White markings on the coat define inclusion for multiple horse breeds, but they may disqualify a horse from registration in other breeds. In domesticated horses (Equus caballus), 35 KIT alleles are associated with or cause depigmentation and white spotting. It is a common misconception among the general public that a horse can possess only two KIT variants. To correct this misconception, we used BEAGLE 5.4-phased NGS data to identify 15 haplotypes possessing two or more KIT variants previously associated with depigmentation phenotypes. We sourced photos for 161 horses comprising 12 compound genotypes with three or more KIT variants and employed a standardized method to grade depigmentation, yielding average white scores for each unique compound genotype. We found that 7 of the 12 multi-variant haplotypes resulted in significantly more depigmentation relative to the single-variant haplotypes (ANOVA). It is clear horses can possess more than two KIT variants, and future work aims to document phenotypic variations for each compound genotype.

Spotting the Pattern: A Review on White Coat Color in the Domestic Horse

Traits such as shape, size, and color often influence the economic and sentimental value of a horse. Around the world, horses are bred and prized for the colors and markings that make their unique coat patterns stand out from the crowd. The underlying genetic mechanisms determining the color of a horse's coat can vary greatly in their complexity. For example, only two genetic markers are used to determine a horse's base coat color, whereas over 50 genetic variations have been discovered to cause white patterning in horses. Some of these white-causing mutations are benign and beautiful, while others have a notable impact on horse health. Negative effects range from slightly more innocuous defects, like deafness, to more pernicious defects, such as the lethal developmental defect incurred when a horse inherits two copies of the Lethal White Overo allele. In this review, we explore, in detail, the etiology of white spotting and its overall effect on the domestic horse to Spot the Pattern of these beautiful (and sometimes dangerous) white mutations.

Genetic characterization of Macaca arctoides: A highlight of key genes and pathways

When compared to the approximately 22 other macaque species, Macaca arctoides has many unique phenotypes. These traits fall into various phenotypic categories, including genitalia, coloration, mating, and olfactory traits. Here we used a previously identified whole genome set of 690 outlier genes to look for possible genetic explanations of these unique traits. Of these, 279 genes were annotated miRNAs, which are non-coding. Patterns within the remaining outliers in coding genes were investigated using GO (n = 370) and String (n = 383) analysis, which showed many interconnected immune-related genes. Further, we compared the outliers to candidate pathways associated with M. arcotides' unique phenotypes, revealing 10/690 outlier genes that overlapped these four pathways: hedgehog signaling, WNT signaling, olfactory, and melanogenesis. Of these, genes in all pathways except olfactory had higher F_ST values than the rest of the genes in the genome based on permutation tests. Overall, our results point to many genes each having a small impact on phenotype, working in tandem to cause large systemic changes. Additionally, these results may indicate pleiotropy. This seems to be especially true with the development and coloration of M. arctoides. Our results highlight that development, melanogenesis, immune function, and miRNAs may be heavily involved in M. arctoides' evolutionary history.

Basal Reactivity Evaluated by Infrared Thermography in the "Caballo de Deporte Español" Horse Breed According to Its Coat Color

Horses have been valued for their diversity of coat color since prehistoric times. In particular, the pleiotropic effect that coat color genes have on behavior determines the way the horse perceives and reacts to its environment. The primary aim of this study was to evaluate the influence of coat color on basal reactivity assessed with infrared thermography as eye temperature at rest (ETR), determine their relation with the results obtained by these horses in Show Jumping competitions and to estimate the genetic parameters for this variable to test its suitability for genetic selection. A General Linear Model (GLM) and Duncan post-hoc analysis indicated differences in ETR due to coat color, sex, age, location, and breed-group factors. A Spearman’s rank correlation of 0.11 (p < 0.05) was found with ranking, indicating that less reactive horses were more likely to achieve better rankings. Heritability values ranged from 0.17 to 0.22 and were computed with a model with genetic groups and a model with residual variance heterogeneity. Breeding values were higher with the last genetic model, thus demonstrating the pleiotropic effect of coat color. These results indicate that ETR has a suitable genetic basis to be used in the breeding program to select for basal reactivity due to coat color.

Roan coat color in livestock

Since domestication, a wide variety of phenotypes including coat color variation has developed in livestock. This variation is mostly based on selective breeding. During the beginning of selective breeding, potential negative consequences did not become immediately evident due to low frequencies of homozygous animals and have been occasionally neglected. However, numerous studies of coat color genetics have been carried out over more than a century and, meanwhile, pleiotropic effects for several coat color genes, including disorders of even lethal impact, were described. Similar coat color phenotypes can often be found across species, caused either by conserved genes or by different genes. Even in the same species, more than one gene could cause the same or similar coat color phenotype. The roan coat color in livestock species is characterized by a mixture of white and colored hair in cattle, pig, sheep, goat, alpaca, and horse. So far, the genetic background of this phenotype is not fully understood, but KIT and its ligand KITLG (MGF) are major candidate genes in livestock species. For some of these species, pleiotropic effects such as subfertility in homozygous roan cattle or homozygous embryonic lethality in certain horse breeds have been described. This review aims to point out the similarities and differences of the roan phenotype across the following livestock species: cattle, pig, sheep, goat, alpaca, and horse; and provides the current state of knowledge on genetic background and pleiotropic effects.

Review: Balancing Selection for Deleterious Alleles in Livestock

Harmful alleles can be under balancing selection due to an interplay of artificial selection for the variant in heterozygotes and purifying selection against the variant in homozygotes. These pleiotropic variants can remain at moderate to high frequency expressing an advantage for favorable traits in heterozygotes, while harmful in homozygotes. The impact on the population and selection strength depends on the consequence of the variant both in heterozygotes and homozygotes. The deleterious phenotype expressed in homozygotes can range from early lethality to a slightly lower fitness in the population. In this review, we explore a range of causative variants under balancing selection including loss-of-function variation (i.e., frameshift, stop-gained variants) and regulatory variation (affecting gene expression). We report that harmful alleles often affect orthologous genes in different species, often influencing analogous traits. The recent discoveries are mainly driven by the increasing genomic and phenotypic resources in livestock populations. However, the low frequency and sometimes subtle effects in homozygotes prevent accurate mapping of such pleiotropic variants, which requires novel strategies to discover. After discovery, the selection strategy for deleterious variants under balancing selection is under debate, as variants can contribute to the heterosis effect in crossbred animals in various livestock species, compensating for the loss in purebred animals. Nevertheless, gene-assisted selection is a useful tool to decrease the frequency of the harmful allele in the population, if desired. Together, this review marks various deleterious variants under balancing selection and describing the functional consequences at the molecular, phenotypic, and population level, providing a resource for further study.

Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features

Background

A large number of pig breeds are distributed around the world, their features and characteristics vary among breeds, and they are valuable resources. Understanding the underlying genetic mechanisms that explain across-breed variation can help breeders develop improved pig breeds.

Results

In this study, we performed GWAS using a standard mixed linear model with three types of genome variants (SNP, InDel, and CNV) that were identified from public, whole-genome, sequencing data sets. We used 469 pigs of 57 breeds, and we identified and analyzed approximately 19 million SNPs, 1.8 million InDels, and 18,016 CNVs. We defined six biological phenotypes by the characteristics of breed features to identify the associated genome variants and candidate genes, which included coat color, ear shape, gradient zone, body weight, body length, and body height. A total of 37 candidate genes was identified, which included 27 that were reported previously (e.g., PLAG1 for body weight), but the other 10 were newly detected candidate genes (e.g., ADAMTS9 for coat color).

Conclusion

Our study indicated that using GWAS across a modest number of breeds with high density genome variants provided efficient mapping of complex traits.

Supplementary Information

Supplementary information accompanies this paper at 10.1186/s40104-020-00520-8.

Genetics and Evolution of Mammalian Coat Pigmentation

The diversity of mammalian coat colors, and their potential adaptive significance, have long fascinated scientists as well as the general public. The recent decades have seen substantial improvement in our understanding of their genetic bases and evolutionary relevance, revealing novel insights into the complex interplay of forces that influence these phenotypes. At the same time, many aspects remain poorly known, hampering a comprehensive understanding of these phenomena. Here we review the current state of this field and indicate topics that should be the focus of additional research. We devote particular attention to two aspects of mammalian pigmentation, melanism and pattern formation, highlighting recent advances and outstanding challenges, and proposing novel syntheses of available information. For both specific areas, and for pigmentation in general, we attempt to lay out recommendations for establishing novel model systems and integrated research programs that target the genetics and evolution of these phenotypes throughout the Mammalia.

Coat Color Roan Shows Association with KIT Variants and No Evidence of Lethality in Icelandic Horses

Roan (Rn) horses show a typical seasonal change of color. Their body is covered with colored and white hair. We performed a descriptive statistical analysis of breeding records of Icelandic horses to challenge the hypothesis of roan being lethal in utero under homozygous condition. The roan to non-roan ratio of foals from roan × roan matings revealed homozygous roan Icelandic horses to be viable. Even though roan is known to be inherited in a dominant mode and epistatic to other coat colors, the causative mutation is still unknown. Nevertheless, an association between roan phenotype and the KIT gene was shown for different horse breeds. In the present study, we identified KIT variants by Sanger sequencing, and show that KIT is also associated with roan in the Icelandic horse breed.

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.

Genome-wide association analysis reveals QTL and candidate mutations involved in white spotting in cattle

BACKGROUND

White spotting of the coat is a characteristic trait of various domestic species including cattle and other mammals. It is a hallmark of Holstein-Friesian cattle, and several previous studies have detected genetic loci with major effects for white spotting in animals with Holstein-Friesian ancestry. Here, our aim was to better understand the underlying genetic and molecular mechanisms of white spotting, by conducting the largest mapping study for this trait in cattle, to date.

RESULTS

Using imputed whole-genome sequence data, we conducted a genome-wide association analysis in 2973 mixed-breed cows and bulls. Highly significant quantitative trait loci (QTL) were found on chromosomes 6 and 22, highlighting the well-established coat color genes KIT and MITF as likely responsible for these effects. These results are in broad agreement with previous studies, although we also report a third significant QTL on chromosome 2 that appears to be novel. This signal maps immediately adjacent to the PAX3 gene, which encodes a known transcription factor that controls MITF expression and is the causal locus for white spotting in horses. More detailed examination of these loci revealed a candidate causal mutation in PAX3 (p.Thr424Met), and another candidate mutation (rs209784468) within a conserved element in intron 2 of MITF transcripts expressed in the skin. These analyses also revealed a mechanistic ambiguity at the chromosome 6 locus, where highly dispersed association signals suggested multiple or multiallelic QTL involving KIT and/or other genes in this region.

CONCLUSIONS

Our findings extend those of previous studies that reported KIT as a likely causal gene for white spotting, and report novel associations between candidate causal mutations in both the MITF and PAX3 genes. The sizes of the effects of these QTL are substantial, and could be used to select animals with darker, or conversely whiter, coats depending on the desired characteristics.

Genomic Analysis Suggests KITLG is Responsible for a Roan Pattern in two Pakistani Goat Breeds

The roan coat color pattern is described as the presence of white hairs intermixed with pigmented hairs. This kind of pigmentation pattern has been observed in many domestic species, including the goat. The molecular mechanisms and inheritance that underlie this pattern are known for some species and the KITLG gene has been shown associated with this phenotype. To date, no research effort has been carried out to find the gene(s) that control(s) roan coat color pattern in goats. In the present study, after genotyping with the GoatSNP50 BeadChip, 35 goats that showed a roan pattern and that belonged to two Pakistan breeds (Group A) were analyzed and then compared to 740 goats of 39 Italian and Pakistan goat breeds that did not have the same coat color pattern (Group B). Runs of homozygosity-based and XP-EHH analyses were used to identify unique genomic regions potentially associated with the roan pattern. A total of 3 regions on chromosomes 5, 6, and 12 were considered unique among the group A versus group B comparisons. The A region > 1.7 Mb on chromosome 5 was the most divergent between the two groups. This region contains six genes, including the KITLG gene. Our findings support the hypothesis that the KITLG gene may be associated with the roan phenotype in goats.

Analysis of ROH patterns in the Noriker horse breed reveals signatures of selection for coat color and body size

Overlapping runs of homozygosity (ROH islands) shared by the majority of a population are hypothesized to be the result of selection around a target locus. In this study we investigated the impact of selection for coat color within the Noriker horse on autozygosity and ROH patterns. We analyzed overlapping homozygous regions (ROH islands) for gene content in fragments shared by more than 50% of horses. Long‐term assortative mating of chestnut horses and the small effective population size of leopard spotted and tobiano horses resulted in higher mean genome‐wide ROH coverage (S_ROH) within the range of 237.4–284.2 Mb, whereas for bay, black and roan horses, where rotation mating is commonly applied, lower autozygosity (S_ROH from 176.4–180.0 Mb) was determined. We identified seven common ROH islands considering all Noriker horses from our dataset. Specific islands were documented for chestnut, leopard spotted, roan and bay horses. The ROH islands contained, among others, genes associated with body size (ZFAT, LASP1 and LCORL/NCAPG), coat color (MC1R in chestnut and the factor PATN1 in leopard spotted horses) and morphogenesis (HOXB cluster in all color strains except leopard spotted horses). This study demonstrates that within a closed population sharing the same founders and ancestors, selection on a single phenotypic trait, in this case coat color, can result in genetic fragmentation affecting levels of autozygosity and distribution of ROH islands and enclosed gene content.

Exploring differentially expressed genes associated with coat color in goat skin using RNA-seq

Fur color in domestic goats is an important, genetically determined characteristic that is associated with economic value. This study was designed to perform a comprehensive expression profiling of genes expressed in the skin tissues from Laiwu Black goat and Lubei White goat. Comparisons of black and white goat skin transcriptomes revealed 102 differentially expressed genes (DEGs), of which 38 were upregulated and 64 downregulated in black skin compared with white skin. Among the DEGs, we identified six genes involved in pigmentation, including agouti signaling protein (ASIP), CAMP responsive element binding protein 3-like 1 (CREB3L1), dopachrome tautomerase (DCT), premelanosome protein (PMEL), transient receptor potential cation channel subfamily M member 1 (TRPM1), and tyrosinase-related protein 1 (TYRP1). Notably, there were no significant differences in the expression of melanocortin 1 receptor, microphthalmia-associated transcription factor, tyrosinase, and KIT proto-oncogene receptor tyrosine kinase between the black and white skin samples, whereas ASIP expression was detected only in white skin. PMEL, TRPM1, TYRP1, and DCT showed higher expression in black goat skin, but ASIP and CREB3L1 had higher expression in white goat skin. Quantitative polymerase chain reaction results for PMEL, TRPM1, DCT, TYRP1, and CREB3L1 expression were consistent with those for RNA-seq. These results will expand our understanding of the complex molecular mechanisms of skin physiology and melanogenesis in goats, and provide a foundation for future studies.

Domestic animals as models for biomedical research

Domestic animals are unique models for biomedical research due to their long history (thousands of years) of strong phenotypic selection. This process has enriched for novel mutations that have contributed to phenotype evolution in domestic animals. The characterization of such mutations provides insights in gene function and biological mechanisms. This review summarizes genetic dissection of about 50 genetic variants affecting pigmentation, behaviour, metabolic regulation, and the pattern of locomotion. The variants are controlled by mutations in about 30 different genes, and for 10 of these our group was the first to report an association between the gene and a phenotype. Almost half of the reported mutations occur in non-coding sequences, suggesting that this is the most common type of polymorphism underlying phenotypic variation since this is a biased list where the proportion of coding mutations are inflated as they are easier to find. The review documents that structural changes (duplications, deletions, and inversions) have contributed significantly to the evolution of phenotypic diversity in domestic animals. Finally, we describe five examples of evolution of alleles, which means that alleles have evolved by the accumulation of several consecutive mutations affecting the function of the same gene.

Constitutive activation of the ERK pathway in melanoma and skin melanocytes in Grey horses

Background

Constitutive activation of the ERK pathway, occurring in the vast majority of melanocytic neoplasms, has a pivotal role in melanoma development. Different mechanisms underlie this activation in different tumour settings. The Grey phenotype in horses, caused by a 4.6 kb duplication in intron 6 of Syntaxin 17 (STX17), is associated with a very high incidence of cutaneous melanoma, but the molecular mechanism behind the melanomagenesis remains unknown. Here, we investigated the involvement of the ERK pathway in melanoma development in Grey horses.

Methods

Grey horse melanoma tumours, cell lines and normal skin melanocytes were analyzed with help of indirect immunofluorescence and immunoblotting for the expression of phospho-ERK1/2 in comparison to that in non-grey horse and human counterparts. The mutational status of BRAF, RAS, GNAQ, GNA11 and KIT genes in Grey horse melanomas was determined by direct sequencing. The effect of RAS, RAF and PI3K/AKT pathways on the activation of the ERK signaling in Grey horse melanoma cells was investigated with help of specific inhibitors and immunoblotting. Individual roles of RAF and RAS kinases on the ERK activation were examined using si-RNA based approach and immunoblotting.

Results

We found that the ERK pathway is constitutively activated in Grey horse melanoma tumours and cell lines in the absence of somatic activating mutations in BRAF, RAS, GNAQ, GNA11 and KIT genes or alterations in the expression of the main components of the pathway. The pathway is mitogenic and is mediated by BRAF, CRAF and KRAS kinases. Importantly, we found high activation of the ERK pathway also in epidermal melanocytes, suggesting a general predisposition to melanomagenesis in these horses.

Conclusions

These findings demonstrate that the presence of the intronic 4.6 kb duplication in STX17 is strongly associated with constitutive activation of the ERK pathway in melanocytic cells in Grey horses in the absence of somatic mutations commonly linked to the activation of this pathway during melanomagenesis. These findings are consistent with the universal importance of the ERK pathway in melanomagenesis and may have valuable implications for human melanoma research.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2407-14-857) contains supplementary material, which is available to authorized users.

The KIT gene is associated with the english spotting coat color locus and congenital megacolon in Checkered Giant rabbits (Oryctolagus cuniculus)

The English spotting coat color locus in rabbits, also known as Dominant white spotting locus, is determined by an incompletely dominant allele (En). Rabbits homozygous for the recessive wild-type allele (en/en) are self-colored, heterozygous En/en rabbits are normally spotted, and homozygous En/En animals are almost completely white. Compared to vital en/en and En/en rabbits, En/En animals are subvital because of a dilated (“mega”) cecum and ascending colon. In this study, we investigated the role of the KIT gene as a candidate for the English spotting locus in Checkered Giant rabbits and characterized the abnormalities affecting enteric neurons and c-kit positive interstitial cells of Cajal (ICC) in the megacolon of En/En rabbits. Twenty-one litters were obtained by crossing three Checkered Giant bucks (En/en) with nine Checkered Giant (En/en) and two en/en does, producing a total of 138 F1 and backcrossed rabbits. Resequencing all coding exons and portions of non-coding regions of the KIT gene in 28 rabbits of different breeds identified 98 polymorphisms. A single nucleotide polymorphism genotyped in all F1 families showed complete cosegregation with the English spotting coat color phenotype (θ = 0.00 LOD  = 75.56). KIT gene expression in cecum and colon specimens of En/En (pathological) rabbits was 5–10% of that of en/en (control) rabbits. En/En rabbits showed reduced and altered c-kit immunolabelled ICC compared to en/en controls. Morphometric data on whole mounts of the ascending colon showed a significant decrease of HuC/D (P<0.05) and substance P (P<0.01) immunoreactive neurons in En/En vs. en/en. Electron microscopy analysis showed neuronal and ICC abnormalities in En/En tissues. The En/En rabbit model shows neuro-ICC changes reminiscent of the human non-aganglionic megacolon. This rabbit model may provide a better understanding of the molecular abnormalities underlying conditions associated with non-aganglionic megacolon.

Pleiotropic effects of coat colour-associated mutations in humans, mice and other mammals

The characterisation of the pleiotropic effects of coat colour-associated mutations in mammals illustrates that sensory organs and nerves are particularly affected by disorders because of the shared origin of melanocytes and neurocytes in the neural crest; e.g. the eye-colour is a valuable indicator of disorders in pigment production and eye dysfunctions. Disorders related to coat colour-associated alleles also occur in the skin (melanoma), reproductive tract and immune system. Additionally, the coat colour phenotype of an individual influences its general behaviour and fitness. Mutations in the same genes often produce similar coat colours and pleiotropic effects in different species (e.g., KIT [reproductive disorders, lethality], EDNRB [megacolon] and LYST [CHS]). Whereas similar disorders and similar-looking coat colour phenotypes sometimes have a different genetic background (e.g., deafness [EDN3/EDNRB, MITF, PAX and SNAI2] and visual diseases [OCA2, RAB38, SLC24A5, SLC45A2, TRPM1 and TYR]). The human predilection for fancy phenotypes that ignore disorders and genetic defects is a major driving force for the increase of pleiotropic effects in domestic species and laboratory subjects since domestication has commenced approximately 18,000 years ago.

The role of humans in facilitating and sustaining coat colour variation in domestic animals

Though the process of domestication results in a wide variety of novel phenotypic and behavioural traits, coat colour variation is one of the few characteristics that distinguishes all domestic animals from their wild progenitors. A number of recent reviews have discussed and synthesised the hundreds of genes known to underlie specific coat colour patterns in a wide range of domestic animals. This review expands upon those studies by asking how what is known about the causative mutations associated with variable coat colours, can be used to address three specific questions related to the appearance of non wild-type coat colours in domestic animals. Firstly, is it possible that coat colour variation resulted as a by-product of an initial selection for tameness during the early phases of domestication? Secondly, how soon after the process began did domestic animals display coat colour variation? Lastly, what evidence is there that intentional human selection, rather than drift, is primarily responsible for the wide range of modern coat colours? By considering the presence and absence of coat colour genes within the context of the different pathways animals travelled from wild to captive populations, we conclude that coat colour variability was probably not a pleiotropic effect of the selection for tameness, that coat colours most likely appeared very soon after the domestication process began, and that humans have been actively selecting for colour novelty and thus allowing for the proliferation of new mutations in coat colour genes.

The genetic inheritance of the blue-eyed white phenotype in alpacas (Vicugna pacos)

White-spotting patterns in mammals can be caused by mutations in the gene KIT, whose protein is necessary for the normal migration and survival of melanocytes from the neural crest. The alpaca (Vicugna pacos) blue-eyed white (BEW) phenotype is characterized by 2 blue eyes and a solid white coat over the whole body. Breeders hypothesize that the BEW phenotype in alpacas is caused by the combination of the gene causing gray fleece and a white-spotting gene. We performed an association study using KIT flanking and intragenic markers with 40 unrelated alpacas, of which 17 were BEW. Two microsatellite alleles at KIT-related markers were significantly associated (P < 0.0001) with the BEW phenotype (bew1 and bew2). In a larger cohort of 171 related individuals, we identify an abundance of an allele (bew1) in gray animals and the occurrence of bew2 homozygotes that are solid white with pigmented eyes. Association tests accounting for population structure and familial relatedness are consistent with a proposed model where these alleles are in linkage disequilibrium with a mutation or mutations that contribute to the BEW phenotype and to individual differences in fleece color.

Identification of genes related to white and black plumage formation by RNA-Seq from white and black feather bulbs in ducks

To elucidate the genes involved in the formation of white and black plumage in ducks, RNA from white and black feather bulbs of an F(2) population were analyzed using RNA-Seq. A total of 2,642 expressed sequence tags showed significant differential expression between white and black feather bulbs. Among these tags, 186 matched 133 annotated genes that grouped into 94 pathways. A number of genes controlling melanogenesis showed differential expression between the two types of feather bulbs. This differential expression was confirmed by qPCR analysis and demonstrated that Tyr (Tyrosinase) and Tyrp1 (Tyrosinase-related protein-1) were expressed not in W-W (white feather bulb from white dorsal plumage) and W-WB (white feather bulb from white-black dorsal plumage) but in B-B (black feather bulb from black dorsal plumage) and B-WB (black feather bulb from white-black dorsal plumage) feather bulbs. Tyrp2 (Tyrosinase-related protein-2) gene did not show expression in the four types of feather bulbs but expressed in retina. C-kit (The tyrosine kinase receptor) expressed in all of the samples but the relative mRNA expression in B-B or B-WB was approximately 10 fold higher than that in W-W or W-WB. Additionally, only one of the two Mitf isoforms was associated with plumage color determination. Downregulation of c-Kit and Mitf in feather bulbs may be the cause of white plumage in the duck.

Exclusion of candidate genes for coat colour phenotypes of the American mink (Neovison vison)

In a previous project, we screened the American mink Bacterial Artificial Chromosome library, CHORI-231, for genes potentially involved in various coat colour phenotypes in the American mink. Subsequently, we 454 sequenced the inserts containing these genes and developed microsatellite markers for each of these genes. Here, we describe a lack of association between three different 'roan-type' phenotypes represented by Cross, Stardust and Cinnamon in American mink and six different genes that we considered to be potentially linked to these phenotypes. Thus, c-KIT (HUGO-approved symbol KIT), ATOH-1 (HUGO-approved symbol ATOH1) and POMC were excluded as potential candidates for these three phenotypes. In addition, MITF and SLC24A5 were excluded for Cross and Cinnamon, and KITL (HUGO-approved symbol KITLG) for Cross and Stardust. Although most of these genes have been implicated as the cause of similar phenotypes in other mammals, including horses, pigs, cows, dogs, cats, mice and humans, they do not appear to be responsible for comparable phenotypes found in American mink.

[Effects of Kit gene on coat depigmentation in white horses]

Coat color of horse is an important basis for both species identification and individual recognition and is also one of the important references traits for breeding. Therefore, the research on the mechanism of coat fading has become an important part of horses' coat color study. It has been found that the white phenotype is closely related to the mutation of kit gene, which is located on chromosome 3. Investigated results showed that the formation of the epidermal melanoblast and melanin relies on the expression of kit gene, which determines the presence of white phenotype. Nevertheless, studies results have shown that the mutation of kit gene in the white horse exhibited significant differences among species. Horses that the coat color completely faded are very rare and are found occasionally in a few species. However, a larger number of horses that coat color completely faded, called Mongolian white horse, are found in West Ujimqin , Xilin Gol League, Inner Mongolia. Therefore, genetic mechanism of color fading in Mongolian white horses is still not clear. No typical mutations have been observed in 21 exons of kit gene in Mongolian white horse. This paper summarized recent international studies on molecular mechanism of color fading and tried to lay the foundation for the study of formation mechanism of Mongolian white horse. The aim of this review is to provide some valuable references to horses coat color research and breeding.

Novel alternative splicing by exon skipping in KIT associated with whole-body roan in an intercrossed population of Landrace and Korean Native pigs

The KIT locus has been suggested to be a strong candidate region linked with whole-body roan in the F(2) population produced by intercrosses between Landrace and Korean Native pigs. In this manuscript, we report the finding of a novel alternative splicing event in the porcine KIT gene that results in the skipping of exon 5 in the I(Rn) allele. KIT mRNAs that lack exon 5 were identified in the large intestine and skin, suggesting that the mechanism responsible for the skipping of exon 5 may be tissue specific. A U(26) repeat in intron 5 showed complete linkage (LOD = 11.8) with the roan phenotype and absolute association with the black phenotype of the Korean Native pig (KNP) population samples, inferring that the repeat pattern may alter the complementary base-pairing-mediated looping-out of introns 4 and 5, which may mediate the exon 5-skipping event. Although the sample size in our study was relatively small, we speculate that the R3 allele containing the U(26) repeat is a causative element for the roan phenotype via alternative control of the exon skipping in our roan pedigree.

Colours of domestication

During the last decade, coat colouration in mammals has been investigated in numerous studies. Most of these studies addressing the genetics of coat colouration were on domesticated animals. In contrast to their wild ancestors, domesticated species are often characterized by a huge allelic variability of coat-colour-associated genes. This variability results from artificial selection accepting negative pleiotropic effects linked with certain coat-colour variants. Recent studies demonstrate that this selection for coat-colour phenotypes started at the beginning of domestication. Although to date more than 300 genetic loci and more than 150 identified coat-colour-associated genes have been discovered, which influence pigmentation in various ways, the genetic pathways influencing coat colouration are still only poorly described. On the one hand, similar coat colourations observed in different species can be the product of a few conserved genes. On the other hand, different genes can be responsible for highly similar coat colourations in different individuals of a species or in different species. Therefore, any phenotypic classification of coat colouration blurs underlying differences in the genetic basis of colour variants. In this review we focus on (i) the underlying causes that have resulted in the observed increase of colour variation in domesticated animals compared to their wild ancestors, and (ii) the current state of knowledge with regard to the molecular mechanisms of colouration, with a special emphasis on when and where the different coat-colour-associated genes act.

Genetic architecture of complex traits and accuracy of genomic prediction: coat colour, milk-fat percentage, and type in Holstein cattle as contrasting model traits

Prediction of genetic merit using dense SNP genotypes can be used for estimation of breeding values for selection of livestock, crops, and forage species; for prediction of disease risk; and for forensics. The accuracy of these genomic predictions depends in part on the genetic architecture of the trait, in particular number of loci affecting the trait and distribution of their effects. Here we investigate the difference among three traits in distribution of effects and the consequences for the accuracy of genomic predictions. Proportion of black coat colour in Holstein cattle was used as one model complex trait. Three loci, KIT, MITF, and a locus on chromosome 8, together explain 24% of the variation of proportion of black. However, a surprisingly large number of loci of small effect are necessary to capture the remaining variation. A second trait, fat concentration in milk, had one locus of large effect and a host of loci with very small effects. Both these distributions of effects were in contrast to that for a third trait, an index of scores for a number of aspects of cow confirmation ("overall type"), which had only loci of small effect. The differences in distribution of effects among the three traits were quantified by estimating the distribution of variance explained by chromosome segments containing 50 SNPs. This approach was taken to account for the imperfect linkage disequilibrium between the SNPs and the QTL affecting the traits. We also show that the accuracy of predicting genetic values is higher for traits with a proportion of large effects (proportion black and fat percentage) than for a trait with no loci of large effect (overall type), provided the method of analysis takes advantage of the distribution of loci effects.

Testes bioquímico (albumina e proteína de ligação da vitamina D) e molecular (gene KIT) para detecção de marcadores genéticos para pelagem tobiana em cavalos Pampa e Paint

Foram utilizados 159 cavalos Pampa, registrados na Associação Brasileira dos Criadores de Cavalo Pampa, e um grupo-controle, de 32 cavalos da raça Paint, ambos os grupos provenientes de plantéis de diferentes regiões brasileiras, com o objetivo de comparar os testes bioquímico e molecular para detecção de marcadores genéticos para pelagem tobiana em cavalos Pampa. Houve diferença significativa (P<0,001) entre os testes bioquímico e molecular, nos cavalos Pampa, mas o mesmo fato não ocorreu com os da raça Paint. Os resultados mostraram que o marcador molecular (KIT) foi mais eficiente na identificação dos prováveis cavalos homozigotos do que os marcadores bioquímicos albumina (Al) e proteína de ligação da vitamina D (Gc), em ambas as raças.

The untranslated side of hair and skin mammalian pigmentation: Beyond coding sequences

For several decades, tremendous advances in studying skin and hair pigmentation of mammals have been made using Mendelian genetics principles. A number of loci and their associated traits have been extensively examined, crossings performed, and phenotypes well documented. Continuously improving PCR techniques allowed the molecular cloning and sequencing of the first pigmentation genes at the end of the 20th century, a period followed by an intense effort to detect and describe polymorphisms in the coding regions and correlate allelic combinations with the observed melanogenic phenotypes. However, a number of phenotypes and biological events could not be elucidated solely by analysis of the coding regions of genes. Messenger RNA isolation, characterization and quantification techniques allowed groups to move ahead and investigate molecular mechanisms whose secrets lay within the noncoding regions of pigmentation genes transcripts such as MC1R, ASIP, or Mitf. The untranslated elements contain specific nucleotidic sequences and structures that dramatically influence the mRNA half-life and processing thus impacting protein translation and melanin production. As we are progressively uncovering the complex processes regulating melanocyte biology, unraveling complete mRNA structures and understanding mechanisms beyond coding regions has become critical.

Genetic heterogeneity at the bovine KIT gene in cattle breeds carrying different putative alleles at the spotting locus

According to classical genetic studies, piebaldism in cattle is largely influenced by the allelic series at the spotting locus (S), which includes the S(H) (Hereford pattern), S(+) (non-spotted) and s (spotted) alleles. The S locus was mapped on bovine chromosome 6 in the region containing the KIT gene. We investigated the KIT gene, analysing its variability and haplotype distribution in cattle of three breeds (Angus, Hereford and Holstein) with different putative alleles (S(+), S(H) and s respectively) at the S locus. Resequencing of a whole of 0.485 Mb revealed 111 polymorphisms. The global nucleotide diversity was 0.087%. Tajima's D-values were negative for all breeds, indicating putative directional selection. Of the 28 inferred haplotypes, only five were observed in the Hereford breed, in which one was the most frequent. Coalescent simulation showed that it is highly unlikely (P < 10E-6) to obtain this low number of haplotypes conditionally on the observed number of segregating SNPs. Therefore, the neutral model could be rejected for the Hereford breed, suggesting that a selection sweep occurred at the KIT locus. Twelve haplotypes were inferred in Holstein and Angus. For these two breeds, the neutral model could not be rejected. High heterogeneity of the KIT gene was confirmed from a phylogenetic analysis. Our results suggest a role of the KIT gene in determining the S(H) allele(s) in the Hereford, but no evidence of selective sweep was obtained in Holstein, suggesting that complex mechanisms (or other genes) might be the cause of the spotted phenotype in this breed.

Seven novel KIT mutations in horses with white coat colour phenotypes

White coat colour in horses is inherited as a monogenic autosomal dominant trait showing a variable expression of coat depigmentation. Mutations in the KIT gene have previously been shown to cause white coat colour phenotypes in pigs, mice and humans. We recently also demonstrated that four independent mutations in the equine KIT gene are responsible for the dominant white coat colour phenotype in various horse breeds. We have now analysed additional horse families segregating for white coat colour phenotypes and report seven new KIT mutations in independent Thoroughbred, Icelandic Horse, German Holstein, Quarter Horse and South German Draft Horse families. In four of the seven families, only one single white horse, presumably representing the founder for each of the four respective mutations, was available for genotyping. The newly reported mutations comprise two frameshift mutations (c.1126_1129delGAAC; c.2193delG), two missense mutations (c.856G>A; c.1789G>A) and three splice site mutations (c.338-1G>C; c.2222-1G>A; c.2684+1G>A). White phenotypes in horses show a remarkable allelic heterogeneity. In fact, a higher number of alleles are molecularly characterized at the equine KIT gene than for any other known gene in livestock species.

Allelic heterogeneity at the equine KIT locus in dominant white (W) horses

White coat color has been a highly valued trait in horses for at least 2,000 years. Dominant white (W) is one of several known depigmentation phenotypes in horses. It shows considerable phenotypic variation, ranging from approximately 50% depigmented areas up to a completely white coat. In the horse, the four depigmentation phenotypes roan, sabino, tobiano, and dominant white were independently mapped to a chromosomal region on ECA 3 harboring the KIT gene. KIT plays an important role in melanoblast survival during embryonic development. We determined the sequence and genomic organization of the approximately 82 kb equine KIT gene. A mutation analysis of all 21 KIT exons in white Franches-Montagnes Horses revealed a nonsense mutation in exon 15 (c.2151C>G, p.Y717X). We analyzed the KIT exons in horses characterized as dominant white from other populations and found three additional candidate causative mutations. Three almost completely white Arabians carried a different nonsense mutation in exon 4 (c.706A>T, p.K236X). Six Camarillo White Horses had a missense mutation in exon 12 (c.1805C>T, p.A602V), and five white Thoroughbreds had yet another missense mutation in exon 13 (c.1960G>A, p.G654R). Our results indicate that the dominant white color in Franches-Montagnes Horses is caused by a nonsense mutation in the KIT gene and that multiple independent mutations within this gene appear to be responsible for dominant white in several other modern horse populations.

Mice Transgenic for KitV620A: Recapitulation of Piebaldism but not Progressive Depigmentation Seen in Humans with this Mutation

Piebaldism is an autosomal dominant genetic pigmentary disorder, characterized by congenital white hair and patches located on the forehead, anterior trunk, and extremities. Most piebald patients have a mutation of the KIT gene, which encodes a tyrosine kinase receptor involved in pigment cell development. The white hair and patches of such patients are already completely formed at birth and do not usually expand thereafter. This stability of pigmented spots also applies to Kit(W) and Kitl(Sl) mutant mice. However, two novel cases of piebaldism were reported in 2001, in which both mother and daughter having a novel Val620Ala mutation in their KIT gene showed progressive depigmentation. To prepare an animal model of this mutation, to explore undefined functions of KIT signaling for maintaining pigmented melanocytes in the skin or more specifically the integrity of the melanocyte stem cell system in the postnatal skin, we produced transgenic mice expressing Val620Ala Kit. These mice well mimicked the white spotting pattern of patients; however, no change in this pattern was observed after birth, even after increasing the transgene expression by various means. Here, we report the unexpectedly extremely stable maintenance of the melanocyte stem cell system under stringent conditions for KIT signaling.

Exon skipping in the KIT gene causes a Sabino spotting pattern in horses

Sabino (SB) is a white spotting pattern in the horse characterized by white patches on the face, lower legs, or belly, and interspersed white hairs on the midsection. Based on comparable phenotypes in humans and pigs, the KIT gene was investigated as the origin of the Sabino phenotype. In this article we report the genetic basis of one type of Sabino spotting pattern in horses that we call Sabino 1, with the alleles represented by the symbols SB1 and sb1. Transcripts of KIT were characterized by reverse transcriptase polymerase chain reaction (RT-PCR) and sequencing cDNA from horses with the genotypes SB1/SB1, SB1/sb1, and sb1/sb1. Horses with the Sabino 1 trait produced a splice variant of KIT that did not possess exon 17. Genomic DNA sequencing of KIT revealed a single nucleotide polymorphism (SNP) caused by a base substitution for T with A in intron 16, 1037 bases following exon 16. The SNP associated with SB1 was designated KI16+1037A. This substitution eliminated a MnlI restriction site and allowed the use of PCR-RFLP to characterize individuals for this base change. Complete linkage was observed between this SNP and Sabino 1 in the Tennessee Walking Horse families (LOD = 9.02 for Theta = 0). Individual horses from other breeds were also tested. All five horses homozygous for this SNP were white, and all 68 horses with one copy of this SNP either exhibited the Sabino 1 phenotype or were multipatterned. Some multipatterned individuals appeared white due to the additive effect of white spotting patterns. However, 13 horses with other Sabino-type patterns did not have this SNP. Based on these results we propose the following: (1) this SNP, found within intron 16, is responsible for skipping of exon 17 and the SB1 phenotype, (2) the White and Sabino phenotypes are heterogeneous and this mechanism is not the only way to produce the pattern described as "Sabino" or "White," and (3) homozygosity for SB1 results in a complete or nearly completely white phenotype.

Linked markers exclude KIT as the gene responsible for appaloosa coat colour spotting patterns in horses

The appaloosa coat colour pattern of the horse is similar to that caused by the rump-white (Rw) gene in the mouse. In the mouse Rw colour pattern is the result of an inversion involving the proto-oncogene c-kit (KIT). Therefore, we investigated KIT as a candidate gene that encodes the appaloosa coat colour gene (Lp) in horses. KIT plays a critical role in haematopoiesis, gametogenesis, and melanogenesis and encodes a transmembrane tyrosine kinase receptor that belongs to the PDGF/CSF-1/c-KIT receptor subfamily. Half-sib families segregating for Lp were uninformative for a reported polymorphism in KIT. However, KIT is located on horse chromosome 3 close to albumin (ALB), serum carboxylesterase (ES), vitamin D-binding protein (GC) and microsatellite markers ASB23, LEX007, LEX57, and UCDEQ437. Indeed, KIT and ASB23 were localized to ECA3q21-22.1 and 3q22.1-22.3, respectively, by fluorescent in situ hybridization. Family studies were conducted to investigate linkage of Lp to these markers using eight half-sib families in which Appaloosa stallions were mated to solid coloured mares. Linkage of Lp to the chromosome region containing ES, ALB, GC, ASB23, UCDEQ437, LEX57, and LEX007 was investigated by a multipoint linkage analysis using the computer program GENEHUNTER. LOD scores over the interval under investigation ranged from -4.28 to -12.48, with a score of -12.48 at the location for ASB23. Therefore, it was concluded that appaloosa (Lp) is not linked to any of the tested markers on ECA3, and thus Lp is unlikely to be the product of KIT.