Coat Color Pigmentation Research Articles

Whole Genome Resequencing Reveals Genetic Diversity and Selection Signatures of Ethiopian Indigenous Cattle Adapted to Local Environments

Cattle are among the most important domesticated bovid species in the world, of which Ethiopia possesses large populations adapted to different agro-ecologies and production systems. Though several molecular population genetic studies have been done on Ethiopian indigenous cattle, genomic diversity and selection signatures pertinent to adaptation to the different local environments have yet to be comprehensively characterized. Here, the whole genome sequences of 151 samples from 14 Ethiopian indigenous cattle populations were analyzed to assess genomic diversity and differentiation as well as signatures of positive selection (using Hp, iHS, FST, and XP-CLR) in comparison to Sudanese zebu, Asian zebu, Ankole, and African and European taurine cattle. High genomic differentiation was observed between Ethiopian and non-Ethiopian cattle populations, while low genomic differentiation and inbreeding were present between and within Ethiopian cattle populations. Sixteen genome regions overlapping with 40 candidate genes were commonly identified by at least three genome scan methods. High frequencies of missense SNPs in ITPR2, CHADL, GNAS, STING1, and KIT genes with high haplotype differentiations were observed in Ethiopian cattle compared to non-Ethiopian cattle. The candidate genes were significantly associated with several biological functions and molecular pathways responsible for nutrient metabolism, skeletal development, immune response, reproduction, water balance, coat color pigmentation, and circulatory homeostasis. Our results provide new insights into the adaptation of the Ethiopian indigenous cattle to the country’s diverse environments.

INFLUENCE OF QUALITATIVE TRAITS ON THE PERFORMANCE OF WEST AFRICAN DWARF GOATS

Data on coat colour pigmentation and incidence of wattle were combined with production records of 1407 West African dwarf goats to study their influence on litter traits and body weight. There was no significant (P>0.05) difference among coat colours for litter size at birth and at weaning and birth weight. Basic white coloured goats were significantly (P <0.05) heavier at weaning and one year of age than the basic brown and black goats. The trend was that the weight decreased with increased pigmentation. Presence or absence of wattle did not exert any influence on the traits studied except yearling body weight Bilaterally wattled goats were lighter (P<0.01) than unilaterally wattled and non wattled goats.

Skin transcriptome profiles associated with black- and white-coated regions in Boer and Macheng black crossbred goats

To increase the current understanding of the gene-expression profiles in different skin regions associated with different coat colors and identify key genes for the regulation of color patterns in goats, we used the Illumina RNA-Seq method to compare the skin transcriptomes of the black- and white-coated regions containing hair follicles from the Boer and Macheng Black crossbred goat, which has a black head and a white body. Six cDNA libraries derived from skin samples of the white-coated region (n = 3) and black-coated region (n = 3) were constructed from three full-sib goats. On average, we obtained approximately 76.5 and 73.5 million reads for skin samples from black- and white-coated regions, respectively, of which 75.39% and 76.05% were covered in the genome database. A total of 165 differentially expressed genes (DEGs) were detected between these two color regions, among which 110 were upregulated and 55 were downregulated in the skin samples of white- vs. black-coated regions. The results of Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses revealed that some of these DEGs may play an important role in controlling the pigmentation of skin or hair follicles. We identified three key DEGs, i.e., Agouti, DCT, and TYRP1, in the pathway related to melanogenesis in the different skin regions of the crossbred goat. DCT and TYRP1 were downregulated and Agouti was upregulated in the skin of the white-coated region, suggesting a lack of mature melanocytes in this region and that Agouti might play a key developmental role in color-pattern formation. All data sets (Gene Expression Omnibus) are available via public repositories. In addition, MC1R was genotyped in 200 crossbred goats with a black head and neck. Loss-of-function mutations in MC1R as well as homozygosity for the mutant alleles were widely found in this population. The MC1R gene did not seem to play a major role in determining the black head and neck in our crossbred goats. Our study provides insights into the transcriptional regulation of two distinct coat colors, which might serve as a key resource for understanding coat color pigmentation in goats. The region-specific expression of Agouti may be associated with the distribution of pigments across the body in Boer and Macheng Black crossbred goats.

TRP‑2 mediates coat color pigmentation in sheep skin.

Tyrosinase-related protein 2 (TRP-2) is one of the most important members of the tyrosinase family, and is a key enzyme involved in melanin biosynthesis. In the present study, a skin transcriptome profile, immunohistochemistry, western blotting and reverse transcription-quantitative polymerase chain reaction were used to investigate TRP-2 expression in sheep with different coat colors, namely, black, white and black-white. TRP-2 was overexpressed in melanocytes in order to study the effect of TRP-2 on melanin production. Results revealed differing TRP-2 levels in sheep of different coat colors and in various parts of the coat with different colors in the same sheep. TRP-2 expression levels in dark-colored areas were significantly increased compared with light-colored areas in piebald sheep. TRP-2 overexpression may regulate melanogenesis and significantly increase melanogenesis associated transcription factor expression in vitro. Therefore, TRP-2 may affect melanin production in sheep, and different expression levels determine coat color. The results may provide novel approaches for developing therapeutic strategies for skin diseases associated with pigmentation disorders.

Phenotypic and genetic categorization of qualitative traits in extensively managed local goat (Capra aegagrus) population of Niger State, Nigeria

A study on the distribution and frequencies of coat colour, wattle, beard, horn, and hair type using 375 extensively managed local goats was carried out in the three administrative zones of Niger state, Nigeria. The animals were scored for coat colour pigmentation pattern, presence or absence of wattle, beard, horn, hair type and extra teat. The study showed that light brown is the predominant colour in zones A (43.24%) and zone C (47.57%). Dark brown colour was predominant in zone B (37.82%) followed by light brown (31.09%). The observed frequencies for wattle (Waw) and extra teat (Ete) were above (p < 0.01) the expected Mendelian value of 75% for a dominant gene in all the zones (90.34, 86.55, 87.39 percent for wattle and 91.73, 96.64, 98.21, percent for extra teat in zones A, B, and C, respectively). The gene frequency for beard (Brb) were significantly lower (p < 0.01) than the expected Mendelian value of 75% for a dominant gene in zone A (66.20%) and zone B (55.46%), but was higher in zone C (83.78%). The gene frequency for polledness (Pop) was 0.00% for all the zones. The gene frequency for soft hair.was more than (p < 0.01) the expected Mendelian value of 75% for dominant genes in zone C (87.33%) but fell short in zone A (60.69%) and zone B (43.70%), respectively. It was concluded that coat colour variation exist in local goats reared extensively in Niger state.

It’s in our roots

It’s in our roots

Human hair melanins: what we have learned and have not learned from mouse coat color pigmentation

Hair pigmentation is one of the most conspicuous phenotypes in humans. Melanocytes produce two distinct types of melanin pigment: brown to black, indolic eumelanin and yellow to reddish brown, sulfur-containing pheomelanin. Biochemically, the precursor tyrosine and the key enzyme tyrosinase and the tyrosinase-related proteins are involved in eumelanogenesis, while only the additional presence of cysteine is necessary for pheomelanogenesis. Other important proteins involved in melanogenesis include P protein, MATP protein, α-MSH, agouti signaling protein (ASIP), MC1R (the receptor for MSH and ASIP), and SLC7A11, a cystine transporter. Many studies have examined the effects of loss-of-function mutations of those proteins on mouse coat color pigmentation. In contrast, much less is known regarding the effects of mutations of the corresponding proteins on human hair pigmentation except for MC1R polymorphisms that lead to pheomelanogenesis. This perspective will discuss what we have/have not learned from mouse coat color pigmentation, with special emphasis on the significant roles of pH and the level of cysteine in melanosomes in controlling melanogenesis. Based on these data, a hypothesis is proposed to explain the diversity of human hair pigmentation.

Human hair melanins: what we have learned and have not learned from mouse coat color pigmentation

Hair pigmentation is one of the most conspicuous phenotypes in humans. Melanocytes produce two distinct types of melanin pigment: brown to black, indolic eumelanin and yellow to reddish brown, sulfur-containing pheomelanin. Biochemically, the precursor tyrosine and the key enzyme tyrosinase and the tyrosinase-related proteins are involved in eumelanogenesis, while only the additional presence of cysteine is necessary for pheomelanogenesis. Other important proteins involved in melanogenesis include P protein, MATP protein, α-MSH, agouti signaling protein (ASIP), MC1R (the receptor for MSH and ASIP), and SLC7A11, a cystine transporter. Many studies have examined the effects of loss-of-function mutations of those proteins on mouse coat color pigmentation. In contrast, much less is known regarding the effects of mutations of the corresponding proteins on human hair pigmentation except for MC1R polymorphisms that lead to pheomelanogenesis. This perspective will discuss what we have/have not learned from mouse coat color pigmentation, with special emphasis on the significant roles of pH and the level of cysteine in melanosomes in controlling melanogenesis. Based on these data, a hypothesis is proposed to explain the diversity of human hair pigmentation.

A brief history of mammalian coat colour genetics.

Abstract The study of coat colour genes of mammals can be traced back to the rediscovery of Mendel's laws in 1900. A phenotypic homology of coat colour loci based on a phenotypic similarity of allelic series has been demonstrated and is known as comparative coat colour genetics . This homology has been verified by molecular genetics. Loci controlling coat colour in mammals are numerous: more than 280 have been discovered in genetic analysis of the mouse, the leading laboratory species. Loci for which mutants have been kept in breeding species (mainly farm animals) are less numerous because only viable alleles have been saved. The colour loci are highly pleiotropic, being involved not only in coat colour pigmentation but also in many other biological processes. The comparative study of DNA chains of numerous variants in several species may help to follow evolution at the locus level in mammals. The colour mutants that segregate in those domesticated populations termed the primary populations may be used as markers to follow genetic dynamics after domestication.

Multiple splice variants within the bovine silver homologue (SILV) gene affecting coat color in cattle indicate a function additional to fibril formation in melanophores

BackgroundThe silver homologue(SILV) gene plays a major role in melanosome development. SILV is a target for studies concerning melanoma diagnostics and therapy in humans as well as on skin and coat color pigmentation in many species ranging from zebra fish to mammals. However, the precise functional cellular mechanisms, in which SILV is involved, are still not completely understood. While there are many studies addressing SILV function upon a eumelaneic pigment background, there is a substantial lack of information regarding the further relevance of SILV, e.g. for phaeomelanosome development.ResultsIn contrast to previous results in other species reporting SILV expression exclusively in pigmented tissues, our experiments provide evidence that the bovine SILV gene is expressed in a variety of tissues independent of pigmentation. Our data show that the bovine SILV gene generates an unexpectedly large number of different transcripts occurring in skin as well as in non-pigmented tissues, e.g. liver or mammary gland. The alternative splice sites are generated by internal splicing and primarily remove complete exons. Alternative splicing predominantly affects the repeat domain of the protein, which has a functional key role in fibril formation during eumelanosome development.ConclusionThe expression of the bovine SILV gene independent of pigmentation suggests SILV functions exceeding melanosome development in cattle. This hypothesis is further supported by transcript variants lacking functional key elements of the SILV protein relevant for eumelanosome development. Thus, the bovine SILV gene can serve as a model for the investigation of the putative additional functions of SILV. Furthermore, the splice variants of the bovine SILV gene represent a comprehensive natural model to refine the knowledge about functional domains in the SILV protein. Our study exemplifies that the extent of alternative splicing is presumably much higher than previously estimated and that alternatively spliced transcripts presumably can generate molecules of deviating function compared to their constitutive counterpart.

Effect of the viable-yellow (A(vy)) agouti allele on skin tumorigenesis and humoral hypercalcemia in v-Ha-ras transgenic TGxAC mice.

We previously reported that papillomas can arise from the follicular epithelium of v-Ha-ras transgenic TGxAC mice. Since the viable-yellow mutation (A(vy)) of the mouse agouti gene which regulates coat color pigmentation by acting within the micro-environment of the hair follicle has been shown to function as a tumor promoter in the liver, we hypothesized that it may also play a role in TGxAC skin tumorigenesis. Endogenous agouti protein product was detected in the outer root sheath of anagen hair follicles following plucking of the hair shaft, but not in the interfollicular epithelium, in TGxAC mice on an FVB/N genetic background. It was also detected in papillomas from these mice produced by 12-O-tetradecanoylphorbol-13-acetate (TPA) treatment or plucking. Expression of the A(vy) allele in the v-Ha-ras transgenic TGxAC mouse line results in an approximately 2-fold increase in papilloma development compared with controls which did not carry the A(vy) allele following twice-weekly treatment with 1.25, 2.5 or 5.0 microg TPA. In addition, TPA-treated, papilloma-bearing F1 mice which carried the A(vy) allele, but not F1 mice which did not carry the A(vy) allele, exhibited a syndrome of humoral hypercalcemia mediated by parathyroid hormone-related protein (PTHrP) that led to weight loss, hypercalcemia and hypophosphatemia. Thus, we conclude that the A(vy) allele can influence the development of skin tumors and PTHrP-mediated humoral hypercalcemia in v-Ha-ras transgenic TGxAC mice.

Molecular structure and chromosomal mapping of the human homolog of the agouti gene.

The agouti (a) locus in mouse chromosome 2 normally regulates coat color pigmentation. The mouse agouti gene was recently cloned and shown to encode a distinctive 131-amino acid protein with a consensus signal peptide. Here we describe the cloning of the human homolog of the mouse agouti gene using an interspecies DNA-hybridization approach. Sequence analysis revealed that the coding region of the human agouti gene is 85% identical to the mouse gene and has the potential to encode a protein of 132 amino acids with a consensus signal peptide. Chromosomal assignment using somatic-cell-hybrid mapping panels and fluorescence in situ hybridization demonstrated that the human agouti gene maps to chromosome band 20q11.2. This result revealed that the human agouti gene is closely linked to several traits, including a locus called MODY (for maturity onset diabetes of the young) and another region that is associated with the development of myeloid leukemia. Initial expression studies with RNA from several adult human tissues showed that the human agouti gene is expressed in adipose tissue and testis.

Molecular characterization of the mouse agouti locus

The agouti (a) locus acts within the microenvironment of the hair follicle to regulate coat color pigmentation in the mouse. We have characterized a gene encoding a novel 131 amino acid protein that we propose is the one gene associated with the agouti locus. This gene is normally expressed in a manner consistent with a locus function, and, more importantly, its structure and expression are affected by a number of representative alleles in the agouti dominance hierarchy. In addition, we found that the pleiotropic effects associated with the lethal yellow (Ay) mutation, which include pronounced obesity, diabetes, and the development of neoplasms, are accompanied by deregulated overexpression of the agouti gene in numerous tissues of the adult animal.

Brachyury - a gene affecting mouse gastrulation and early organogenesis

Mouse embryos that are homozygous for the Brachyury (T) deletion die at mid-gestation. They have prominent defects in the notochord, the allantois and the primitive streak. Expression of the T gene commences at the onset of gastrulation and is restricted to the primitive streak, mesoderm emerging from the streak, the head process and the notochord. Genetic evidence has suggested that there may be an increasing demand for T gene function along the rostrocaudal axis. Experiments reported here indicate that this may not be the case. Instead, the gradient in severity of the T defect may be caused by defective mesoderm cell movements, which result in a progressive accumulation of mesoderm cells near the primitive streak. Embryonic stem (ES) cells which are homozygous for the T deletion have been isolated and their differentiation in vitro and in vivo compared with that of heterozygous and wild-type ES cell lines. In +/+<-->T/T ES cell chimeras the Brachyury phenotype is not rescued by the presence of wild-type cells and high level chimeras show most of the features characteristic of intact T/T mutants. A few offspring from blastocysts injected with T/T ES cells have been born, several of which had greatly reduced or abnormal tails. However, little or no ES cell contribution was detectable in these animals, either as coat colour pigmentation or by isozyme analysis. Inspection of potential +/+<-->T/T ES cell chimeras on the 11th or 12th day of gestation, stages later than that at which intact T/T mutants die, revealed the presence of chimeras with caudal defects.(ABSTRACT TRUNCATED AT 250 WORDS)