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Background and Aim: Coat color is a phenotypic trait that is affected by many functional genes. In addition, coat color is an important characteristic of breeds in livestock. This study aimed to determine functional genes for coat color patterns in Sumatran native cattle in Indonesia using a genome-wide association study method. Materials and Methods: A bovine single nucleotide polymorphism (SNP) 50K BeadChip was used for the investigation. A total of 46 Sumatran native cattle of three colors as follows: Brown (36 animals), white (9 animals), and black (1 animal), were used as experimental animals. Results: Results showed that the SNP markers ARS-BFGL-NGS-75486 (p = 2.46 × 10-7) and BTB-01992588 (p = 1.06 × 10-5) were selected as two genetic markers for coat color variation in animals under study, which were located at the cytoplasmic FMR1-interacting protein 2 (CYFIP2) gene at BTA7 and small G protein signaling modulator 1(SGSM1) genes at BTA17, respectively. The polymorphic informative content values of both SNP markers were 0.33 (ARSBFGL-NGS-75486) and 0.13 (BTB-01992588). In this study, a genetic marker for coat color patterns in Sumatran native cattle was obtained based on the haplotypes of both SNP markers. Conclusion: It can be concluded that CYFIP2 and SGSM1 are two coloration genes that affect the phenotype characteristics of Sumatran native cattle. [ABSTRACT FROM AUTHOR]

Background: Colored wool from cashmere goats is increasingly popular among consumers, but the transcriptomic differences between coat colors are poorly understood. Objectives: This study aimed to screen for coat color regulation-associated genes in cashmere goats to ascertain their underlying molecular mechanisms. Methods: Transcriptomic sequencing of skin tissues from black (BC), brown (YC), and white cashmere (WC) goats was performed. Immunohistochemistry and western blotting were used to validate SLC24A4 and DCT expression, two essential genes identified for coat color determination. Results: We identified 6,518 differentially expressed genes (DEGs) in the BC vs. WC group (3,919 upregulated, 2,599 downregulated). Next, 5,593 DEGs were identified in the YC vs. WC group (3,629 upregulated, 1,964 downregulated). Finally, 4,538 DEGs were expressed in both groups, with 1,980 and 1,055 DEGs exclusively expressed in either group. Functions and pathways associated with hair color were enriched, including melanosomes, melanocyte migration, melanin biosynthesis processes and functions, and melanogenesis pathways. TYRP1, SLC24A4, PMEL, OCA2, and DCT were significantly upregulated in BC goat skin, while ASIP was significantly upregulated in YC skin. Additionally, KIT, POMC, SLC24A5, Wnt3a, and EDN3 were DEGs for different coat colors. Immunohistochemistry revealed SLC24A4 and DCT expression in dermal papillae, inner and outer root sheaths, and the hair follicle matrix. Western blotting showed that SLC24A4 protein levels were highest in BC goat skin. DCT protein levels were also highest in BC goat skin, albeit not significantly. Conclusion: These results further our understanding of coat color regulation in cashmere goats, establishing a foundation for their molecular breeding. [ABSTRACT FROM AUTHOR]

Cattle coat color is governed by numerous genes, notably the tyrosinase gene (TYR). This study analyzed coat color anomalies like albinism and white spotting in Bali cattle. It aims to discern the TYR gene's diversity, expression patterns, and correlation with coat color abnormalities. The research encompassed 189 cattle, including those with standard coat color (n=53), white-spotted (n=11), and albino (n=17) Bali cattle, as well as Simmental (n=37), Limousin (n=14), Madura (n=21), and Peran-akan Ongole (PO) cattle (n=36). Total DNA was extracted and the TYR gene in exon 1 was amplified using forward and reverse primers with a target amplicon length of 994 bp. Direct sequencing unveiled TYR gene diversity, analyzed using BioEdit and MEGA6 software to identify SNPs. PCR-RFLP was used for SNP genotyping, while qPCR analyzed TYR gene expression. Two mutations (SNP g. 939A>G and SNP g. 887C>T) were discovered in Bali cattle TYR exon 1. SNP g. 939A>G exhibited polymorphism, with the highest GG genotype frequency in standard Bali cattle, indicating a high G allele frequency. Conversely, Madura, Simmental, Limousin, and PO cattle had the lowest allele fre-quency. Chi-square (χ² test) results showed non-significance across all cattle types. TYR gene expres-sion differed significantly between standard Bali cattle and albinos (p

Identifying when kittens are in fearful emotional states is crucial to protecting welfare, preventing behavioral issues, and ensuring caretaker and researcher assessments are accurate. Research is needed to confirm if kittens have fully developed fear responses similar to those of adult cats when they are in situations that evoke fear. To assess which behaviors kittens show when they are avoiding novel and startling stimuli, kittens (5 to 8 weeks old; n = 46) completed trials involving exposure to such stimuli, alternating with blank control trials. Trials were separated into immediate responses (during a short stimulus presentation or equivalent control period), and delayed responses (after stimulus removal). Mixed regression models, with litter and kitten as random intercepts, were used to model durations and frequencies of behaviors. Across both time phases, kittens displayed significantly longer durations of arched back, piloerection, freezing, and tail tucking, shorter durations of eating, and greater rates of putting their ears back during fear trials compared to blank trials. During stimulus presentations, kittens displayed significantly shorter durations of retreating to a hutch and greater rates of flinching, whereas after stimulus removal, kittens displayed significantly longer durations of crouching and shorter durations of upright tail. Responses were also affected by kitten coat color, sex, and being mother-reared. Thus, fear behaviors in 5-to-8-week-old kittens are fully developed and similar to what is observed in adult cats. These results allow for accurate identification of fear in kittens, with the goal of improving research on kitten fear development and kitten welfare.

Objective Coat color is an important characteristic and economic trait in domestic sheep. In this study, we explored the potential mechanisms and the signaling pathways involved in coat color regulation for sheep. Methods Isobaric tags for relative and absolute quantification (iTRAQ) technology was used to catalog global protein expression profiles in skin of sheep with black versus white coat color. Immunofluorescence was used to observe the expression localization of differential protein. Western blot and quantitative real time polymerase chain reaction (qRT-PCR) were used to evaluate their role in the coat color formation of sheep. Results A total of 136 differential proteins were obtained in different coat colors, including 101 up-regulated and 35 down-regulated. Pigmentation function entries were enriched through gene ontology annotation. Tyrosine metabolism and platelet activation signaling pathway were extracted by Kyoto encyclopedia of genes and genomes analysis. Apolipoprotein A-1 (APOA1) and fibrinogen alpha chain (FGA) were found to be critical differential proteins by the interaction of differential proteins in the direct-interaction network diagram. Strikingly, twenty candidate differential proteins were screened, from which beta-actin (ACTB) protein showed higher expression in white sheep skin, while albumin (ALB), APOA1, MAOA (amine oxidase) and FGA proteins showed higher expression in black sheep skin, which was validated by immunofluorescence, western blot, and qRT-PCR. Conclusion This study identified several novel proteins that may be involved in the coat color formation of sheep. The white and black sheep skin proteome profiles obtained provide a valuable resource for future research to understand the network of protein expression controlling skin physiology and melanogenesis in sheep.

Simple Summary: We performed a genome-wide selection sweep analysis on 50 domesticated yaks to investigate the genetic basis of coat color phenotypes. We identified numerous candidate genes (e.g., PLCB1, LEF1, and DTNBP1) that play key roles in melanin synthesis. Unique candidate genes for different coat color groups may explain the variations in coat color. Additionally, a range of selected genes associated with melanin and pigment deposition were identified within the ROH islands. This study provides a solid theoretical basis for understanding yak coat color. Although coat color is an important economic phenotype in domesticated yaks (Bos grunniens), its genetic basis is not yet fully understood. In this study, a genome-wide selective sweep and high-frequency runs of homozygosity (ROH) identification were performed on 50 yaks with different coat colors to investigate candidate genes (CDGs) related to coat color. The results suggested that 2263 CDGs were identified from the 5% interaction windows of the FST and θπ ratio, along with 2801 and 2834 CDGs from black and brown yaks with iHS, respectively. Furthermore, 648 and 691 CDGs from black and brown yaks, which were widely enriched in pathways related to melanogenesis, melanocyte differentiation, and melanosome organization via GO and KEGG functional enrichment, respectively, were confirmed on the basis of the intersection of three parameters. Additionally, the genome of brown yaks presented more ROH, longer ROH fragments, and higher inbreeding levels than those of black yaks. Specifically, a large number of genes related to melanin synthesis and regulation (e.g., UST, TCF25, and AHRR) from the ROH islands were confirmed to be under strong selection. In summary, the results of this study enhance the understanding of the genetic basis for determining yak coat color. [ABSTRACT FROM AUTHOR]

Cats with a distinctive white hair pattern of unknown molecular cause have been discovered in the Finnish domestic cat population. Based on the unique appearance of these cats, we have named this phenotype salmiak ("salty licorice"). The use of a commercially available panel test to genotype four salmiak‐colored cats revealed the absence of all known variants associated with white‐haired phenotypic loci: full White (W), Spotting (Ws) and the Birman white Gloves associated (wg) allele of the KIT proto‐oncogene (KIT) gene. Whole‐genome sequencing on two salmiak‐colored cats was conducted to search for candidate causal variants in the KIT gene. Despite a lack of coding variants, visual inspection of the short read alignments revealed a large ~95 kb deletion located ~65 kb downstream of the KIT gene in the salmiak cats. Additional PCR genotyping of 180 domestic cats and three salmiak‐colored cats confirmed the homozygous derived variant genotype fully concordant with the salmiak phenotype. We suggest the newly identified variant be designated as wsal for "w salmiak". [ABSTRACT FROM AUTHOR]

Four dominant coat color phenotypes are found in fallow deer (Dama dama). Brown is the most common. Black, menil, and white occur with varying frequencies. In order to gain insights into the molecular genetic background of these phenotypes, 998 fallow animals (772 brown, 62 black, 126 menil, and 38 white) were examined for mutations in the ASIP, MC1R, TYR, and SLC45A2 genes. In ASIP, two mutations (ASIP-M-E2, located at the boundary from exon 2 to intron 2; and ASIP-M-E3, an InDel of five nucleotides) were found, leading to black fallow deer being either homozygous or heterozygous in combination. There were also two mutations found in MC1R. Whereby the mutation MC1R-M1 (leucine to proline, L48P) homozygous leads to a white coat, while the mutation MC1R-M2 (glycine to aspartic acid, G236D) homozygous is associated with the menil phenotype. When both mutations occur together in a heterozygous character state, it results in a menil coat. Since the mutations in the two genes are only present alternatively, 36 genotypes can be identified that form color clusters to which all animals can be assigned. No mutations were found in the TYR and SLC45A2 genes. Our investigations demonstrate that the four dominant coat colors in fallow deer can be explained by ASIP and MC1R mutations only. [ABSTRACT FROM AUTHOR]

Simple Summary: At birth, wild boars and their hybrid offspring usually have camouflage coat colors with juvenile stripes (the black/dark longitudinal stripes separated by yellow/light ones) on their back and two side flanks, and the juvenile stripes disappear at 4–5 months old. To study the mechanism of juvenile stripe maintenance, piglets with juvenile stripes were produced by crossing a wild boar with three Duroc sows. Through picture recording and pigment extraction, we observed that the stripe tended to disappear within approximately 70 days. Furthermore, whole-transcriptome comparison between two adjacent stripes (dark and light) on the back revealed that ZIC4, ssc-miR-532-3p and ENSSSCG00000056225 might play a role in the formation of stripes. The present study laid the foundation for future research on the molecular mechanisms underlying juvenile stripes. Coloration is a crucial trait that allows species to adapt and survive in different environments. Wild boars exhibit alternating black (dark) and yellow (light) longitudinal stripes on their back during their infancy (juvenile stripes), and as adults, they transform into uniform wild-type coat color. Aiming to record the procedure of juvenile stripes disappearing, piglets (WD) with juvenile stripes were produced by crossing a wild boar with Duroc sows, and photos of their coat color were taken from 20 d to 220 d. The pigments in the hairs from the black and yellow stripes were determined. Furthermore, the differentially expressed genes between the black and yellow stripes were investigated in 5 WD with the age of 30 d using whole-transcriptome sequencing to explore the genetic mechanism of the juvenile stripes. The juvenile stripes started to disappear at about 70 d, and stripes were not distinguished with the naked eye at about 160 d; that is, the juvenile stripe completely disappeared. A hotspot of a differentially expressing (DE) region was found on chromosome 13, containing/covering 2 of 13 DE genes and 8 of 10 DE lncRNAs in this region. A network among ZIC4, ssc-miR-532-3p, and ENSSSCG00000056225 might regulate the formation of juvenile stripes. Altogether, this study provides new insights into spatiotemporal coat color pattern. [ABSTRACT FROM AUTHOR]

Introduction1: Sheep are the main source of wool and its fiber characteristics, such as diameter, length, and color, which are determined by genetics and environmental factors, are key features in the economic value of sheep wool. In sheep, white wool has the highest economic value due to its dyeability. Therefore, identifying the mechanisms responsible for coat color determination is very important from an economic perspective. In general, the coat color is determined based on the amounts and types of melanin produced and released by the melanocytes in the skin tissue (Ito et al., 2000). The genetic basis and genes involved in coat color are well understood in rodents, although many of these genes are incorporated in coat color regulation in other species; including Sheep also have a common role. In Iran, the Lori Bakhtiari sheep is one of the most important breeds of sheep in terms of the use of its wool in the textile and carpet industries. In his breed, the dominant coat of the wool is white, although sometimes a percentage of dark brown and pale brown is also observed (Saadat Nouri, M. & Siah Mansour, 1368). However, in this breed, some animals have black spots on their coat, which leads to a decrease in wool quality. Since MC1R, ASIP, KLF4 and MITF genes play an important role in controlling and determining coat color in mammals, the purpose of this study was to investigate the expression of these genes in two phenotypes of white and black spots in the skin tissue of Lori Bakhtiari sheep. Materials and Methods: Skin samples were obtained from both white and dark parts of 14 white-coated sheep with black spots and total RNA was extracted. The quality and quantity of extracted RNAs were evaluated by agarose gel electrophoresis and spectrophotometer. Extracted RNA samples were exposed to DNase1 enzyme digestion to remove the possible contamination of genomic DNA. Also, the quality of synthesized cDNA was evaluated using 1% agarose gel. In this research, in order to amplify a fragment of the studied genes, using the mRNA sequence of these genes in the GenBank database, appropriate primers were designed by Primer3plus software. To evaluate the relative expression of the target genes, β-actin and GAPDH genes were used as reference genes to normalize the data. Finally, BestKeeper and REST 2009 V2.0.13 software were used for the analysis of gene expression data. Results and Discussion: Based on the descriptive results of Ct values, MC1R and MITF genes revealed minimum and maximum expression stability among the target genes in skin samples with standard deviations of 1.34 and 3.62, respectively. In addition, the reference genes (β-actin and GAPDH) showed the highest stability among all the studied genes. No significant differences were observed in mRNA levels of MC1R, ASIP, KLF4, and MITF genes in the spotted skin tissue compared to the white part of the skin (p>0.05). However, the expression of the ASIP gene was more than 2 times in the spotted part compared to the white skin, but this difference was not significant (p=0.21). In addition, the MC1R gene showed minimum expression differences in black spots and white parts of the skin tissue. In addition, the MITF and MC1R genes showed the highest and lowest levels of expression in skin samples of Lori Bakhtiari breed sheep with average Ct of 25.86 and 30.42, respectively. However, among all the studied genes, the lowest mRNA level was observed for the GAPDH gene with an average Ct of 35.96. Conclusion: Mammalian coat color results from various factors such as the degree and distribution of melanin pigment and the interaction between genotype and environment (B. Li et al., 2018). In addition, melanogenesis is a complex process that includes melanocyte growth, melanosome formation, melanin synthesis, melanin transport, and melanosome release (Ito & Wakamatsu, 2011). According to the conducted studies, a large number of genes are involved in the mechanism of coat color determination, but two genes, MC1R and ASIP, play an essential role in the regulation and control of coat color (Searle, 1968). In our study, no significant difference was observed in the expression of MC1R, ASIP, KFL4, and MITF genes in the spotted compared to the white part of the skin tissue in Lori Bakhtiari sheep. These results showed that the development of skin spots is not under the control of the studied genes in Lori Bakhtiari sheep, and genes or other factors can play roles in the creation of dark spots in this breed. [ABSTRACT FROM AUTHOR]

Taurine and indicine gray cattle represent relevant livestock resources in many countries of the world. A gray coat color and pigmented skin, which are common in most of the gray cattle breeds, have been demonstrated to confer better adaptation to solar radiation and thermal stresses. In a previous study adopting the FST-outlier approach with BayeScan v2.0, we identified differentially selected genomic regions in a set of gray cattle breeds, including the Podolica Italiana, and contrasted these findings with four non-gray cattle breeds. More supported signals were detected on bovine chromosomes (BTAs) 2, 4, 14, and 26 that encompassed more than fifty genes known to be directly or indirectly related to one or more steps in pigment biology. In the present study, we aimed to validate the previously observed signals using the same methodological approach on three new Podolica Italiana sample sets (N = 30 animals each). These animals were selected from the ANABIC genetic station during performance tests as being representative of the Podolica Italiana population at three different timeframes separated by approximately 10 years each. We typed these samples to the loci of 23,027 quality-controlled single-nucleotide polymorphisms. We also analyzed the dataset using the haplotype-based approach available in hapFLK v1.4 software. Both the FST-outlier and hapFLK approaches validated the abovementioned signals on BTAs 2, 4, 14, and 26. Moreover, both methods detected additional supported regions on BTAs 7 and 18 that included a total of 42 genes, of which most were already known from literature to be implicated in pigmentation traits.

The variability of camel hair fibers physical-mechanical properties across sampling body areas and phaneroptics continue to be relatively unexplored topics in scientific literature. With the aim to valorize camel hair fibers, the present investigation has examined, through discriminant canonical analysis, fiber properties of Canarian camel hair regarding the body region sampled by comparing them with Merino sheep wool, world’s most demanded textile fiber. Additionally, camel hair attribute differences depending on phaneroptics such as coat or eye color and particularities have been determined. Diameter at the base of the fiber is higher for adult camels and increases from the mid-region to the back of the animal. Besides, the highest variability in both staple length and mean diameter was found for camel shoulder and hump fibers. Camel tail dock was the region with the finest fibers but also the one accounting for the highest percentage of residual dirt. Coat color and particularities were unlikely to significantly (p

Introduction: Sheep are the main source of wool and its fiber characteristics, such as diameter, length, and color, which are determined by genetics and environmental factors, are key features in the economic value of sheep wool. In sheep, white wool has the highest economic value due to its dyeability, thus, the identification of mechanisms responsible for coating color determination is very important from an economic point of view. In general, the coat color is determined based on the amounts and types of melanin produced and released by the melanocytes in the skin tissue (Ito et al., 2000). The genetic basis and genes involved in coat color are well understood in rodents, although many of these genes are incorporated in coat color regulation in other species; including Sheep also have a common role. In Iran, the Lori Bakhtiari sheep is one of the most important breeds of sheep in terms of the use of its wool in the textile and carpet industries. In his breed, the dominant coat of the wool is white, although sometimes a percentage of dark brown and pale brown is also observed (Saadat Nouri, M. & Siah Mansour, 1368). However, in this breed, some animals have black spots on their coat, which leads to a decrease in wool quality. Since MC1R, ASIP, KLF4 and MITF genes play an important role in controlling and determining coat color in mammals, the purpose of this study was to investigate the expression of these genes in two phenotypes of white and black spots in the skin tissue of Lori Bakhtiari sheep.Materials and Methods: Skin samples were obtained from both white and dark parts of 14 white-coated sheep with black spots and total RNA was extracted. The quality and quantity of extracted RNAs were evaluated by agarose gel electrophoresis and spectrophotometer. Extracted RNA samples were exposed to DNase1 enzyme digestion to remove the possible contamination of genomic DNA. Also, the quality of synthesized cDNA was evaluated using 1% agarose gel. In this research, in order to amplify a fragment of the studied genes, using the mRNA sequence of these genes in the GenBank database, appropriate primers were designed by Primer3plus software. To evaluate the relative expression of the target genes, β-actin and GAPDH genes were used as reference genes to normalize the data. Finally, BestKeeper and REST 2009 V2.0.13 software were used for the analysis of gene expression data.Results and Discussion: Based on the descriptive results of Ct values, MC1R and MITF genes revealed minimum and maximum expression stability among the target genes in skin samples with standard deviations of 1.34 and 3.62, respectively. In addition, the reference genes (β-actin and GAPDH) showed the highest stability among all the studied genes. No significant differences were observed in mRNA levels of MC1R, ASIP, KLF4, and MITF genes in the spotted skin tissue compared to the white part of the skin (p>0.05). However, the expression of the ASIP gene was more than 2 times in the spotted part compared to the white skin, but this difference was not significant (p=0.21). In addition, the MC1R gene showed minimum expression differences in black spots and white parts of the skin tissue. In addition, the MITF and MC1R genes showed the highest and lowest levels of expression in skin samples of Lori Bakhtiari breed sheep with average Ct of 25.86 and 30.42, respectively. However, among all the studied genes, the lowest mRNA level was observed for the GAPDH gene with an average Ct of 35.96.Conclusion: Mammalian coat color results from various factors such as the degree and distribution of melanin pigment and the interaction between genotype and environment (B. Li et al., 2018). In addition, melanogenesis is a complex process that includes melanocyte growth, melanosome formation, melanin synthesis, melanin transport, and melanosome release (Ito & Wakamatsu, 2011). According to the conducted studies, a large number of genes are involved in the mechanism of coat color determination, but two genes, MC1R and ASIP, play an essential role in the regulation and control of coat color (Searle, 1968). In our study, no significant difference was observed in the expression of MC1R, ASIP, KFL4, and MITF genes in the spotted compared to the white part of the skin tissue in Lori Bakhtiari sheep. These results showed that the development of skin spots is not under the control of the studied genes in Lori Bakhtiari sheep, and genes or other factors can play roles in the creation of dark spots in this breed.

This study aimed to assess the presence of single nucleotide polymorphisms (SNPs) in the exon 1 region of the tyrosinase (TYR) gene in Bali cattle with abnormal coat color. This study analyzed 43 Bali cattle, 26 individuals with typical or standard coat color, and 17 individuals with albinism. The genetic diversity of the TYR gene was determined via direct sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) techniques. The sequence data of the TYR gene were scrutinized using BioEdit and MEGA10 software to detect single nucleotide polymorphisms (SNPs) related to different types of coat color features in Bali cattle. The genetic diversity information was derived from computations performed using PopGen 1.32 software. The results showed that exon 1 of the TYR gene was affected by the new SNP g.939A>G, which is polymorphic in Bali cattle. In conclusion, the SNP c.939A>G can be further analyzed for use as a candidate-assisted selection (MAS) for abnormal coat color in Bali cattle.

The aim of this study was to identify polymorphisms in the entire coding regions of the Melanocortin 1 Receptor (MC1R) gene and their possible associations with coat color variants of the Black Bengal goat (BBG) of Bangladesh. Forty blood samples representing five distinct color variants of BBG (Solid Black, Toggenburg, Dutch Belt, White and Brown) were collected from Bangladesh Livestock Research Institute, Savar, Dhaka. Two PCR amplicons that harbored entire coding region were sequenced both forward and reverse directions. Multiple sequence alignment identified four single nucleotide polymorphisms (SNPs) based on Capra hircus reference sequence (MT186778.1). Among them, only one was identified as synonymous type (c.183C>T; p.61A) and the remaining three were non-synonymous in nature (c.676A>G, c.748G>T, and c.801C>G), causing amino acid substitutions as p.K226E, p.V250F, and p.C267W, respectively. Twelve haplotypes were defined by four substitutions where four haplotypes (Hap6, Hap7, Hap8, and Hap9) were found white-color goat-specific involving c.801C>G mutation that might be associated with white coat color phenotype of BBG. Furthermore, white goats had the highest haplotype (0.879±0.08) and nucleotide diversity (0.0017±0.0002). The UPGMA phylogenetic tree revealed two separate clusters, one of which included all color variants of BBG and major domestic goat populations (Capra hircus) from various countries. The haplotype sharing features suggest that the coat color phenotypes of BBG were not solely attributable to the MC1R gene. However, more detailed investigation with large samples from diverse populations across the country was required to draw a precise conclusion. [ J Adv Biotechnol Exp Ther 2024; 7(1.000): 95-105]

Simple Summary: Color and body size traits are considered the key parameters influence the economic value of animals. In recent years, advancement in the genetic basis of coat colors in equines has received considerable attention among animal breeders. In addition, coat color plays a significant role in breed identification and selection, as well as animal health and disease. The current review concisely provides information on the role of melanin pigments and key candidate genes associated with coat color phenotypes in equines. Furthermore, the review also highlights the importance of coat color in equine breeding and health. Variation in coat color among equids has attracted significant interest in genetics and breeding research. The range of colors is primarily determined by the type, concentration, and distribution of melanin pigments, with the balance between eumelanin and pheomelanin influenced by numerous genetic factors. Advances in genomic and sequencing technologies have enabled the identification of several candidate genes that influence coat color, thereby clarifying the genetic basis of these diverse phenotypes. In this review, we concisely categorize coat coloration in horses and donkeys, focusing on the biosynthesis and types of melanin involved in pigmentation. Moreover, we highlight the regulatory roles of some key candidate genes, such as MC1R, TYR, MITF, ASIP, and KIT, in coat color variation. Moreover, the review explores how coat color relates to selective breeding and specific equine diseases, offering valuable insights for developing breeding strategies that enhance both the esthetic and health aspects of equine species. [ABSTRACT FROM AUTHOR]

Camouflage expressed by animals is an adaptation to local environments that certain animals express to maximize survival and fitness. Animals at higher latitudes change their coat color according to a seasonally changing environment, expressing a white coat in winter and a darker coat in summer. The timing of molting is tightly linked to the appearance and disappearance of snow and is mainly regulated by photoperiod. However, due to climate change, an increasing mismatch is observed between the coat color of these species and their environment. Here, we conducted an experiment in northern Sweden, with white and brown decoys to study how camouflage (mis)‐match influenced (1) predator attraction to decoys, and (2) predation events. Using camera trap data, we showed that mismatching decoys attracted more predators and experienced a higher likelihood of predation events in comparison to matching decoys, suggesting that camouflage mismatched animals experience increased detection by predators. These results provide insight into the function of a seasonal color coat and the need for this adaptation to maximize fitness in an environment that is exposed to high seasonality. Thus, our results suggest that, with increasing climate change and reduced snow cover, animals expressing a seasonal color coat will experience a decrease in survival. Research Highlights: Camouflage mismatched decoys attracted more predators in comparison to camouflage matched decoys.Camouflage mismatched decoys experienced a higher likelihood and faster occurrence of predator events than matched decoys. [ABSTRACT FROM AUTHOR]

The coat color phenotype 'sable' occurs in the English Cocker Spaniel dog breed. It closely resembles other canine color patterns known as domino/grizzle/pied (eA allele) and grizzle/domino (eG allele) determined by variants in the melanocortin 1 receptor gene (MC1R; 'extension' or E locus), a key multi‐allele regulator of coat color. We examined genetic variation in MC1R, and found one new non‐synonymous variant, c.250G>A (p.(Asp84Asn)), consistently associated with the English Cocker Spaniel 'sable' phenotype. We propose calling this newly identified allele eH and further show that the eA, eH and eG (previously known as EG) alleles associate with similar phenotypes in dogs impacting genotypes regulated by beta‐defensin 103 gene (CBD103; K locus) and agouti signaling protein gene (ASIP; A locus) in the absence of the EM and E alleles. This suggests that all three alleles are putative reduced‐function variants of the MC1R gene. We propose the revised and updated E locus dominance hierarchy to be EM > E > eA/eH/eG > e1–3. [ABSTRACT FROM AUTHOR]

Pigment production and distribution is controlled through multiple genes, resulting in a wide range of coat color phenotypes in dogs. Dogs that produce only the pheomelanin pigment vary in intensity from white to deep red. The Poodle breed has a wide range of officially recognized coat colors, including the pheomelanin-based white, cream, apricot, and red coat colors, which are not fully explained by the previously identified genetic variants involved in pigment intensity. Here, a genome-wide association study for pheomelanin intensity was performed in Poodles which identified an association on canine chromosome 18. Whole-genome sequencing data revealed an SNN retrocopy insertion (SNNL1) in apricot and red Poodles within the associated region on chromosome 18. While equal numbers of melanocytes were observed in all Poodle skin hair bulbs, higher melanin content was observed in the darker Poodles. Several genes involved in melanogenesis were also identified as highly overexpressed in red Poodle skin. The most differentially expressed gene however was GPR22, which was highly expressed in red Poodle skin while unexpressed in white Poodle skin (log2 fold change in expression 6.1, P

Abstract Background Jianli pig, a renowned indigenous breed in China, has the characteristics of a two-end black (TEB) coat color, excellent meat quality, strong adaptability and increased prolificacy. However, there is limited information available regarding the genetic diversity, population structure and genomic regions under selection of Jianli pig. On the other hand, the genetic mechanism of TEB coat color has remained largely unknown. Results In this study, the whole genome resequencing of 30 Jianli pigs within a context of 153 individuals representing 13 diverse breeds was performed. The population structure analysis revealed that Jianli pigs have close genetic relationships with the Tongcheng pig breed, their geographical neighbors. Three methods (observed heterozygosity, expected heterozygosity, and runs of homozygosity) implied a relatively high level of genetic diversity and, a low inbreeding coefficient in Jianli compared with other pigs. We used Fst and XP-EHH to detect the selection signatures in Jianli pigs compared with Asian wild boar. A total of 451 candidate genes influencing meat quality (CREBBP, ADCY9, EEPD1 and HDAC9), reproduction (ESR1 and FANCA), and coat color (EDNRB, MITF and MC1R), were detected by gene annotation analysis. Finally, to fine-map the genomic region for the two-end black (TEB) coat color phenotype in Jianli pigs, we performed three signature selection methods between the TEB coat color and no-TEB coat color pig breeds. The current study, further confirmed that the EDNRB gene is a candidate gene for TEB color phenotype found in Chinese pigs, including Jinhua pigs, and the haplotype harboring 25 SNPs in the EDNRB gene may promote the formation of TEB coat color. Further ATAC-seq and luciferase reporter assays of these regions suggest that the 25-SNPs region was a strong candidate causative mutation that regulates the TEB coat color phenotype by altering enhancer function. Conclusion Our results advanced the understanding of the genetic mechanism behind artificial selection, and provided further resources for the protection and breeding improvement of Jianli pigs.

Simple Summary: There are few reports on local pig breeds in Guizhou province. In this work, the population structure, genetic diversity, and selection characteristics of three foreign pig breeds and seven Guizhou local pig breeds were studied. Principal component analysis, adjacent tree analysis, and ADMIXTURE analysis showed that Chinese and Western pig breeds had different ancestral sources. Jianhe White Xiang pig (JHBX) had a distant genetic relationship with the other six local pig breeds in Guizhou province and had unique genetic characteristics. The genetic diversity of the JHBX population was low, and the genetic diversity of the remaining six Chinese native pig populations was generally at a moderate level. In addition, we also screened the candidate genes that affect the coat color phenotype of pigs in Guizhou province through selection signals. Our findings will advance our understanding of the genetic mechanisms underlying these germplasm characteristics. The local pig breeds in Guizhou possess exceptional meat quality, robust adaptability, and resilience to harsh feeding conditions, making them ideal for producing high-quality pork. With over 10 local pig breeds in the region, we focused on 7 specific breeds: Baixi pigs (BX), Congjiang Xiang pigs (CJX), Guanling pigs (GL), Jianhe White Xiang pigs (JHBX), Jiangkou Luobo pigs (JKLB), Kele pigs (KL), and Qiandong Hua pigs (QDH). Unfortunately, these breeds face threats such as introduced species and inbreeding, resulting in a decline in population size and numbers. To better protect and utilize these breeds, we employed genome-wide single-nucleotide polymorphism (SNP) markers to investigate the population structure, genetic diversity, and selection characteristics of 283 pigs across these seven breeds. Our findings revealed distinct ancestral sources between Chinese and Western pig breeds, as demonstrated by principal component analysis, adjacent tree analysis, and ADMIXTURE analysis. Notably, JHBX exhibited a distant genetic relationship from the other six local pig breeds in Guizhou province, showcasing unique genetic characteristics. While the genetic diversity of the six Chinese native pig populations, excluding JHBX, was generally moderate in Guizhou province, the JHBX population displayed low genetic diversity. Therefore, it is imperative to intensify selection efforts to prevent inbreeding decline in JHBX while further enhancing the protection measures for the other six pig populations. Additionally, we identified candidate genes influencing the size disparity among pigs in Guizhou province through signal selection. Our study outcomes serve as a reference for developing effective conservation and utilization plans for pig breeds in Guizhou province and deepen our understanding of the genetic mechanisms underlying pig body size. [ABSTRACT FROM AUTHOR]

Simple Summary: The understanding of coat color genetics in the domestic horse has advanced largely in the last few years. Specifically, many alleles influencing equine white spotting have been described in the last few decades. White spotting phenotypes can range from small white facial spots to an entirely white horse. Although white markings may be the most obvious phenotype, many white-causing alleles also cause adverse health defects, including sterility, deafness, and blindness. Many white spotting alleles are considered embryonic lethal in the homozygous state, causing obstacles in the breeding process. This review aims to concisely summarize recent research related to the genetics of equine white spotting phenotypes. 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. [ABSTRACT FROM AUTHOR]

Dezhou donkey is one of the representative local breeds in China, which is mainly divided into two strains: Sanfen and Wutou. There are obvious differences in coat color between the two strains. The former shows light points around the eyes, around the muzzle and under the belly, while the latter is completely solid black. In this study, genome‐wide association analysis was performed for the differences in coat color traits between the Sanfen (n = 97) and Wutou (n = 108) strains using a novel donkey 40K liquid chip developed based on GenoBaits technology, to identify genomic regions and causal genes that could explain this variation. We also used FST and The cross‐population composite likelihood ratio test (XPCLR) analyses to explore selected regions related to coat color differences. We identified one significant region on chromosome 15, with the most significant SNP located within the agouti signaling protein (ASIP) gene. At the same time, both FST and XPCLR methods detected the same selected region on chromosome 15, and ASIP was the gene with the strongest signal. ASIP and melanocortin 1 receptor (MC1R) control the ratio of eumelanin to pheomelanin through their protein activity. They are deeply involved in the process of melanosome organation and melanogenesis, thus affecting mammals' coat color variation. We used a range of genome‐wide approach to identify the genetic basis of coat color variation in Dezhou donkeys. The results provide a supplement to the color variation study in Chinese donkeys at the genome‐wide level, and preliminarily verified the reliability of the Molbreeding Donkey No. 1 40K liquid chip. [ABSTRACT FROM AUTHOR]

Abstract Background Coat color, as a distinct phenotypic characteristic of pigs, is often subject to preference and selection, such as in the breeding process of new breed. Shanxia long black pig was derived from an intercross between Berkshire boars and Licha black pig sows, and it was bred as a paternal strain with high-quality meat and black coat color. Although the coat color was black in the F1 generation of the intercross, it segregated in the subsequent generations. This study aims to decode the genetic basis of coat color segregation and develop a method to distinct black pigs from the spotted in Shanxia long black pig. Results Only a QTL was mapped at the proximal end of chromosome 6, and MC1R gene was picked out as functional candidate gene. A total of 11 polymorphic loci were identified in MC1R gene, and only the c.67_68insCC variant was co-segregating with coat color. This locus isn’t recognized by any restriction endonuclease, so it can’t be genotyped by PCR-RFLP. The c.370G > A polymorphic locus was also significantly associated with coat color, and has been in tightly linkage disequilibrium with the c.67_68insCC. Furthermore, it is recognized by BspHI. Therefore, a PCR-RFLP method was set up to genotype this locus. Besides the 175 sequenced individuals, another more 1,391 pigs were genotyped with PCR-RFLP, and all of pigs with GG (one band) were black. Conclusion MC1R gene (c.67_68insCC) is the causative gene (mutation) for the coat color segregation, and the PCR-RFLP of c.370G > A could be used in the breeding program of Shanxia long black pig.

Although coat color is an important economic phenotype in domesticated yaks (Bos grunniens), its genetic basis is not yet fully understood. In this study, a genome-wide selective sweep and high-frequency runs of homozygosity (ROH) identification were performed on 50 yaks with different coat colors to investigate candidate genes (CDGs) related to coat color. The results suggested that 2263 CDGs were identified from the 5% interaction windows of the FST and θπ ratio, along with 2801 and 2834 CDGs from black and brown yaks with iHS, respectively. Furthermore, 648 and 691 CDGs from black and brown yaks, which were widely enriched in pathways related to melanogenesis, melanocyte differentiation, and melanosome organization via GO and KEGG functional enrichment, respectively, were confirmed on the basis of the intersection of three parameters. Additionally, the genome of brown yaks presented more ROH, longer ROH fragments, and higher inbreeding levels than those of black yaks. Specifically, a large number of genes related to melanin synthesis and regulation (e.g., UST, TCF25, and AHRR) from the ROH islands were confirmed to be under strong selection. In summary, the results of this study enhance the understanding of the genetic basis for determining yak coat color.

Coloration is a crucial trait that allows species to adapt and survive in different environments. Wild boars exhibit alternating black (dark) and yellow (light) longitudinal stripes on their back during their infancy (juvenile stripes), and as adults, they transform into uniform wild-type coat color. Aiming to record the procedure of juvenile stripes disappearing, piglets (WD) with juvenile stripes were produced by crossing a wild boar with Duroc sows, and photos of their coat color were taken from 20 d to 220 d. The pigments in the hairs from the black and yellow stripes were determined. Furthermore, the differentially expressed genes between the black and yellow stripes were investigated in 5 WD with the age of 30 d using whole-transcriptome sequencing to explore the genetic mechanism of the juvenile stripes. The juvenile stripes started to disappear at about 70 d, and stripes were not distinguished with the naked eye at about 160 d; that is, the juvenile stripe completely disappeared. A hotspot of a differentially expressing (DE) region was found on chromosome 13, containing/covering 2 of 13 DE genes and 8 of 10 DE lncRNAs in this region. A network among ZIC4, ssc-miR-532-3p, and ENSSSCG00000056225 might regulate the formation of juvenile stripes. Altogether, this study provides new insights into spatiotemporal coat color pattern.

Objective Pigment production and distribution are controlled through multiple proteins, resulting in different coat color phenotypes of sheep. Methods The expression distribution of vimentin (VIM) and transthyretin (TTR) in white and black sheep skins was detected by liquid chromatography–electrospray ionization tandem MS (LC–ESI–MS/MS), gene ontology (GO) statistics, immunohistochemistry, Western blot, and quantitative real time polymerase chain reaction (qRT-PCR) to evaluate their role in the coat color formation of sheep. Results LC–ESI–MS/MS results showed VIM and TTR proteins in white and black skin tissues of sheep. Meanwhile, GO functional annotation analysis suggested that VIM and TTR proteins were mainly concentrated in cellular components and biological process, respectively. Further research confirmed that VIM and TTR proteins were expressed at significantly higher levels in black sheep skins than in white sheep skins by Western blot, respectively. Immunohistochemistry notably detected VIM and TTR in hair follicle, dermal papilla, and outer root sheath of white and black sheep skins. qRT-PCR results also revealed that the expression of VIM and TTR mRNAs was higher in black sheep skins than in white sheep skins. Conclusion The expression of VIM and TTR were higher in black sheep skins than in white sheep skins and the transcription and translation were unanimous in this study. VIM and TTR proteins were expressed in hair follicles of white and black sheep skins. These results suggested that VIM and TTR were involved in the coat color formation of sheep.

Objective: The goal of this study was to characterize and investigate the effect of single nucleotide polymorphisms (SNPs) or InDels in tyrosinase related protein 1 (TYRP1), dopachrome tautomerase (DCT), and Ras-related protein 38 (RAB38) genes on coat color in South American camelids. TYRP1 is among one of the major regulators of pigmentation in mammals. DCT is a pigment cell-specific gene that plays an important role in the melanin synthesis pathway and the expression of skin color. RAB38 is involved in the transport of tyrosinase (TYR) and TYRP1, which are key enzymes in melanin production. Methods: Five fleece color tones from 327 alpacas (white, black, brown, gray and light fawn) were investigated to characterize and identify polymorphisms that play a role in coat color. Among the SNPs and Indels identified in the coding region, statistical analysis was performed to determine the association between the polymorphisms and fleece color in camelids, as well as the determination of allelic frequencies. Results: Twenty two polymorphisms in the coding region, seven of them were nonsynonymous, eleven were synonymous, three located in the 5’UTR region and one deletion in the 3’UTR region were identified in the TYRP1 gene; in the DCT gene were identified twenty two polymorphisms, where five of them were non-synonymous, twelve were synonymous, one polymorphism in the 5’UTR region and four in the 3’UTR region; in adition, in the RAB38 gene six polymorphisms were identified, one was nonsynonymous, two were synonymous, in addition to three polymorphisms in the 3’UTR region were found in the RAB38 gene. There were low to moderate polymorphisms in the populations. Significant differences (P<0.001) were found with color fiber in the alpaca populations studied for TYRP1 and DCT genes. [ABSTRACT FROM AUTHOR]

The identification of candidate genes related to pigmentation and under selective sweep provides insights into the genetic basis of pigmentation and the evolutionary forces that have shaped this variation. The selective sweep events in the genes responsible for normal coat color in Indian cattle groups are still unknown. To find coat color genes displaying signs of selective sweeps in the indigenous cattle, we compiled a list of candidate genes previously investigated for their association with coat color and pigmentation. After that, we performed a genome-wide scan of positive selection signatures using the BovineSNP50K Bead Chip in 187 individuals of seven indigenous breeds. We applied a wide range of methods to find evidence of selection, such as Tajima's D, CLR, iHS, varLD, ROH, and FST. We found a total of sixteen genes under selective sweep, that were involved in coat color and pigmentation physiology. These genes are CRIM1 in Gir, MC1R in Sahiwal, MYO5A, PMEL and POMC in Tharparkar, TYRP1, ERBB2, and ASIP in Red Sindhi, MITF, LOC789175, PAX3 and TYR in Ongole, and IRF2, SDR165 and, KIT in Nelore, ADAMTS19 in Hariana. These genes are related to melanin synthesis, the biology of melanocytes and melanosomes, and the migration and survival of melanocytes during development. [ABSTRACT FROM AUTHOR]

Simple Summary: Coat color and birth weight are important traits in beef cattle and have a significant impact on breed identification and adult body weight. In this study, genome-wide association analysis (GWAS) of Simmental × Holstein (F1) crossbred cattle revealed that calves with lighter coat color had higher birth weight. Further analysis indicated that mutations in the premelanosome protein (PMEL) gene resulted in a lighter coat color, while the birth weights of individuals heterozygous for this gene were significantly higher than those of the pure genotype. Therefore, mutations in PMEL can result in a lighter coat color, and lighter coat color may, thus, have a selective effect on calf birth weight. Coat color and birth weight, as easily selected traits in cattle, play important roles in cattle breeding. Therefore, we carried out a genome-wide association study on birth weight and coat color to identify loci or potential linkage regions in 233 Simmental × Holstein crossbred beef cattle. The results revealed that nine SNPs were significantly associated with coat color (rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, PMEL_1, rs134930689, rs383170073, rs109924971, and rs109146332), and these were in RNF41, ZC3H10, ERBB3, PMEL, and OR10A7 on BTA5. Interestingly, rs137169378, rs110022687, rs136002689, Hypotrichosis_PMel17, and PMEL_1 showed strong linkage disequilibrium (r2 > 0.8) and were significantly associated with coat color. Notably, Hypotrichosis_PMel17 and PMEL_1 were located in the gene PMEL (p = 2.22 × 10−18). Among the five significant SNPs associated with coat color, the birth weight of heterozygous individuals (AB) was greater than that of homozygous individuals (AA). Notably, the birth weight of heterozygous individuals with Hypotrichosis_PMel17 and PMEL_1 genotypes was significantly greater than that of homozygous individuals (0.01 < p < 0.05). Interestingly, the two loci were homozygous in black/white individuals and heterozygous in gray/white individuals, and the birth weight of heterozygous brown/white individuals (43.82 ± 5.25 kg) was greater than that of homozygous individuals (42.58 ± 3.09 kg). The birth weight of calves with the parental color (41.95 ± 3.53 kg) was significantly lower than that of calves with a non-parental color (43.54 ± 4.78 kg) (p < 0.05), and the birth weight of gray/white individuals (49.40 ± 7.11 kg) was the highest. Overall, PMEL appears to be a candidate gene affecting coat color in cattle, and coat color may have a selective effect on birth weight. This study provides a foundation for the breeding of beef cattle through GWAS for coat color and birth weight. [ABSTRACT FROM AUTHOR]

The transcriptome data of skin cells from domestic cats with brown, orange, and white coats were analyzed using a public database to investigate the possible relationship between coat color‐related gene expression and squamous cell carcinoma risk, as well as the mechanism of deafness in white cats. We found that the ratio of the expression level of genes suppressing squamous cell carcinoma to that of genes promoting squamous cell carcinoma might be considerably lower than the theoretical estimation in skin cells with orange and white coats in white‐spotted cat. We also found the possibility of the frequent production of KIT lacking the first exon (d1KIT) in skin cells with white coats, and d1KIT production exhibited a substantial negative correlation with the expression of SOX10, which is essential for melanocyte formation and adjustment of hearing function. Additionally, the production of d1KIT was expected to be due to the insulating activity of the feline endogenous retrovirus 1 (FERV1) LTR in the first intron of KIT by its CTCF binding sequence repeat. These results contribute to basic veterinary research to understand the relationship between cat skin coat and disease risk, as well as the underlying mechanism. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: Coat color, as a distinct phenotypic characteristic of pigs, is often subject to preference and selection, such as in the breeding process of new breed. Shanxia long black pig was derived from an intercross between Berkshire boars and Licha black pig sows, and it was bred as a paternal strain with high-quality meat and black coat color. Although the coat color was black in the F1 generation of the intercross, it segregated in the subsequent generations. This study aims to decode the genetic basis of coat color segregation and develop a method to distinct black pigs from the spotted in Shanxia long black pig. Results: Only a QTL was mapped at the proximal end of chromosome 6, and MC1R gene was picked out as functional candidate gene. A total of 11 polymorphic loci were identified in MC1R gene, and only the c.67_68insCC variant was co-segregating with coat color. This locus isn't recognized by any restriction endonuclease, so it can't be genotyped by PCR-RFLP. The c.370G > A polymorphic locus was also significantly associated with coat color, and has been in tightly linkage disequilibrium with the c.67_68insCC. Furthermore, it is recognized by BspHI. Therefore, a PCR-RFLP method was set up to genotype this locus. Besides the 175 sequenced individuals, another more 1,391 pigs were genotyped with PCR-RFLP, and all of pigs with GG (one band) were black. Conclusion: MC1R gene (c.67_68insCC) is the causative gene (mutation) for the coat color segregation, and the PCR-RFLP of c.370G > A could be used in the breeding program of Shanxia long black pig. [ABSTRACT FROM AUTHOR]

Feline leishmanial infection is reported worldwide, but the epidemiological role of domestic cats in the leishmaniasis cycle remains unclear, and cats might act as cryptic reservoir hosts in endemic areas with no feline leishmaniosis cases. Considering that, a serological screening for anti-Leishmania spp. antibodies was performed by indirect immunofluorescence antibody test (IFAT) in 389 necropsied cats' serum samples from a new visceral leishmaniasis transmission area with no feline leishmanial infection reported to unveil if the cats are being exposed to the parasite. The overall seroprevalence for Leishmania spp. was 11.05% (43/389). No association was found between sex, neutering status, age group, breed, coat length, feline immunodeficiency virus (FIV) infection, and Leishmania spp. antibody detection. A positive association was found with coat color (cats within the orange spectrum with white [particolor]) (OR = 2.47, CI 95% 1 – 6.13, P = 0.044) and a negative association (OR = 0.38, CI 95% 0.18 – 0.79, P = 0.01) between feline leukemia virus (FeLV) infection and IFAT positivity for Leishmania spp. Therefore, it is concluded that the seroprevalence found was greater than 10%, indicating contact of the protozoan with cats in the region served. [ABSTRACT FROM AUTHOR]

White spotting is an iconic feature of the American Paint Horse. The American Paint Horse Association (APHA) is dedicated to recording pedigree and performance of this stock-type breed, while preserving its distinctive coat color and conformation. Here, the depigmented proportion of the coat (% white coat) was measured using digital photograph analysis of 1195 registered American Paint Horses. Genotypes for nine white-spotting polymorphisms commonly found in Paint Horses, and two pigment-producing loci MCIR and ASIP genes, were also provided by the APHA. White-coat percent significantly increased in horses with more white-spotting alleles present, regardless of the number of loci bearing those alleles, likely due to a strong additive genetic effect at each white-spotting locus, as well as an additive epistatic effect among white spotting loci. Paint Horses with a chestnut base coat color (genotype e/e at MC1R) possessed a significantly higher white coat percentage, suggesting confirming an epistatic interaction between pigmentation signaling genes and loci for white spotting. The APHA registry categories of Regular versus Solid Paint-Bred also differed in their median white coat percentage (p < 0.0001), but not in the overall ranges of this phenotype, reenforcing the importance of the regional patterns of the depigmentation in the definition of the desired APHA phenotype. Multi-locus phenotype prediction models for white-coat percentage performed only moderately well, and improvements in the sample size and the number of loci genotyped will likely be needed before such an approach could be used practically by APHA breeders. In the future, models that enable phenotype prediction based on genotypes, and automated phenotype assessment could increase the production of valuable visual traits in the American Paint Horse population and improve the APHA member experience during the registration process. [ABSTRACT FROM AUTHOR]

This paper represents the fundamental report of the survey of genome-wide changes of four Chinese indigenous donkey breeds, Dezhou (DZ), Guangling (GL), North China (NC), and Shandong Little donkey (SDL), and the findings will prove usefully for identification of biomarkers that perhaps predict or characterize the growth and coat color patterns. Three genomic regions in CYP3A12, TUBGCP5, and GSTA1 genes, were identified as putative selective sweeps in all researched donkey populations. The loci of candidate genes that may have contributed to the phenotypes in body size (ACSL4, MSI2, ADRA1B, and CDKL5) and coat color patterns (KITLG and TBX3) in donkey populations would be found in underlying strong selection signatures when compared between large and small donkey types, and between different coat colors. The results of the phylogenetic analysis, FST, and principal component analysis (PCA) supported that each population cannot clearly deviate from each other, showing no obvious population structure. We can conclude from the population history that the formation processes between DZS and NC, GL, and SDL are completely different. The genetic variants discovered here provide a rich resource to help identify potential genomic markers and their associated molecular mechanisms that impact economically important traits for Chinese donkey breeding programs. [ABSTRACT FROM AUTHOR]

Background and Aim: Coat color variations in cattle are known to be influenced by the melanocortin 1 receptor (MC1R) and receptor tyrosine kinase (KIT) genes. The presence of coat color abnormalities, such as white spots and albinism, in Bali cattle was the focus of this study. This study aimed to identify single nucleotide polymorphisms (SNPs) in the coding region of MC1R and exons 2 and 3 of KIT associated with coat color abnormalities in Bali cattle. Materials and Methods: The study included the analysis of 48 Bali cattle, including 20 individuals with standard coat color, 15 with white spots, and 13 with albinism. Total DNA was extracted using a DNA Extraction Kit, and MC1R (coding region) and KIT (exons 2 and 3) gene amplifications were analyzed using forward and reverse primers with polymerase chain reaction product lengths of 1071, 234, and 448 bp, respectively. The determination of MC1R and KIT gene diversity was analyzed through direct sequencing. Melanocortin 1 receptor and KIT gene sequence data were analyzed using BioEdit and MEGA6 to identify SNPs associated with standard and abnormal coat color phenotypes (white-spotted and albino) in Bali cattle. Results: No SNPs associated with coat color abnormalities were found in the coding region of MC1R and exons 2 and 3 of KIT genes in Bali cattle. However, the intron two regions of KIT contained the SNP g.70208534A>G, which showed a high degree of diversity. The AA genotype frequency was highest in albino Bali cattle, whereas the G allele frequency was highest and the A allele frequency was lowest in white-spotted Bali cattle. Conclusion: The results indicated that standard, white-spotted, and albino coat colors in Bali cattle could not be distinguished by analyzing the MC1R and KIT genes.

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.

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

ObjectiveThe goal of this study was to characterize and investigate the effect of single nucleotide polymorphisms (SNPs) or InDels in tyrosinase related protein 1 (TYRP1), dopachrome tautomerase (DCT), and Ras-related protein 38 (RAB38) genes on coat color in South American camelids. TYRP1 is among one of the major regulators of pigmentation in mammals. DCT is a pigment cell-specific gene that plays an important role in the melanin synthesis pathway and the expression of skin color. RAB38 is involved in the transport of tyrosinase (TYR) and TYRP1, which are key enzymes in melanin production.MethodsFive fleece color tones from 327 alpacas (white, black, brown, gray and light fawn) were investigated to characterize and identify polymorphisms that play a role in coat color. Among the SNPs and Indels identified in the coding region, statistical analysis was performed to determine the association between the polymorphisms and fleece color in camelids, as well as the determination of allelic frequencies.ResultsTwenty two polymorphisms in the coding region, seven of them were nonsynonymous, eleven were synonymous, three located in the 5’UTR region and one deletion in the 3’UTR region were identified in the TYRP1 gene; in the DCT gene were identified twenty two polymorphisms, where five of them were non-synonymous, twelve were synonymous, one polymorphism in the 5’UTR region and four in the 3’UTR region; in adition, in the RAB38 gene six polymorphisms were identified, one was nonsynonymous, two were synonymous, in addition to three polymorphisms in the 3’UTR region were found in the RAB38 gene. There were low to moderate polymorphisms in the populations. Significant differences (P

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Simple Summary: Hair whorls in horses are a hereditary trait that may be associated with various factors, including the temperament or the coat color of the animals. Hair whorls are described as changes in the hair pattern and may take various forms: circular whorls (spirals of hair with a round epicenter) and linear whorls (a line where the hairs span out on both sides from the center, producing an oval shape similar to a feather). The aim of this study is to estimate the frequency and genetic parameters of the number and position of circular and linear hair whorls (on head, body-neck and limbs) of the Pura Raza Española horse according to different factors such as gender, level of inbreeding, birth period and coat color. In this breed, circular whorls are more prevalent than linear whorls, with both showing a relevant symmetry. The laterality of hair whorls has been also evidenced and are most concentrated on the left-hand side. Most horses, particularly gray ones, showed circular hair whorls below the central line of the eyes; in a previous paper, this was associated with a calmer and more docile temperament. Hair whorls have medium-high heritability and can be included in a breeding program due to their relationship with behavior. Hair whorls are a hereditary feature in horses that may be associated with temperament and coat color. Hair whorls are described as changes in the hair pattern and may take various forms, such as circular and linear whorls. We first carried out a frequency analysis of hair whorls (circular and linear). Next, a Generalized Non-Linear Model was computed to assess the significance of some potential influencing factors, and a genetic parameter estimation was performed. ENDOG software v4.8 was used to estimate the inbreeding coefficient of all the animals analyzed. It was more common to find horses with circular hair whorls than with linear whorls. The heritability ranges obtained were, in general, medium-high for both circular whorls (0.20 to 0.90) and linear whorls (0.44 to 0.84). High positive correlations were found on the between left and right positions, indicating a tendency to symmetry in certain locations. The laterality of hair whorls was also evidenced, with the biggest concentration on the left-hand side, particularly in gray horses, showing circular whorls below the central line of eyes, which has been associated in a previous paper with a calmer and more docile temperament. [ABSTRACT FROM AUTHOR]

MiRNAs as a series of small noncoding RNAs that play a crucial part in regulating coat color and hair follicle development. In the previous Solexa sequencing experiments, there were many miRNAs expressed differentially in alpacas with different coat color, including miR-193b.But the mechanism of miR-193b in mammalian pigmentation is still unknown. In this study, bioinformatics analysis showed that WNT10A and GNAI2 might be the target genes of miR-193b. qRT-PCR showed the expression of miR-193b in white Cashmere goats' skins was obviously lower than that in browns, and the expression of WNT10A and GNAI2 were similar with miR-193b. The protein levels of WNT10A and GNAI2 indicated the same findings. Furthermore, the expression of WNT10A and GNAI2 in keratinocytes were analyzed from mRNA and protein levels, the results manifested that the group of overexpression of miR-193b in HaCaT cells increased the expressions of target genes, and miR-193b inhibition group reduced expressions. Luciferase report assays confirmed that the targeting relationship between miR-193b and target genes (WNT10A and GNAI2), the results showed that miR-193b was positively correlated with target genes. These experimental data showed that miR-193b might participate in adjustment of coat color in skin tissue of Cashmere goat by targeting WNT10A and GNAI2. [ABSTRACT FROM AUTHOR]

A structural variant (SV) in the agouti signaling protein gene (ASIP), namely ASIP‐SV1, has been found to strongly correlate with the darkness of hair coat in specific regions of the body of bulls from the zebu (Bos indicus) Nellore breed. Here we visually analyzed the whole‐genome sequence of zebu and taurine (Bos taurus) cattle to elucidate the extent of spread of ASIP‐SV1 in different cattle populations. Of 216 sequences analyzed, 63 zebu (45.9%) and five taurine (6.3%) animals had at least one copy of ASIP‐SV1. Four of the taurine animals presenting the SV were Romagnola cattle, a breed with history of zebu introgression. The remaining taurine animal was a Simmental, a breed frequently used in crossbreeding. These data provide evidence that ASIP‐SV1 is commonly found in zebu populations, in addition to taurine animals with zebu admixture. [ABSTRACT FROM AUTHOR]

Copyright of Acta Scientiarum Polonorum seria Zootechnica is the property of West Pomeranian University of Technology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

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.

Dogs exhibit a wide variety of coat color types, and many genes have been identified that control pigment production, appearance, and distribution. Some breeds, such as the Nova Scotia Duck Tolling Retriever (NSDTR), exhibit variation in pheomelanin pigment intensity that is not explained by known genetic variants. A genome-wide association study comparing light red to dark red in the NSDTR identified a significantly associated region on canine chromosome 15 (CFA 15:23 Mb-38 Mb). Coverage analysis of whole genome sequence data from eight dogs identified a 6 kb copy number variant (CNV) 152 kb upstream of KITLG. Genotyping with digital droplet PCR (ddPCR) confirmed a significant association between an increased copy number with the dark-red coat color in NSDTR (p = 6.1 × 10-7). The copy number of the CNV was also significantly associated with coat color variation in both eumelanin and pheomelanin-based Poodles (p = 1.5 × 10-8, 4.0 × 10-9) and across other breeds. Moreover, the copy number correlated with pigment intensity along the hair shaft in both pheomelanin and eumelanin coats. KITLG plays an important role in melanogenesis, and variants upstream of KITLG have been associated with coat color variation in mice as well as hair color in humans consistent with its role in the domestic dog.

Objective This work was to determine coat inheritance and evaluate production performance for crossbred pigs from Berkshire×Chenghua (BC) compared with Chinese indigenous Chenghua (CH) pigs. Methods The coat color phenotypes were recorded for more than 16,000 pigs, and the genotypes of melanocortin 1 receptor (MCIR) gene were identified by sequencing. The reproductive performance of 927 crossbred BC F4 gilts and 320 purebred CH gilts was recorded. Sixty pigs of each breed were randomly selected at approximately 60 days of age to determine growth performance during fattening period, which lasted for 150 days for BC pigs and 240 days for CH pigs. At the end of the fattening period, 30 pigs of each breed were slaughtered to determine carcass composition and meat quality. Results The coat color of BC pigs exhibits a “dominant black” hereditary pattern, and all piglets derived from boars or sows genotyped ED1ED1 homozygous for MC1R gene showed a uniform black coat phenotype. The BC F4 gilts displayed a good reproductive performance, showing a higher litter and tear size and were heavier at farrowing litter and at weaning litter than the CH gilts, but they reached puberty later than the CH gilts. BC F4 pigs exhibited improved growth and carcass characteristics with a higher average daily live weight gain, lower feed-to-gain ratio, and higher carcass lean meat rate than CH pigs. Like CH pigs, BC F4 pigs produced superior meat-quality characteristics, showing ideal pH and meat-color values, high intramuscular fat content and water-holding capacity, and acceptable muscle-fiber parameters. C18:1, C16:0, C18:0, and C18:2 were the main fatty acids in M. longissimus lumborum in the two breeds, and a remarkably high polyunsaturated/saturated fatty acid ratio of ~0.39 was observed in the BC F4 pigs. Conclusion The BC F4 pigs exhibit a uniform black coat pattern and acceptable total production performance.

Climate change negatively influences the productive and reproductive abilities of goats. There is a need to understand the relationship between heat stress and genes that may aid in the development of climate-resilient goats. Melanism variation in goats plays a role in thermoregulation, in which the melanogenic genes have a pleiotropic effect on the regulation of physiological responses and behavior that are altered due to heat stress in the animals. Thus, the present study was conducted to establish a possible association between the coat color gene (MC1R) and heat stress characteristics. The physiological responses and cortisol levels were recorded in forty different coat-colored goats. The genotyping of the animals revealed four SNPs at the 183rd (C/T), 332nd (C/G), 748th (G/T), and 801st (C/G) positions, among which the black and brown goat populations had novel SNPs at the 332nd position. Eight haplotypes were constructed, and an association study revealed that haplotypes (CCGG, TCGG, and CCTC) that were linked to white animals had lower cortisol values, rectal temperature, skin temperature, and respiration rate. The multivariate and cluster analyses revealed that the white goats were distinct from the rest of the goats. In addition, the docking results revealed the residues that were forming the interaction complex, which could play a role in melanogenesis in the animals and, in turn, the heat stress ability of the goats. Altogether, the results of the present study could pave the way for more research into coat color genes and their relationship with heat stress traits. [ABSTRACT FROM AUTHOR]