A missense mutation in the agouti signaling protein gene (ASIP) is associated with the no light points coat phenotype in donkeys

Coat colour in marsupials: genetic variants at the ASIP locus determine grey and black fur of the brushtail possum

The possession of fur or hair is a defining characteristic of mammals and can occur in a variety of colours and patterns. While genetic determinants of coat colour are well described in eutherian 'placental' mammals, the other major mammalian infraclass, marsupials, is grossly understudied. The fur of the common brushtail possum (Trichosurus vulpecula), an iconic native mammal found throughout Australia and introduced into Aotearoa New Zealand, possesses two main colour morphs: grey and black. To identify genetic variants associated with coat colour, we performed a genome-wide association study (GWAS) with genotype by sequencing (GBS) data. Single nucleotide variants (SNVs) on chromosome 3, close to the agouti signalling protein (ASIP) gene that controls the temporal and spatial distribution of pigments in eutherian mammals, were identified. Fine-mapping identified a C>T variant at chr3:100483705 that results in a ASIP:p.Arg115Cys missense substitution, and animals homozygous for this variant have black fur. In addition to uncovering the first genetic determinant of coat colour in a natural marsupial population, comparative analysis of ASIP in divergent marsupial species identified the dasyurids as having accelerated evolution, reflecting their well described diversity of coat colour and pattern.

Coloration in Equine: Overview of Candidate Genes Associated with Coat Color Phenotypes

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.

TRPM4 gene variation associated with climatic conditions in Chinese cattle

The transient receptor potential (TRP) superfamily has been reported to play an important role in heat tolerance pathways. Based on the Bovine Genome Variation Database and Selective Signatures, a missense mutation (NC_037345.1: c.2237A > G: p. His746Arg) (rs209689836) was identified in the transient receptor potential cation channel subfamily M member 4 (TRPM4) gene, a member of the TRP family, corresponding to heat tolerance. Here, we explored the prevalence of this variant in 19 native Chinese cattle (comprised of 404 individuals) to determine its possible association with heat tolerance in Chinese cattle by using PCR and DNA sequencing. The distribution of alleles of NC_037345.1: c.2237A > G: p. His746Arg displays significant geographical differences across native Chinese cattle breeds, consistent with the distribution of indicine and taurine cattle in China. Additionally, the association analysis indicated that the G allele was significantly associated with mean annual temperature (T), relative humidity (RH) and temperature humidity index (THI) (p < .05), suggesting that cattle carrying allele G were distributed in regions with higher T, RH, and THI. In conclusion, our results suggested that the mutation of the TRPM4 gene in Chinese cattle might be a candidate locus associated with heat tolerance.

Analysis of the genetic loci of pigment pattern evolution in vertebrates

Vertebrate pigmentation patterns are amongst the best characterised model systems for studying the genetic basis of adaptive evolution. The wealth of available data on the genetic basis for pigmentation evolution allows for analysis of trends and quantitative testing of evolutionary hypotheses. We employed Gephebase, a database of genetic variants associated with natural and domesticated trait variation, to examine trends in how cis-regulatory and coding mutations contribute to vertebrate pigmentation phenotypes, as well as factors that favour one mutation type over the other. We found that studies with lower ascertainment bias identified higher proportions of cis-regulatory mutations, and that cis-regulatory mutations were more common amongst animals harbouring a higher number of pigment cell classes. We classified pigmentation traits firstly according to their physiological basis and secondly according to whether they affect colour or pattern, and identified that carotenoid-based pigmentation and variation in pattern boundaries are preferentially associated with cis-regulatory change. We also classified genes according to their developmental, cellular, and molecular functions. We found a greater proportion of cis-regulatory mutations in genes implicated in upstream developmental processes compared to those involved in downstream cellular functions, and that ligands were associated with a higher proportion of cis-regulatory mutations than their respective receptors. Based on these trends, we discuss future directions for research in vertebrate pigmentation evolution.

Whole-genome sequencing reveals the artificial selection and local environmental adaptability of pigeons (Columba livia)

To meet human needs, domestic pigeons (Columba livia) with various phenotypes have been bred to provide genetic material for our research on artificial selection and local environmental adaptation. Seven pigeon breeds were resequenced and can be divided into commercial varieties (Euro-pigeon, Shiqi, Shen King, Taishen, and Silver King), ornamental varieties (High Fliers), and local varieties (Tarim pigeon). Phylogenetic analysis based on population resequencing showed that one group contained local breeds and ornamental pigeons from China, whereas all commercial varieties were clustered together. It is revealed that the traditional Chinese ornamental pigeon is a branch of Tarim pigeon. Runs of homozygosity (ROH) and linkage disequilibrium (LD) analyses revealed significant differences in the genetic diversity of the three types of pigeons. Genome sweep analysis revealed that the selected genes of commercial breeds were related to body size, reproduction, and plumage color. The genomic imprinting genes left by the ornamental pigeon breeds were mostly related to special human facial features and muscular dystrophy. The Tarim pigeon has evolved genes related to chemical ion transport, photoreceptors, oxidative stress, organ development, and olfaction in order to adapt to local environmental stress. This research provides a molecular basis for pigeon genetic resource evaluation and genetic improvement and suggests that the understanding of adaptive evolution should integrate the effects of various natural environmental characteristics.

Detection of Selection Signatures Underlying Production and Adaptive Traits Based on Whole-Genome Sequencing of Six Donkey Populations

Simple Summary

After a long period of artificial selection, the donkey now presents a variety of body types and production performance values. In this experiment, we performed selective signal scanning on the second-generation resequencing data of six different varieties. The regions and candidate genes related to artificial selection were identified to provide reference for future breeding.

Abstract

Donkeys (Equus asinus) are an important farm animal. After long-term natural and artificial selection, donkeys now exhibit a variety of body sizes and production performance values. In this study, six donkey breeds, representing different regions and phenotypes, were used for second-generation resequencing. The sequencing results revealed more than seven million single nucleotide variants (SNVs), with an average of more than four million SNVs per species. We combined two methods, Z-transformed heterozygosity (ZHp) and unbiased estimates of pairwise fixation index (di) values, to analyze the signatures of selection. We mapped 11 selected regions and identified genes associated with coat color, body size, motion capacity, and high-altitude adaptation. These candidate genes included staining (ASIP and KITLG), body type (ACSL4, BCOR, CDKL5, LCOR, NCAPG, and TBX3), exercise (GABPA), and adaptation to low-oxygen environments (GLDC and HBB). We also analyzed the SNVs of the breed-specific genes for their potential functions and found that there are three varieties in the conserved regions with breed-specific mutation sites. Our results provide data to support the establishment of the donkey SNV chip and reference information for the utilization of the genetic resources of Chinese domestic donkeys.

Genomic Characteristics and Selection Signatures in Indigenous Chongming White Goat (Capra hircus)

The Chongming white goat (CM) is an indigenous goat breed exhibits unique traits that are adapted to the local environment and artificial selection. By performing whole-genome re-sequencing, we generated 14-20× coverage sequences from 10 domestic goat breeds to explore the genomic characteristics and selection signatures of the CM breed. We identified a total of 23,508,551 single-nucleotide polymorphisms (SNPs) and 2,830,800 insertion-deletion mutations (indels) after read mapping and variant calling. We further specifically identified 1.2% SNPs (271,713) and 0.9% indels (24,843) unique to the CM breed in comparison with the other nine goat breeds. Missense (SIFT < 0.05), frameshift, splice-site, start-loss, stop-loss, and stop-gain variants were identified in 183 protein-coding genes of the CM breed. Of the 183, 36 genes, including AP4E1, FSHR, COL11A2, and DYSF, are involved in phenotype ontology terms related to the nervous system, short stature, and skeletal muscle morphology. Moreover, based on genome-wide F ST and pooled heterozygosity (Hp) calculation, we further identified selection signature genes between the CM and the other nine goat breeds. These genes are significantly associated with the nervous system (C2CD3, DNAJB13, UCP2, ZMYND11, CEP126, SCAPER, and TSHR), growth (UCP2, UCP3, TSHR, FGFR1, ERLIN2, and ZNF703), and coat color (KITLG, ASIP, AHCY, RALY, and MC1R). Our results suggest that the CM breed may be differentiated from other goat breeds in terms of nervous system owing to natural or artificial selection. The whole-genome analysis provides an improved understanding of genetic diversity and trait exploration for this indigenous goat breed.

Genetics, Evolution, and Physiology of Donkeys and Mules

The genus Equus is made up of donkeys, horses, and zebras. Despite significant variation in chromosome number across these species, interspecies breeding results in healthy, although infertile, hybrid offspring. Most notable among these are the horse-donkey hybrids, the mule and hinny. Donkeys presently are used for everything from companion animals to beasts of burden. Although closely related from an evolutionary standpoint, differences in anatomy and physiology preclude the assumption that they can be treated identically to the domestic horse. Veterinarians should be aware of these differences and adjust their practice accordingly.

Chromosomal Localization of Candidate Genes for Fiber Growth and Color in Alpaca (Vicugna pacos)

The alpaca (Vicugna pacos) is an economically important and cultural signature species in Peru. Thus, molecular genomic information about the genes underlying the traits of interest, such as fiber properties and color, is critical for improved breeding and management schemes. Current knowledge about the alpaca genome, particularly the chromosomal location of such genes of interest is limited and lags far behind other livestock species. The main objective of this work was to localize alpaca candidate genes for fiber growth and color using fluorescence in situ hybridization (FISH). We report the mapping of candidate genes for fiber growth COL1A1, CTNNB1, DAB2IP, KRT15, KRTAP13-1, and TNFSF12 to chromosomes 16, 17, 4, 16, 1, and 16, respectively. Likewise, we report the mapping of candidate genes for fiber color ALX3, NCOA6, SOX9, ZIC1, and ZIC5 to chromosomes 9, 19, 16, 1, and 14, respectively. In addition, since KRT15 clusters with five other keratin genes (KRT31, KRT13, KRT9, KRT14, and KRT16) in scaffold 450 (Vic.Pac 2.0.2), the entire gene cluster was assigned to chromosome 16. Similarly, mapping NCOA6 to chromosome 19, anchored scaffold 34 with 8 genes, viz., RALY, EIF2S2, XPOTP1, ASIP, AHCY, ITCH, PIGU, and GGT7 to chromosome 19. These results are concordant with known conserved synteny blocks between camelids and humans, cattle and pigs.

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

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

Comparative transcriptome analysis reveals the genetic basis of coat color variation in Pashmina goat

The genetics of coat color variation remains a classic area. Earlier studies have focused on a limited number of genes involved in color determination; however, the complete set of trait determinants are still not well known. In this study, we used high-throughput sequencing technology to identify and characterize intricate interactions between genes that cause complex coat color variation in Changthangi Pashmina goats, producer of finest and costly commercial animal fiber. We systematically identified differentially expressed mRNAs and lncRNAs from black, brown and white Pashmina goat skin samples by using RNA-sequencing technique. A pairwise comparison of black, white and brown skin samples yielded 2479 significantly dysregulated genes (2422 mRNA and 57 lncRNAs). Differentially expressed genes were enriched in melanin biosynthesis, melanocyte differentiation, developmental pigmentation, melanosome transport activities GO terms. Our analysis suggested the potential role of lncRNAs on color coding mRNAs in cis and trans configuration. We have also developed online data repository as a component of the study to provide a central location for data access, visualization and interpretation accessible through http://pcd.skuastk.org/.

Comparative FISH-Mapping of MC1R, ASIP, and TYRP1 in New and Old World Camelids and Association Analysis With Coat Color Phenotypes in the Dromedary (Camelus dromedarius)

Melanocortin 1 receptor (MC1R), the agouti signaling protein (ASIP), and tyrosinase related protein 1 (TYRP1) are among the major regulators of pigmentation in mammals. Recently, MC1R and ASIP sequence variants were associated with white and black/dark brown coat colors, respectively, in the dromedary. Here we confirmed this association by independent sequencing and mutation discovery of MC1R and ASIP coding regions and by TaqMan genotyping in 188 dromedaries from Saudi Arabia and United States, including 38 black, 53 white, and 97 beige/brown/red animals. We showed that heterozygosity for a missense mutation c.901C > T in MC1R is sufficient for the white coat color suggesting a possible dominant negative effect. Likewise, we confirmed that the majority of black dromedaries were homozygous for a frameshift mutation in ASIP exon 2, except for 4 animals, which were heterozygous. In search for additional mutations underlying the black color, we identified another frameshift mutation in ASIP exon 4 and 6 new variants in MC1R including a significantly associated SNP in 3'UTR. In pursuit of sequence variants that may modify dromedary wild-type color from dark-reddish brown to light beige, we identified 4 SNPs and one insertion in TYRP1 non-coding regions. However, none of these were associated with variations in wild-type colors. Finally, the three genes were cytogenetically mapped in New World (alpaca) and Old World (dromedary and Bactrian camel) camelids. The MC1R was assigned to chr21, ASIP to chr19 and TYRP1 to chr4 in all 3 species confirming extensive conservation of camelid karyotypes. Notably, while the locations of ASIP and TYRP1 were in agreement with human-camelid comparative map, mapping MC1R identified a new evolutionary conserved synteny segment between camelid chromosome 21 and HSA16. The findings contribute to coat color genomics and the development of molecular tests in camelids and toward the chromosome level reference assemblies of camelid genomes.

Coat colour phenotype of Qingyu pig is associated with polymorphisms of melanocortin receptor 1 gene

Objective

Qingyu pig, a Chinese indigenous pig breed, exhibits two types of coat colour phenotypes, including pure black and white with black spotting respectively. Melanocortin receptor 1 (MC1R) and agouti signaling protein (ASIP) are two widely reported pivotal genes that significantly affect the regulation of coat colour. The objectives of this study were to investigate whether the polymorphisms of these two genes are associated with coat colour and analyze the molecular mechanism of the coat colour separation in Qingyu pig.

Methods

We studied the phenotype segregation and used polymerase chain reaction amplification and Sanger sequencing to investigate the polymorphism of MC1R and ASIP in 121 Qingyu pigs, consisting of 115 black and 6 white with black spotted pigs.

Results

Coat colour of Qingyu pig is associated with the polymorphisms of MC1R but not ASIP. We only found 2 haplotypes, E^QY and E^qy, based on the 13 observed mutations from MC1R gene. Among which, E^qy presented a recessive inheritance mode in black spotted Qingyu pigs. Further analysis revealed a g.462–463CC insertion that caused a frameshift mutation and a premature stop codon, thus changed the first transmembrane domain completely and lost the remaining six transmembrane domains. Altogether, our results strongly support that the variety of Qingyu pig’s coat colour is related to MC1R.

Conclusion

Our findings indicated that black coat colour in Qingyu pig was dominant to white with black spotted phenotype and MC1R gene polymorphism was associated with coat colour separation in Qingyu pig.

Genome Wide Association Study Identifies New Loci Associated with Undesired Coat Color Phenotypes in Saanen Goats

This paper reports a quantitative genetics and genomic analysis of undesirable coat color patterns in goats. Two undesirable coat colors have routinely been recorded for the past 15 years in French Saanen goats. One fifth of Saanen females have been phenotyped “pink” (8.0%) or “pink neck” (11.5%) and consequently have not been included in the breeding program as elite animals. Heritability of the binary “pink” and “pink neck” phenotype, estimated from 103,443 females was 0.26 for “pink” and 0.21 for “pink neck”. Genome wide association studies (using haplotypes or single SNPs) were implemented using a daughter design of 810 Saanen goats sired by 9 Artificial Insemination bucks genotyped with the goatSNP50 chip. A highly significant signal (-log10pvalue = 10.2) was associated with the “pink neck” phenotype on chromosome 11, suggesting the presence of a major gene. Highly significant signals for the “pink” phenotype were found on chromosomes 5 and 13 (-log10p values of 7.2 and, 7.7 respectively). The most significant SNP on chromosome 13 was in the ASIP gene region, well known for its association with coat color phenotypes. Nine significant signals were also found for both traits. The highest signal for each trait was detected by both single SNP and haplotype approaches, whereas the smaller signals were not consistently detected by the two methods. Altogether these results demonstrated a strong genetic control of the “pink” and “pink neck” phenotypes in French Saanen goats suggesting that SNP information could be used to identify and remove undesired colored animals from the breeding program.