Allele frequencies of TYR and MC1R in Chinese native cattle

In order to estimate the influence of TYR and MC1R on the color of the cattle hide, the MC1R and TYR in Luxi Yellow, Bohai Black, China Holstein black‐white and China Holstein red‐white cattle (20 animals of each of the four breeds) were sequenced. The comparison of TYR among the four hide color phenotypes revealed no sequence difference. The sequences of the MC1R coding region revealed three alleles (E^D, E⁺ and e), which were previously reported. Furthermore, we found an important single nucleotide polymorphism at 725 position of the MC1R coding region, which may help in cattle breed identification. A polymerase chain reaction‐restriction fragment length polymorphism was performed to investigate the gene frequencies of the four breeds. Most China Holstein black‐white cattle had E^D and E⁺ alleles (E^D = 0.12, E⁺ = 0.80) and no homozygous e/e and most Bohai Black cattle had E^D and E⁺ alleles (E^D = 0.52, E⁺ = 0.47). Therefore it is consistent with the hypothesis that E^D and E⁺ induce black pigment synthesis. On the other hand, most of the China Holstein red‐white cattle and Luxi Yellow cattle had the e allele (e/e = 0.95). Unexpectedly, the E⁺/e genotype was present in China Holstein red‐white cattle and Luxi Yellow cattle.     

Allele frequencies of the extension locus encoding the melanocortin-1 receptor in Japanese and Korean cattle

In order to estimate the influence of the Extension (E) locus in cattle coat color, the melanocortin‐1 receptor (MC1R) gene in Japanese Black, Japanese Brown and Korean (Hanwoo) cattle were sequenced. The sequences of the coding region revealed three alleles (E^D, E⁺ and e), which were previously reported. Polymerase chain reaction‐restriction fragment length polymorphism was performed to investigate the gene frequencies of the three breeds. Japanese Black was almost composed of E^D and E⁺ individuals, E^D = 0.481 and E⁺ = 0.514, and no homozygous e/e, therefore that is consistent with the hypothesis that E^D and E⁺ induce black pigment synthesis. Allele frequencies between Japanese Brown and Hanwoo were obviously different; however, recessive red e allele frequency was 0.038 for Japanese Brown and 0.948 for Hanwoo, even though both breeds have quite similar coat colors (ranging from yellowish brown to dark brown including a red coat color). This result suggested that other genes are also associated with a coat color of red and brown in cattle.     

MC1R c.310G>‐ and c.871G > A determine the coat color of Kumamoto sub‐breed of Japanese Brown cattle

Coat color is one of the important factors characterizing breeds for domestic animals. Melanocortin 1 receptor (MC1R) is a representative responsible gene for this phenotype. Two single‐nucleotide polymorphisms (SNPs) in bovine MC1R gene, c.296T > C and c.310G>‐, have been well characterized, but these SNPs are not enough to explain cattle coat color. As far as we know, MC1R genotypes of Kumamoto sub‐breed of Japanese Brown cattle have not been analyzed. In the current study, genotyping for c.296T > C and c.310G>‐ was performed to elucidate the role of MC1R in determining the coat color of this sub‐breed. As a result, most animals were e/e genotype, suggesting the coat color of this sub‐breed is derived from the e allele of MC1R gene. However, we found six animals with E/e genotype, which coat color would be black theoretically. Subsequently, sequence comparison was performed with these animals to identify other polymorphisms affecting coat color, elucidating that these animals possessed the A allele of c.871G > A commonly. c.871G > A was a non‐synonymous mutation in the seventh transmembrane domain, suggesting alteration of the function and/or the structure of MC1R protein. Our data indicated that the A allele of c.871G > A might be a loss‐of‐function mutation.     

Genetic variation within coat color genes of MC1R and ASIP in Chinese brownish red Tibetan pigs

Melanocortin receptor 1 (MC1R) and agouti signaling protein (ASIP) are two major genes affecting coat color phenotypes in mammals, and inactivation mutations in the MC1R gene are responsible for red coat color in European pig breeds. Conversely, the gain‐of‐function ASIP mutations block MC1R signaling and lead to the production of red pheomelanin. Chinese Tibetan pigs have three types of coat color phenotypes, including brownish red, solid black and black with patches of brownish red and white. Herein, we investigated variations of the MC1R and ASIP genes in Tibetan pigs. The results showed that the brownish red Tibet pig had the dominant black MC1R allele (E^D1). No loss‐of‐function mutation in MC1R responsible for red coat color in European breeds was observed in this breed. No causal mutation for the red coat color phenotype was found in the coding sequence of the ASIP gene. A novel missense mutation c.157G > A was firstly identified in exon 2 of ASIP, which was further genotyped in 285 pigs from five Chinese breeds and three Western breeds having different coat color phenotypes. Nearly all pigs were GG homozygotes. In conclusion, no functional variant responsible for brownish red coloration was found in the coding region of MC1R and ASIP in Tibetan pigs.     

Inheritance of the lace‐tailed laced plumage pattern of the sebright bantam

1. An investigation was conducted firstly among progeny from a cross between Blue Andalusian and Silver‐spangled Hamburgh bantams, and secondly between crosses of selected progeny of this mating with a Silver Sebright bantam in an effort to determine the genotype of the lace‐tailed laced plumage phenotype of the latter.

2. The genotype of the black‐laced blue and the spangled plumage phenotypes of the Andalusian and the Silver‐spangled Hamburgh had, respectively, been shown to depend on homozygosity of E, Co, db⁺, Ml and Pg, and of co⁺, Db, Ml and Pg together with a black down allele at the E‐locus presumed to be E, but also hypothesised to be E^R. The genes E and E^R are the extended black and birchen‐like allele at the E‐locus whilst Co, Db, Ml and Pg are, respectively, the eumelanin restrictors, Columbian and dark‐brown Columbian, the eumelanin extension melanotic and the pattern gene. The Sebright had been hypothesised to possess the E allele at the E‐locus, and to be homozy‐gous Co, Ml and Pg, a combination shown to be responsible for the black‐tailed laced phenotype of the Wyandotte.

3. Segregation in the F₂ generation varied from that expected if both parental genotypes were E/E, but gave close agreement if the Silver‐spangled Hamburgh was E^R/E^R.

4. A lace‐tailed laced segregant in the F₂ generation of the first mating, presumed to be homozygous E^R, Co, Db, Ml and Pg was mated to a Sebright. The F₁ generation failed to segregate at the 5 loci, thus suggesting the genotype of the lace‐tailed laced phenotype of the Sebright to be homozygous E^R, Co, Db, Ml and Pg. Segregation in the F₂ generation of a mating of the female F₁ with a Silver‐spangled Hamburgh male confirmed the genotype of the lace‐tailed lacing of the Sebright bantam, and demonstrated that of the Silver‐spangled Hamburgh to be homozygous E^R, co⁺, Db, Ml and Pg‐.     

Genetic polymorphism at CSN1S2 locus in two endangered sicilian goat breeds

In this study we surveyed two endangered Sicilian goat breeds (Girgentana and Argentata dell'Etna) for genetic polymorphism at the CSN1S2 locus. In a total of 537 goats, we detected CSN1S2^A, CSN1S2^B, CSN1S2^C° (CSN1S2^C + CSN1S2^E), CSN1S2^D, CSN1S2^F and CSN1S2^O alleles by means of various polymerase chain reaction (PCR), allele specific‐PCR (AS–PCR) and PCR‐restriction fragment length polymorphism (RFLP) reactions with the aim of improving the knowledge of the genetic resource of these two breeds. Three and five alleles, with six and twelve genotypes, were identified at CSN1S2 locus, in Girgentana and Argentata, respectively. Argentata dell'Etna showed a higher degree of genetic variation. The allelic and genotypic distribution seems to be significantly different (p < 0.001) in the two breeds. In Argentata the rare null allele (CSN1S2^O) was found at low frequency (0.033); this genetic peculiarity makes its preservation worthwhile.     

Altered expression of melanocortin-1 receptor (MC1R) in a yellow-coloured wild raccoon dog (Nyctereutes procyonoides)

Background – The melanocortin 1 receptor (MC1R) gene plays a key role in determining coat colour in mammals by controlling the proportion of eumelanin and pheomelanin granules. Wild raccoon dogs have a mixed coat colour, with black to brown and grey hairs. Hypothesis/Objectives – The study was performed to identify the cause of the variant yellow coat colour in a wild raccoon dog. Animals – A wild raccoon dog that showed coat colour change to yellow and four wild‐type raccoon dogs that showed normal coat colour were included. Methods – To identify the cause of the variant yellow coat colour, we examined the sequence of the MC1R gene and its expression at the mRNA and protein levels. Results – The coding region of the MC1R gene of this raccoon dog comprised 954 bp, the same as for wild‐type raccoon dogs and domestic dogs. By comparing the gene with that in the wild‐type raccoon dog, a 2 bp deletion was detected in the 5′‐untranslated region, positioned 152 bp upstream of the start codon. However, there was no significant difference in the mRNA expression level. The yellow raccoon dog revealed a significantly decreased MC1R protein level compared with the wild‐type raccoon dogs, indicating an increase in pheomelanin synthesis. Conclusions and clinical importance – These results suggest that the variant coat colour in the yellow raccoon dog was associated with decreased MC1R function.     

Development of a method for simultaneously genotyping multiple horse coat colour loci and genetic investigation of basic colour variation in Thoroughbred and Misaki horses in Japan

In order to develop a genotyping method that can be used in the registration procedure for Thoroughbreds, we developed a method for simultaneously genotyping multiple coat colour genes on the basis of single nucleotide polymorphism typing by using the SNaPshot^TM technique. This method enabled precise and reasonable detection of causal mutations; it was effective for genotyping of MC1R, ASIP, and SLC45A2 at the Extension (E), Agouti (A), Cream dilution (C) loci, and the possibility of identification of rare variants of MC1R, EDNRB and KIT at the E, Overo (O) and Sabino 1 (SB1) loci, respectively, was also indicated. It was considered that this genotyping method would provide information not only for the registration of Thoroughbreds but also for the preservation of phenotypic characters, such as coat colour, of endangered Misaki native horses in Japan. Therefore, genetic variations at the five coat colour loci were investigated in 1111 Thoroughbred and 99 Misaki native horses. Allele frequencies at the polymorphic E and A loci were estimated, and the proportions of basic coat colours that could be expected in the Thoroughbred population were bay, 0.662; black, 0.070; chestnut, 0.268. In the Misaki population, they were bay, 0.792; black, 0.129; chestnut, 0.080. The data presented were the first of its kind on genetic coat colour variation, and will be important with regard to the registration of Thoroughbreds and the management of Misaki horses.     

Inheritance of the spangled plumage pattern and the marbled chick down phenotypes of the silver‐spangled Hamburgh Bantam

1. An investigation was conducted among the progeny from crosses between Silver‐Spangled and Gold‐Pencilled Hamburgh bantams, and between Silver‐Spangled Hamburgh and Double‐Laced Barnevelder bantams.

2. Two subjects were studied: the relationship between three plumage pattern phenotypes, spangling, transverse‐barring and double‐lacing, all of which are arrangements of eumelanin expressed on a background of phaeomelanic pigmentation and the inheritance of the marbled chick down of the Silver‐Spangled Hamburgh bantam.

3. Examination of the F₂ generations demonstrated that, in conjunction with silver (S) gene(s) and extended black (E) alleles at the E‐locus the silver‐spangled phenotype can be produced by the addition to the genotypes of the Gold‐Pencilled Hamburgh, homozygous e^bc (Db‐ml⁺‐Pg), and Double‐Laced Barnevelder, homozygous e^b (db⁺‐Ml‐Pg), of Sp and Db genes respectively. Consequently Sp and Ml are one and the same gene, for which I retain the symbol Ml, and the genotype of the Silver‐Spangled Hamburgh is homozygous E (Db‐Ml‐Pg), where the buttercup (e^bc) and brown (e^b) are alleles of the E‐locus and Db, Ml, Sp and Pg are respectively the eumelanin restrictor dark‐brown Columbian, the eumelanin extension melanotic, plumage pattern spangling and the pattern gene.

4. The exact correlation between S/‐ E/E Db/Db and the marbled chickdown phenotype demonstrated the latter to be a pleiotropic effect of Db/Db, thus enabling the mapping of Db, Ml and Pg in group 3 on chromosome 1.     

Notes on the “wheaten” plumage phenotype of the domestic fowl

1. A study was made using a Light Sussex bantam hen to determine the allele present at the E locus. Conflicting results occurred on mating with different males suggesting the presence in one case of the dominant allele e^Wh and, in the other, of the recessive e^y.

2. Further examination of these apparently conflicting results suggests the possibility that there may be a single gene producing the wheaten phenotype which appears to be dominant if melanin restriction genes are present at other loci, or recessive by interaction with melanin intensifier genes. This gene may also require the presence of down‐diluting gene(s) to produce the wheaten phenotype.     

Haplotype diversity in MC1R locus between the Min and white-haired pig breeds

In this article, we investigated the genetic variations in the coding region of porcine melanocortin receptor 1 (MC1R) gene in three pig breeds (Min, Yorkshire and Landrace) with black and white coat colors. Six polymorphic sites were found to be significantly associated with coat color. Two blocks were identified in the linkage disequilibrium map, the haplotypes in the first block are nt67/68indelCC and nt67/68indel--, and the haplotypes in the second block are ACCGA and GTTAG. The median-joining network diagram of MC1R haplotypes showed most Min pigs and other Asia domestic breeds own similar haplotypes to ACCGA, while the haplotypes of Europe pig breeds are similar to GTTAG. The phylogenetic analysis of the MC1R CDS further showed Min pigs are close to Laiwu pigs (Shandong, China), which indicated that the black coat color trait of Min pig might be originated and evolved from the black pig breed in Shandong Peninsula of China.     

Molecular characteristics of MC1R gene in tile-grey plumage of domestic chicken

ABSTRACT

1. Tile-grey plumage is a unique and rare feather type of local chicken breeds in China, but its genetic mechanism and corresponding genes remain unknown.

2. In order to identify the genetic basis and molecular characteristics of tile-grey plumage, this experiment investigated variations of melanocortin 1 receptor (MC1R) gene in Yunnan Piao chickens with typical tile-grey plumage characteristics in contrast with three Yunnan local breeds as well as two standard breeds with different plumage colour, and analysed the association between genic variation and tile-grey plumage.

3. Through sequencing and comparison of the entire coding region of the MC1R gene, a total of 10 SNP loci were detected, of which eight were non-synonymous mutations that cause amino acid changes. The gene frequency and genotype frequency of the MC1R mutation sites in different breeds and different plumage colour groups revealed that C69T, T212C and A274G were significantly associated with tile-grey plumage. Eighteen haplotypes of the MC1R gene were constructed based on 10 nucleotide variations and eight amino acid variations. Haplotype distribution and the median joining network in breeds and plumage colour groups revealed a main haplotype (hap2) for tile-grey plumage. Hap2 is unique to the tile-grey feather of Piao chicken, and the individuals carrying this haplotype account for 62.96% of the whole tile-grey chicken.

4. The results of this study are of significance for further analysis of the molecular basis of tile-grey plumage and the selective breeding of tile-grey plumage.     

The coding sequence of the ASIP gene is identical in nine wild-type coloured cattle breeds

The aim of this study was to ascertain the role of the Agouti signaling peptide (ASIP) gene coding region in the Agouti locus variation within wild‐type coat colour in cattle. We determined the Extension genotype in 241 individuals from six Spanish and three French brown cattle breeds representative of wild‐type coat variation. Polymerase chain reaction–single‐strand conformation polymorphism (PCR‐SSCP) analysis was carried out in individuals of each Extension genotypes within the same breed in an attempt to identify variants in the three coding exons of the ASIP gene. No SSCP variants were found. Results were confirmed by sequencing the coding exons of the ASIP gene in 20 individuals. Our results suggest that the ASIP coding region does not play a central role in coat colour variation in cattle.     

Diagnostic value of rectal temperature of African cattle of variable coat colour infected with trypanosomes and tick-borne infections

Diagnosis of major endemic bovine parasitic diseases in sub-Saharan Africa such as trypanosomosis, theileriosis, anaplasmosis, babesiosis and cowdriosis is increasingly relying on clinical diagnosis due to deterioration of veterinary services and laboratory facilities. Pyrexia is a common clinical feature of aforementioned diseases whose detection relies on measurement of rectal temperature. The research undertaken in this study was aimed at assessing the effects of diurnal changes and variable coat colour of indigenous Nkedi Zebu cattle on the diagnostic value of rectal temperature under tropical conditions. The results revealed that variation in rectal temperature was significantly influenced by time of day it was taken and by the coat colour of the Nkedi Zebu cattle (P < 0.001). Rectal temperature experienced diurnal changes: steadily rising to reach a peak at 17.00 h before declining. The mean rectal temperature of unhealthy cattle was significantly higher (P < 0.05) than that of the healthy ones only between 13.00 and 17.00 h of the day. During which period the proportion of unhealthy cattle having a rectal temperature of 39.4 °C or higher was significantly higher than that of healthy ones (P < 0.001). Regarding the variable coat colour of indigenous breeds, rectal temperature among cattle of different coat colours was significantly different (P < 0.05). In conclusion it is important to consider diurnal changes in rectal temperature and differences due to variable coat colour of indigenous African breeds when measuring rectal temperature for assessing pyrexia, during clinical diagnosis of bovine trypanosomosis and tick-borne diseases that are endemic in many countries in sub-Saharan Africa.     

Inheritance of the plumage pattern of the double‐laced Barnevelder bantam

1. An investigation was conducted among the progeny from crosses between Gold‐Laced Wyandotte and Double‐Laced Barnevelder bantams into the genotype of the plumage pattern of the latter.

2. The double‐laced phenotype has been shown to depend upon homozygosity of the linkage of a eumelanin intensifier melanotic Ml with a pattern gene Pg in the presence of either wheaten e^Wh or brown e^b alleles at the E‐locus.

3. Examination of the female F₂ generation demonstrated that the plumage pattern phenotype of the Double‐Laced Barnevelder depended upon homozygosity of e^b(Ml‐Pg).     

Tracing the origin of 'blue Weimaraner' dogs by molecular genetics

Weimaraner dogs are defined by light brown coat colour termed grey including several shadings ranging from silver and deer to mouse grey. In contrast, the so-called blue Weimaraners (BW) with lightened black-pigmented coat have been proposed to represent spontaneous revertants in the Weimaraner breed. In order to investigate the genetic determinants of the characteristic grey coat colour versus those of BW, known variation in coat colour genes including TYRP1 and MLPH were analysed in a number of grey and blue dogs. Variations at the B locus cause grey coat colour in Weimaraners via two non-functional TYRP1 copies (bb) including the b(s), b(d) and b(c) alleles. In all BW, at least one functional TYRP1 allele (Bb or BB genotype) was identified. Defined microsatellite alleles in TYRP1 intron 4 are linked to this functional B allele in BW. These alleles were also detected in various other dog breeds, but not in grey Weimaraners. The combination of a dominant trait for blue versus grey together with a specific TYRP1 haplotype in BW suggests that blue coat colour is not the result of spontaneous (back-) mutation in grey Weimaraners. This inference is even emphasized by the presence of a unique Y-chomosomal haplotype in a male offspring of the supposed ancestor of the BW population which - according to pedigree information - carries a copy of the original Y chromosome. Thus, molecular genetic analyses of coat colours combined with Y-chromosomal haplotypes allow tracing the origin of atypical dogs in respective canine populations.     

Marker-assisted selection for forelimb-girdle muscular anomaly of Japanese Black cattle

Forelimb‐girdle muscular anomaly is a hereditary disorder of Japanese Black cattle characterized by tremors and astasia caused by hypoplasia of the forelimb‐girdle muscles. The locus responsible for this disorder has been mapped on a middle region of bovine chromosome 26. In this study, we applied marker‐assisted selection to identify the carriers of this disorder. Four microsatellite markers, DIK4440, BM4505, MOK2602 and IDVGA‐59, linked to the disorder locus were genotyped in 37 unaffected offspring of a carrier sire. Transmission of the mutant or wild‐type allele of the disorder locus of the sire to the 37 offspring was determined by examining the haplotypes of these markers. The results showed that nine and 18 of the 37 animals possessed the paternally transmitted mutant and wild‐type alleles, respectively, and therefore, the nine animals with the mutant allele were identified as carriers. We concluded that the marker‐assisted selection using these four markers can be applied for the identification of the carriers of forelimb‐girdle muscular anomaly of Japanese Black cattle.     

Single nucleotide polymorphism detection in promoter III of the acetyl-CoA carboxylase-α gene in sheep

Three novel SNPs were identified in the locus OAR292286, encoding the DNA sequence of promoter III of the ovine acetyl‐CoA carboxylase‐α gene, in Italian sheep of four breeds: Gentile di Puglia (25 individuals) and Sopravissana (31) which are triple‐purpose local endangered breeds, Comisana (25) which is a local non‐selected, non‐endangered dairy breed and Sarda (15) which is a popular selected high yielding dairy breed. Variant alleles are: G/T at 1330 bp, C/G at 1338 bp and C/T at 1430 bp. Frequencies of the variant alleles were calculated and chi‐squared analysis of the differences in allele frequency between breed pairs was performed. Allele frequencies of the Sarda breed differ significantly from the other considered breeds.     

DGAT1, GH, GHR, PRL and PRLR polymorphism in water buffalo (Bubalus bubalis)

The polymorphism of several genes has been shown to affect the milk composition traits in dairy cattle, including DGAT1‐exon8 K232A, GH‐intron3 MspI, GH‐exon5 AluI, GHR‐exon8 F279Y, PRL‐exon3 RsaI and PRLR‐exon3 S18N. However, the polymorphism and effects of these genes on the milk traits of water buffalo are still unclear. In this study, four DNA pooling samples from Murrah, Nili‐ravi, Murrah‐Nili‐Swamp crossbreed and Chinese swamp buffalo were constructed, respectively, and polymorphism of these sites was investigated using PCR–Single‐strand conformation polymorphism and sequencing. Twenty‐eight inter‐specific single‐nucleotide polymorphism (SNPs) were found in these six assayed gene fragments between buffalo and dairy cattle, including nine intra‐specific SNPs among buffalo groups. All buffalo fixed a K allele genotype in DGAT1‐exon8, MspI⁺ restriction site(c nucleotide) and AluI⁺ site(c nucleotide) at intron3 and exon5 of GH gene, F allele genotype of F279Y mutation in GHR gene, RsaI^? restriction site at PRL‐exon3/exon4 and N allele genotype of S18N mutation at PRLR‐exon3. It provides an indirect evidence that water buffalo have fixed alleles with genotypes reported in dairy cattle, which is thought to be responsible for high milk fat, high protein content and low milk yield. Moreover, three new intra‐specific SNPs were found including 275th bp (c/t) in DGAT1 of Murrah buffalo, 109th bp (t/a) in PRL‐exon3/exon4 and 43rd bp (c/t) in PRLR‐exon3 of Chinese swamp buffalo. Information provided in this study will be useful in further studies to improve buffalo breeding for better lactation performances.