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.     

Coat colour genes in diversity studies

In this paper we describe the use of polymorphic genes affecting coat colour as a tool in diversity studies of domestic animals. Although phenotypic data has been the main criteria for establishing different breeds, calculation of genetic distances between breeds is normally performed using noncoding microsatellite markers. As anticipated, MC1‐R (melanocyte stimulating hormone receptor) allele frequencies vary greatly between cattle breeds expressing different coat colours. In multicoloured breeds, like Icelandic cattle, a high frequency of the E⁺ allele appears to be essential for colour variation. Whereas black breeds have a high frequency of the dominant acting allele E^D, entirely red breeds have no E^D. Animals being homozygous for the defective allele e occurred frequently in some cattle breeds, indicating that the MC1‐R does not have crucial impact on animal physiology other than coat colour. The E⁺ and e alleles were observed in the closely related river buffalo as well. None of the breeds included in this study express the roan phenotype. Consequently, they were monomorphic at the MGF locus. As for the MC1‐R locus, a correlation to colour pattern was observed for two c‐kit alleles as well, confirming that selection of specific phenotypes strongly affect the allelic variation of underlying loci. Information on genes affecting the phenotype is therefore well suited for describing different breeds of livestock and, consequently, a practical tool in breed conservation.     

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.     

Allele frequencies of gene polymorphisms related to economic traits in Bos taurus and Bos indicus cattle breeds

Allele frequencies of 10 representative polymorphisms for beef and milk traits were investigated for a total of 240 animals from Bos taurus and Bos indicus breeds, including two Japanese groups (Japanese Black and Japanese Brown), two East Asian groups (Korean and Mongolian), three European groups (Holstein, Angus and Hereford) and a Bos indicus group in South Asia (Myanmar, Laos and Cambodia). The Japanese Black revealed unique genetic construction in GH, FASN and SREBP‐1 and the other Asian populations show intermediate frequencies between European and Japanese populations. The Bos indicus group showed low favorable allele frequencies in most of the genes. The study showed the variability and distribution of 10 genes affecting economic traits among world representative cattle breeds. The genetic information would contribute to elucidating the genetic background for worldwide cattle breeds and the possibility of improvement using the markers.     

Reference ranges of hematology and lymphocyte subsets in healthy Korean native cattle (Hanwoo) and Holstein dairy cattle

There are no accurate reference ranges for hematology parameters and lymphocyte subsets in Korean native beef cattle (Hanwoo). This study was performed to establish reliable reference ranges of hematology and lymphocyte subsets using a large number of Hanwoo cattle (n = 350) and to compare differences between Hanwoo and Holstein dairy cattle (n = 334). Additionally, age‐related changes in lymphocyte subsets were studied. Bovine leukocyte subpopulation analysis was performed using mono or dual color flow cytometry. The leukocyte subpopulations investigated in healthy cattle included: CD2⁺ cells, sIgM⁺ cells, MHC class II⁺ cells, CD3⁺CD4⁺ cells, CD3⁺CD8⁺ cells, and WC1⁺ cells. Although Hanwoo and Holstein cattle are the same species, results showed several differences in hematology and lymphocyte subsets between Hanwoo and Holstein cattle. This study is the first report to establish reference ranges of hematology and lymphocyte subsets in adult Hanwoo cattle.     

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.     

Genome‐wide association studies identified variants for taurine concentration in Japanese Black beef

We performed genome‐wide association studies (GWAS) using the BovineSNP50 array to detect significant single nucleotide polymorphisms (SNPs) that may affect the concentration of 22 free amino acids and three peptides in Japanese Black beef cattle. A total of 574 Japanese Black cattle and 40,657 SNPs from the array were used for this study. Genome‐wide significant SNPs were detected for β‐alanine (three SNPs on chromosomes 22 and 29) and taurine (26 SNPs on chromosome 22). Importantly, the top two SNPs for taurine were highly significant (p = 6.2 × 10^?21), and the frequency of the increase‐concentration allele (Q) for taurine was found to be 0.73. The Q allele frequency of this population was similar to that of the other unrelated Japanese Black cattle, but different from that of the other breeds. In addition, the significant SNPs were not associated with carcass traits or fatty acid compositions. Interestingly, the top three of the four most significant SNPs for taurine were located near solute carrier family 6, member 6 (SLC6A6), which is a membrane transporter for taurine. We also found two associated variants in the 5′‐upstream region of SLC6A6; however, they were less significantly associated than the SNPs from the BovineSNP50 array.     

中国黄牛酪氨酸关联蛋白1（TYRP1）基因多态性的研究

[目的]验证TYRP1基因的错义突变(g.1300C>T)与中国黄牛毛色性状是否存在相关性。[方法]采用PCR测序及生物信息学的方法,对991头中国黄牛、48头安格斯牛、104头婆罗门牛的TYRP1基因进行多态性分析。[结果]通过对中国黄牛的等位基因频率和基因型频率的分析,发现此变异与中国黄牛棕色毛色性状不相关。[结论]TYRP1基因的错义突变(g.1300C>T)与中国黄牛棕色表型不相关。该位点可能在一些品种中受到了选择,中国黄牛的棕色表型可能受其他基因调控。     

日本和牛品种形成、将征与评价

介绍日本和牛发展历史以及黑毛和牛、褐毛和牛、无角和牛、日本短角牛四个和牛品种分布、形成、外貌特征、生产性能及发展动向，并对此评价的同时指出了值得我国黄牛改良借鉴的经验。     

Evaluation of genetic diversity in Japanese Brown cattle population by pedigree analysis

The Japanese Brown is the second most common domestic beef breed in Japan. However, nowadays this breed is facing reduction in numbers because of pressure from a profitable domestic breed. This breed is uniformly characterized by its brown coat colour, but is comprised of two isolated sub‐breeds, Kumamoto and Kouchi, each possessing a different gene pool. Pedigree analyses were carried out for the two sub‐breeds using the pedigree records of animals born from 1970 to 2000. The effective population size has been found to be consistently reducing during the last three decades in both sub‐breeds. The current effective sizes were estimated to be 25.5 and 6.0 for the Kumamoto and Kouchi sub‐breeds, respectively. The estimate of the effective number of founders (N_ef) in the Kumamoto sub‐breed decreased from 152.1 to 74.4; that of non‐founders (N_enf), from 41.7 to 5.3; and that of founder genome equivalents (N_ge), from 32.7 to 4.9. The corresponding changes in the Kouchi sub‐breed were from 108.2 to 79.4, 16.2 to 4.1, and 14.1 to 3.9. Increasing differences between the two genetic diversity indices in the sub‐breeds indicate that the greater part of the reduction of genetic diversity can be attributed to genetic drift that accumulated in the non‐founder generations. A comparison with published estimates for several cattle breeds suggests the extremely limited genetic diversity of Japanese Brown. In addition to the avoidance of further reduction of genetic diversity, it will be important to counteract the process of breed decline by establishing a production system to efficiently utilize the unique characteristics of this breed and by developing links between the breed and products with market value.     

Development of discrimination markers between Japanese domestic and imported beef

In the meat industry, correct labeling of beef origins or breed is required to assure quality and safety. This paper describes the development of discrimination markers between Japanese domestic and imported beef from the United States (US) and Australia (AUS) based on a bovine 50K single nucleotide polymorphism (SNP) array using a total of 110 samples: Japanese Black (n = 50), Japanese Holstein (n = 50) and US cattle (n = 10). Genotyping information revealed 1081 SNPs as candidate markers that were polymorphic only in US cattle. The genotyping results by PCR – restriction length polymorphism in Japanese Black (n = 300) and Holstein cattle (n = 146) revealed that 11 SNPs had alleles specific to US cattle. Their allelic frequencies in US cattle (n = 108) ranged from 0.097 to 0.250 with an average of 0.178 and the combined identification probability of US cattle was 0.987. In addition, we also verified the applicability of these US‐specific markers to AUS cattle. Their allelic frequencies in AUS cattle (n = 280) ranged from 0.063 to 0.224 with an average of 0.137 and the combined identification probability of AUS cattle was 0.963. In conclusion, a set of these markers could be useful for discriminating between Japanese domestic and imported beef and would contribute to identify origins and prevent falsified labeling of beef.     

The T allele at the g.1471620G>T in the EDG1 gene associated with high marbling in Japanese Black cattle is at a low frequency in breeds not selected for marbling

Our previous study detected a single nucleotide polymorphism (SNP), g.1471620G > T , in the 5' flanking region of the endothelial differentiation sphingolipid G-protein-coupled receptor 1 ( EDG1 ) gene, which has been considered as a positional functional candidate for the gene responsible for marbling, and showed association of the g.1471620G > T SNP with marbling in Japanese Black beef cattle. In the present study, we investigated the allele frequency distribution of the g.1471620G > T SNP among the 5 cattle breeds, Japanese Black, Japanese Brown, Japanese Short Horn, Holstein, and Brown Swiss breeds. The T allele at the g.1471620G > T SNP associated with high marbling was found at high frequency in Japanese Black breed that has been subjected to a strong selection for high marbling, while the allele was absent or at very low frequencies in the other breeds that have not been strongly selected for high marbling. Based on this finding, we hypothesized that the pressure of the strong selection for high marbling in Japanese Black breed has increased the frequency of the T allele at the g.1471620G > T SNP in the EDG1 .     

Genetic structure and relationships of 16 Asian and European cattle populations using DigiTag2 assay

In this study, we genotyped 117 autosomal single nucleotide polymorphisms using a DigiTag2 assay to assess the genetic diversity, structure and relationships of 16 Eurasian cattle populations, including nine cattle breeds and seven native cattle. Phylogenetic and principal component analyses showed that Bos taurus and Bos indicus populations were clearly distinguished, whereas Japanese Shorthorn and Japanese Polled clustered with European populations. Furthermore, STRUCTURE analysis demonstrated the distinct separation between Bos taurus and Bos indicus (K=2), and between European and Asian populations (K=3). In addition, Japanese Holstein exhibited an admixture pattern with Asian and European cattle (K=3‐5). Mongolian (K=13‐16) and Japanese Black (K=14‐16) populations exhibited admixture patterns with different ancestries. Bos indicus populations exhibited a uniform genetic structure at K=2‐11, thereby suggesting that there are close genetic relationships among Bos indicus populations. However, the Bhutan and Bangladesh populations formed a cluster distinct from the other Bos indicus populations at K=12‐16. In conclusion, our study could sufficiently explain the genetic construction of Asian cattle populations, including: (i) the close genetic relationships among Bos indicus populations; (ii) the genetic influences of European breeds on Japanese breeds; (iii) the genetic admixture in Japanese Holstein, Mongolian and Japanese Black cattle; and (iv) the genetic subpopulations in Southeast Asia.     

The assessment of genetic diversity within and among the eight subpopulations of Japanese Black cattle using 52 microsatellite markers

Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise F_ST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.     

Allelic frequencies and association with carcass traits of six genes in local subpopulations of Japanese Black cattle

Marker‐assisted selection (MAS) is expected to accelerate the genetic improvement of Japanese Black cattle. However, verification of the effects of the genes for MAS in different subpopulations is required prior to the application of MAS. In this study, we investigated the allelic frequencies and genotypic effects for carcass traits of six genes, which can be used in MAS, in eight local subpopulations. These genes are SCD, FASN and SREBP1, which are associated with the fatty acid composition of meat, and NCAPG, MC1R and F11, which are associated with carcass weight, coat color and blood coagulation abnormality, respectively. The frequencies of desirable alleles of SCD and FASN were relatively high and that of NCAPG was relatively low, and NCAPG was significantly associated with several carcass traits, including carcass weight. The proportions of genotypic variance explained by NCAPG to phenotypic variance were 4.83 for carcass weight. We thus confirmed that NCAPG is a useful marker for selection of carcass traits in these subpopulations. In addition, we found that the desirable alleles of six genes showed no negative effects on carcass traits. Therefore, selection using these genes to improve target traits should not have negative impacts on carcass traits.     

Development of SNP markers for individual identification and parentage test in a Japanese Black cattle population

This study describes the development of efficient single nucleotide polymorphism (SNP) markers for individual identification and parentage tests in a Japanese Black cattle population. An amplified fragment length polymorphism method was employed to detect informative candidate markers, and yielded 44 SNP markers from 220 primer combinations. 29 unlinked SNPs were finally selected as diagnostic markers. The allelic frequencies for each marker were estimated by using PCR‐RFLP in the Japanese Black population. Based on the frequency data, the estimated identity power of these markers was 2.73 × 10^?12. Parentage exclusion probabilities, when both suspected parents' genotypes were known and when only one suspected parent was genotyped, were estimated as 0.96929 and 0.99693, respectively. This panel of SNP markers is theoretically sufficient for individual identification, and would also be a powerful tool for a parentage test in Japanese Black cattle. The markers could contribute to the management of the beef industry in Japan.     

Conception rate of Holstein and Japanese Black cattle following embryo transfer in southwestern Japan

This study aimed to quantify and compare conception rates to embryo transfer (ET) of Holstein and Japanese Black cattle in southwestern Japan. A 10‐year retrospective epidemiological survey was conducted. The recipient numbers for Holstein and Japanese Black cattle was 621 and 527, respectively. Conception rates of Holstein and Japanese Black cattle during the study period were 45.4% and 42.3%, respectively. There was no significant difference between both breeds. However, a different trend of conception rate to ET in Holstein and Japanese Black cattle was observed. In Holstein cattle, conception rate in August to October was lower than in the other months and was significantly lower (p < .05) than in April. Particularly, conception rate in October of Holstein cattle was the lowest (31.0%). In Japanese Black cattle, conception rates in December (24.2%) and January (31.3%) were lower than in the other months. Conception rate of Japanese Black cattle declined as the temperature–humidity index (THI) decreased, exhibiting significantly lower levels in the ≤45 THI class than in any other THI class (p < .05). By contrast, in Holstein cattle, no relationship was observed between conception rate and THI on the day of ET. These observations suggest the importance of appropriate management that considers seasonal reactivity in each breed.     

Bos indicus type of growth hormone receptor gene is retained in Japanese Black cattle

The growth hormone receptor (GHR) gene is responsible for growth and carcass traits, and polymorphisms associated with the variation of meat production are thought to occur in the liver‐specific promoter of the GHR gene in cattle. The aim of this study was to analyse the structure of the liver‐specific promoter of GHR in Japanese Black cattle, as the relationship between GHR polymorphism and meat production is poorly understood in this breed. Typically in European cattle, the LINE‐1 element, a family of retrotransposons, is inserted in the liver‐specific promoter. However, a short GHR promoter without the LINE‐1 sequence was found in the Japanese Black breed as in Bos indicus cattle. The frequency of the short allele was approximately 60%. In addition, 24 of 29 Holstein/Japanese Black crosses carried the short allele from their sire. The present result suggests that the short allele for GHR may be a candidate marker for improving meat production of Japanese Black cattle.     

Genetic structure of milk protein polymorphisms and effects on milk production traits in a local dairy cattle

The milk protein genetic structure of the Reggiana dairy local cattle with remarkable milk quality properties was analysed and compared with the structure of Italian Friesian and Italian Brown cattle. A total of 1138 individual milk samples from the three breeds were typed by isoelectrofocusing. Polymorphism was found at the α_s1‐casein (CSN1S1), β‐casein (CSN2), κ‐casein (CSN3), and β‐lactoglobulin (LGB) loci. High frequencies were observed for some casein alleles in Reggiana (CSN1S1*C, 25%; CSN2*B: 28%) with considerable differences to those observed in a survey carried out 30 years before. A great variation among breeds was observed for casein haplotype frequencies and high linkage disequilibrium was detected at the three polymorphic casein loci CSN1S1‐CSN2‐CSN3. The prevalent haplotypes were CA²B (23%; Reggiana), BA²A (48%; Italian Friesian) and BA²B (51%; Italian Brown). Higher G_ST values between breeds were observed when haplotype frequencies were considered instead of gene frequencies. In the Reggiana cattle, the occurrence of two casein alleles at a rather high frequency (CSN1S1*C, CSN2*B) allowed to estimate the effects of rare casein haplotypes on milk traits. The CA²B haplotype was associated with a significantly higher milk protein and fat content and a significantly higher protein per cent was found also for the BA¹B haplotype.