The Origins of Domesticated Cattle

The origin of domestic cattle has perplexed archaeologists for more than a century. Researchers have proposed various theories, which offer alternative spatial and chronological models for the origin and spread of domesticated cattle. One point of discussion is whether domestic cattle had a single or multiple origins; however, most authorities considered that the first steps towards cattle domestication were taken in southwest Asia and that domesticated cattle entered Europe with pastoralists migrating from this region. Domesticated taurine cattle were thought to have entered Africa in successive waves from southwest Asia, while zebu cattle migrated into Africa at a later date from Arabia and the Indian subcontinent. Analysis of mitochondrial DNA (mtDNA) shows that taurine and zebu cattle divergence before the Holocene and were probably domesticated independently. Recent mtDNA sequence data shows that African and European taurine cattle were probably domesticated independently, but that there was a process of genetic introgression between taurine and zebu cattle in Africa. Ancient DNA studies over the last 10 years suggest that Northern European aurochsens apparently contributed little or nothing to domestic cattle while Southern European aurochsens apparently made a significant input. However, Middle Eastern aurochsen, unfortunately not typed yet, are expected to be to be very similar to European breeds as well, both because archeological data suggest that the major center of domestication for European Bos taurus breeds was the Fertile Crescent (9), and also because a mtDNA sequence from a Syrian specimen dated at 8,000–9,000 years ago shows a typical European haplotype found both in modern breeds and the Italian aurochsen. Evidence seems to suggest that small to moderate levels of local gene flow from wild Bos primigenius females in selected breeds were either accepted or may be reinforced by Neolithic breeders.     

Complete mitogenome reveals genetic divergence and phylogenetic relationships among Indian cattle (Bos indicus) breeds

Indigenous cattle of India belong to the species, Bos indicus and they possess various adaptability and production traits. However, little is known about the genetic diversity and origin of these breeds. To investigate the status, we sequenced and analyzed the whole mitochondrial DNA (mtDNA) of seven Indian cattle breeds. In total, 49 single-nucleotide variants (SNVs) were identified among the seven breeds analyzed. We observed a common synonymous SNV in the COII gene (m.7583G?>?A) of all the breeds studied. The phylogenetic analysis and genetic distance estimation showed the close genetic relationship among the Indian cattle breeds, whereas distinct genetic differences were observed between Bos indicus and Bos taurus cattle. Our results indicate a common ancestor for European Zwergzebu breed and South Indian cattle. The estimated divergence time demonstrated that the Bos indicus and Bos taurus cattle lineages diverged 0.92 million years ago. Our study also demonstrates that ancestors of present zebu breeds originated in South and North India separately ～30,000 to 20,000 years ago. In conclusion, the identified genetic variants and results of the phylogenetic analysis may provide baseline information to develop appropriate strategies for management and conservation of Indian cattle breeds.     

Geographical partitioning of goat diversity in Europe and the Middle East

Thirty microsatellite markers were analysed in 1426 goats from 45 traditional or rare breeds in 15 European and Middle Eastern countries. In all populations inbreeding was indicated by heterozygosity deficiency (mean FIS = 0.10). Genetic differentiation between breeds was moderate with a mean FST value of 0.07, but for most (c. 71%) northern and central European breeds, individuals could be assigned to their breeds with a success rate of more than 80%. Bayesian-based clustering analysis of allele frequencies and multivariate analysis revealed at least four discrete clusters: eastern Mediterranean (Middle East), central Mediterranean, western Mediterranean and central/northern Europe. About 41% of the genetic variability among the breeds could be explained by their geographical origin. A decrease in genetic diversity from the south-east to the north-west was accompanied by an increase in the level of differentiation at the breed level. These observations support the hypothesis that domestic livestock migrated from the Middle East towards western and northern Europe and indicate that breed formation was more systematic in north-central Europe than in the Middle East. We propose that breed differentiation and molecular diversity are independent criteria for conservation.     

Phylogenetic relationships of Northeast Asian cattle to other cattle populations determined using mitochondrial DNA D-loop sequence polymorphism

Phylogenetic relationships of Northeast Asian cattle to various other cattle breeds including Bos taurus, Bos indicus, and Bison bison were assessed using mtDNA D-loop sequences. A neighbor-joining tree was constructed using sequences determined for 4 Cheju Black, 4 Cheju Yellow, 4 Korean Yellow cattle (Bos taurus), and 2 American Brahman cattle (Bos indicus), and also published sequences for 31 Japanese Black cattle, 45 European breed cattle, 6 African zebus, 2 African taurines, and 6 Indian zebus. Five American bisons (Bison bison) were used as an outgroup. The neighbor-joining tree showed that American bisons and Indian zebus are clearly separate from other cattle breeds, respectively, and African cattle clustered together, although with a low bootstrap probability (<50%). Results indicate that cattle in Northeast Asia, Europe, and Africa are closely related to each other–suggesting their recent divergence, but are separate from Indian zebus.     

MspI Allelic Pattern of Bovine Growth Hormone Gene in Indian Zebu Cattle (Bos indicus) Breeds

The MspI allelic variation in intron III of the bovine growth hormone (bGH) gene was explored using PCR-RFLP in 750 animals belonging to 17 well-recognized breeds of Indian zebu cattle (Bos indicus) reared in different geographic locations of the country. Restriction digestion analysis of a 329-bp PCR fragment of the bGH intron III region with MspI restriction enzyme revealed two alleles (MspI− and MspI+) and two genotypes (−/− and +/−) across the 17 cattle breeds studied. The allelic frequency varied from 0.67 to 0.94 for MspI (−) and from 0.06 to 0.33 for MspI (+) across the 17 breeds, with a combined average frequency of 0.87 and 0.13, respectively. No animal with +/+ genotype was detected across the samples analyzed. The chi-square test showed that the difference in MspI allelic frequency was not significant (p > 0.05), regardless of the geographic origin, coat color, or utility of the cattle breed. The high MspI (−) allele frequencies obtained for Indian zebu cattle in this study are in sharp contrast to those reported for taurine breeds from northern Europe, Mediterranean countries, and America. Findings of this study further substantiate the hypothesis that the MspI (−) allele has an Indian origin.     

Chemical classification of cattle. 2. Phylogenetic tree and specific status of the Zebu

Phylogenetic trees for the ten major breed groups of cattle were constructed by Farris's (1972) maximum parsimony method, or Fitch & Margoliash's (1967) method, which averages ou the deviation over the entire assemblage. Both techniques yield essentially identical trees. The phylogenetic tree for the ten major cattle breed groups can be superimposed on a map of Europe and western Asia, the root of the tree being close to the 'fertile crescent' in Asia Minor, believed to be a primary centre of bovine domestication.
For some but not all protein variants there is a cline of gene frequencies as one proceeds from the British Isles and northwest Europe towards southeast Europe and Asia Minor, with the most extreme gene frequencies in the Zebu breeds of India. It is not clear to what extent the observed clines are primary or secondary, i.e., consequent to the initial migrations of cattle towards the end of the Pleistocene or consequent to the many migrations of man with his domesticated cattle. Such clines as exist are not in themselves sufficient to prove either selection versus genetic drift or to establish taxonomic ranking. Contrary to some suggestions in the literature, the biochemical evidence supports Linnaeus's original conclusions: Bos taurus and Bos indicus are distinct species.     

Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub-saharan African cattle breeds

We report for the first time, and for the whole of sub-Saharan Africa, the geographical distribution and the frequency of an indicine and a taurine Y specific allele amongst African cattle breeds. A total of 984 males from 69 indigenous African populations from 22 countries were analysed at the microsatellite locus INRA 124. The taurine allele is probably the oldest one on the continent. However, the taurine and the indicine alleles were present in 291 males (30%), and 693 males (70%), respectively. More particularly, 96% of zebu males (n = 470), 50% of taurine males (n = 263), 29% of sanga males (crossbreed Bos taurus x Bos indicus, n = 263) and 95% of zebu x sanga crossbred males (n = 56) had the indicine allele. The Borgou, a breed classified as zebu x taurine cross showed only the zebu allele (n = 12). The indicine allele dominates today in the Abyssinian region, a large part of the Lake Victoria region and the sahelian belt of West Africa. All the sanga males (n = 64) but only one from the Abyssinian region had the indicine allele. The taurine allele is the commonest only among the sanga breeds of the southern African region and the trypanotolerant taurine breeds of West Africa. In West Africa and in the southern Africa regions, zones of introgression were detected with breeds showing both Y chromosome alleles. Our data also reveal a pattern of male zebu introgression in Mozambique and Zimbabwe, probably originating from the Mozambique coast. The sanga cattle from the Lake Victoria region and the Kuri cattle of Lake Chad, cattle populations surrounded by zebu breeds were, surprisingly, completely devoid of the indicine allele. Human migration, phenotypic preferences by the pastoralists, adaptation to specific habitats and to specific diseases are the main factors explaining the present-day distribution of the alleles in sub-Saharan Africa.     

Biochemical polymorphism in Egyptian Baladi cattle and their relationship with other breeds

Gene frequencies were estimated in a sample of Baladi cattle for milk proteins, blood proteins and blood groups. Gene frequency estimates of Bos taurus, Bos indicus and Sanga breeds were assembled from the literature. The gene frequencies were utilized for estimating the genetic distance between the breeds and breed groups. The Egyptian Baladi cattle appeared to be closer to Bos taurus breeds than to the Sanga. They are far removed from Zebus.     

Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers

Twenty-seven domesticated yellow cattle breeds of China and three introduced cattle breeds were analysed by means of 30 microsatellite markers to determine the level of genetic variation within and among populations as well as the population structure. In all, 480 microsatellite alleles were observed across the 30 breeds with the mean number of alleles per locus of 9.093 for native breeds and 6.885 for the three introduced breeds. Mean F -statistics (0.08) for Chinese native cattle breeds implied that 92% of the total genetic variation was from genetic differentiation within each breed and 8% of the genetic variation existed among breeds. A phylogenetic tree was constructed based on Nei's genetic distances, and three clusters were obtained. According to the tree, the three introduced breeds were distinct from the 27 native breeds. The indigenous cattle breeds were divided into two clusters, one cluster including five humpless breeds and the other cluster containing 22 humped breeds. This study identifies multiple origins of yellow cattle of China from Bos taurus and Bos indicus . Furthermore, population structure analysis implies that there are possibly five independent original domestications for yellow cattle in China. Four of five origins were four different Bos indicus types, mainly in areas of the Chang Jiang, the Zhu Jiang River basin, the Yellow River and the Huai River basin. The other origin was for Bos taurus type of Mongolian descent, mainly located in Northwestern China, the Mongolian plateau and Northeastern China or north of the Great Wall.     

Geographic distribution of haplotype diversity at the bovine casein locus

The genetic diversity of the casein locus in cattle was studied on the basis of haplotype analysis. Consideration of recently described genetic variants of the casein genes which to date have not been the subject of diversity studies, allowed the identification of new haplotypes. Genotyping of 30 cattle breeds from four continents revealed a geographically associated distribution of haplotypes, mainly defined by frequencies of alleles at CSN1S1 and CSN3. The genetic diversity within taurine breeds in Europe was found to decrease significantly from the south to the north and from the east to the west. Such geographic patterns of cattle genetic variation at the casein locus may be a result of the domestication process of modern cattle as well as geographically differentiated natural or artificial selection. The comparison of African Bos taurus and Bos indicus breeds allowed the identification of several Bos indicus specific haplotypes (CSN1S1*C-CSN2*A²-CSN3*A_I/CSN3*H) that are not found in pure taurine breeds. The occurrence of such haplotypes in southern European breeds also suggests that an introgression of indicine genes into taurine breeds could have contributed to the distribution of the genetic variation observed.     

Sequence comparison of mitochondrial tRNA genes and origin of light strand replication in Bos taurus and Nellore (Bos indicus) breeds

Although the complete bovine mitochondrial DNA molecule has been previously sequencedand sequence comparisons of the mitochondrial displacement loop have been performed, detailed sequence information is limited on coding regions of mitochondrial DNA within and among breeds of Bos taurus and Bos indicus. This study analysed polymorphism of the mitochondrial DNA transfer RNA genes for trypto-phan, alanine, asparagine, cysteine, tyrosine and the origin of light strand replication among Ayrshire, Canadian, Belgium Blue, Brown Swiss, Hereford, Jersey, Limousine, Piedmon-taise, Red Angus, Simmental (Bos taurus) and a Nellore (Bos indicus). Nucleotide sequence analysis of a 420-bp fragment of mitochondrial DNA comprising the five transfer RNA genes showed 100% homology among single individuals of the Bos taurus breeds. The Nellore breed showed guanine to adenine substitutions in the DHU arm of asparagine tRNA and in the origin of light-strand replication. This equates to a 0.5% sequence difference between the Nellore andBos taurus breeds and may reflect an independent evolutionary origin of the species.     

Comparative gene frequencies of nucleoside phosphorylase from cattle of Bos taurus and Bos indicus derivation in Brazil

1. Two nucleoside phosphorylase (NP) phenotypes were detected in 844 animals from four distinct genetic groups of Bos taurus and Bos indicus derivation. 2. Bos indicus breeds like Guzerat (Kankrej), Gir, Nellore (Ongole) and Indubrazil presented an NP-H frequency of 1.00, 0.928, 0.776 and 0.754 respectively, while the Canchim breed, a Bos taurus-Bos indicus crossbred cattle (5/8 Charolais-3/8 Zebu) presented a frequency of 0.372. 3. The high frequency detected from the NP-H allele in the Bos indicus breeds strongly suggests that this enzyme is a genetic marker for cattle and that it probably has a very high frequency in all Indian breeds.     

Characterization and genetic analysis of bovine αs1-casein I variant

The aim of this study was to identify the molecular genetic origin underlying the I variant of α_s1-casein and to develop a DNA-based test for this polymorphism as a tool for genetic analyses independent of milk sample testing. All coding exons and flanking regions of the α _{s 1} -casein gene were sequenced in DNA samples from cattle of known α _{s 1} -casein genotypes ( BI , CI , II , CC ), determined by isoelectric focusing of milk samples. A nucleotide substitution (A>T) in exon 11 (g.19836A>T) leads to the exchange of Glu with Asp at amino acid position 84 of the mature protein (p.Glu84Asp) and perfectly co-segregated with the presence of the α_s1-casein I variant in the milk of the analysed animals. Genotyping of a total of 680 DNA samples from 31 Bos taurus and Bos indicus cattle breeds and from Bos grunniens , Bison bison and Bison bonasus by restriction fragment length polymorphism analysis revealed the occurrence of Asp at position 84 at low frequencies in Bos taurus and Bos indicus breeds and established its origin from the α _s1-casein C variant (p.Glu192Gly). Ten different intragenic haplotypes in the gene region from intron 8 to intron 12 were observed by sequencing, of which two occurred in Bison bison and one in Bison bonasus only. Using available casein gene complex information, an association of Asp at position 84 to β-casein A ² and κ-casein B was shown in the Bos indicus breed Banyo Gudali . Taken together, we can postulate that the α _s1-casein variant I is caused by a non-synonymous nucleotide substitution in exon 11 of the gene and that it originated within Bos indicus and spread to Bos taurus subsequently.     

A microsatellite survey of cattle from a centre of origin: the Near East

Eight humpless cattle breeds from the Near East, three from Europe, one from West Africa and two zebu breeds from India were screened with 20 microsatellite loci. Breeds from the Near East revealed considerable levels of introgression from zebu cattle, which was apparent most in populations from the East and which declined in populations further West. This nonrandom pattern is suggestive of the introduction of zebu cattle from the East. Notwithstanding the overlay of zebu alleles, it was possible to demonstrate that Near Eastern cattle exhibited significantly higher levels of allelic diversity than breeds from other regions, which is consistent with the view that this region represents a primary domestication centre for Bos taurus cattle. The hypothesis that B. taurus and B. indicus cattle have separate domestic origins is also supported by the survey, a large genetic divergence being apparent between the nonhybrid taurine and zebu groups.     

Admixture analysis of South Asian cattle

We present population genetic analysis of microsatellite variation in seven Bos indicus cattle breeds from a variety of locations in South Asia. This is the first such study focusing within this area, which is one of the postulated centres of origin of domestic cattle. An estimate of the influence of Bos taurus ancestry was carried out using three approaches: by the systematic selection of population-associated alleles for B. taurus and examination of their frequency; by examining the truncation of genetic distances from European populations; and by a model-based Bayesian admixture analysis. These analyses revealed a B. taurus influence in the Indian subcontinent; part of a gradation which stretches from Europe through the Near East towards Indian and which may be of ancient origin.     

Polymorphism of mitochondrial DNA (mtDNA) in cattle and buffaloes

Mitochondrial DNA (mtDNA) from two breeds of cattle, viz., [Hariana (Bos indicus), Holstein (Bos taurus)] and Indian water buffalo (Bubalis bubalus), was analyzed using 13 restriction endonucleases which recognized an average of about 40 six-base sites. Polymorphism among cattle was detected with six of these enzymes. The two Holstein differed at six sites, whereas the Hariana breed (Bos indicus) did not show any site polymorphism. Surprisingly, the Hariana type differed by only one site from one of the Holstein types. The total size of buffalo mtDNA was estimated to be 16.4 kb. Polymorphism within the Murrah buffalo breed was observed with respect to aBglI site. Scarcely any of the restriction fragments of buffalo mtDNA matched those of cattle mtDNA.     

Analysis of Genetic Variation at the Prolactin-RsaI (PRL-RsaI) Locus in Indian Native Cattle Breeds (Bos indicus)

This study assessed the distribution pattern of allelic variants at the prolactin-RsaI locus in 23 Indian native cattle breeds (Bos indicus). PCR-RFLP genotyping of a 156?bp fragment of prolactin (PRL) in exon 3 revealed the predominance of the heterozygous AB genotype (mean frequency 0.58) irrespective of utility type (dairy, dual, draft), geographic region (northern, central, southern), and coat color (red, gray) of the breeds analyzed. The overall frequencies of homozygous AA (0.22) and BB (0.20) genotypes were in a similar range. The PRL (A) and PRL (B) alleles exhibited similar gene frequencies (means 0.52 and 0.48, respectively). The existing profile of the PRL-RsaI gene locus in a large set of Indian native cattle breeds was different from that of Bos taurus and cattle breeds of other countries, where either the BB genotype and PRL (B) allele or the AA genotype and PRL (A) allele have been reported to be more prevalent.     

中国黄牛品种多样性及其保护

总结关于中国黄牛起源和品种多样的文献,依据头颅骨分类,毛色,血液蛋白多态性,体型体态,梁色体组型,线粒体DNA和考古论证的资料可知,在各地的牛种中,中国的无峰牛来自于两种原牛,在长城以北有长角型的普通牛的分支土雷诺蒙古利亚（truano-mognolia)和青藏高原有矮型的短角型普通牛（draft pimigenius),有峰牛来自于三种原牛,来自北非,西亚的瘤牛,印度瘤牛和东南亚瘤牛,这些牛的后裔大多以混血种形态存在,关中和中原地区牛受西亚瘤牛的影响,胸垂较发达,多皱折,体格圈套 ,云南部分高峰牛受印度瘤牛影响,东南地区高峰牛为古代准牛属爪哇牛被东南亚瘤牛吸收杂交的后裔,属矮小型,体躯体而皱折贫乏,肩峰属头位,耳端较尖而不下垂,在起源上,藏牛为原始种,海南高峰牛（zebu sinsis)为一个瘤牛的发源地,云南高峰牛是一个特殊种,击阳牛是含有非洲瘤牛血淮的特殊种,全国的黄牛在总体上可分为两大系统三大类型,根据体态特征分为无峰,低身和有峰三种,按地理分布为蒙古,黄淮和长珠三组,现代国民经济发展引进30个外国品种,加速了地方品种的灭绝,本文还提出了农牛保种应以特殊品种和边缘地区以及特有生态区牛种为主要的主张。     

Genetic diversity and genomic signatures of selection among cattle breeds from Siberia,eastern and northern Europe

Domestication in the near eastern region had a major impact on the gene pool of humpless taurine cattle (Bos taurus). As a result of subsequent natural and artificial selection, hundreds of different breeds have evolved, displaying a broad range of phenotypic traits. Here, 10 Eurasian B. taurus breeds from different biogeographic and production conditions, which exhibit different demographic histories and have been under artificial selection at various intensities, were investigated using the Illumina BovineSNP50 panel to understand their genetic diversity and population structure. In addition, we scanned genomes from eight breeds for signatures of diversifying selection. Our population structure analysis indicated six distinct breed groups, the most divergent being the Yakutian cattle from Siberia. Selection signals were shared (experimental P‐value < 0.01) with more than four breeds on chromosomes 6, 7, 13, 16 and 22. The strongest selection signals in the Yakutian cattle were found on chromosomes 7 and 21, where a miRNA gene and genes related to immune system processes are respectively located. In general, genomic regions indicating selection overlapped with known QTL associated with milk production (e.g. on chromosome 19), reproduction (e.g. on chromosome 24) and meat quality (e.g. on chromosome 7). The selection map created in this study shows that native cattle breeds and their genetic resources represent unique material for future breeding.