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.     

Satellite DNA polymorphisms and AFLP correlate with Bos indicus-taurus hybridization

We describe satellite DNA variation that detects hybridization of Bos indicus (zebu or indicine cattle) and Bos taurus (taurine cattle) in African cattle populations. On Southern blots hybridized to a satellite III probe, relative intensities of Hinfl fragments correlated with the taurine-zebu composition in hybrid animals as deduced from AFLP genotyping of the same animals and previous data on microsatellite allele frequencies. Similar results were obtained by PCR-RFLP analysis of a zebu-specific mutation in the repeat unit of satellite 1.711b. Analysis of individuals from 20 African cattle breeds indicate that the centromeric satellites of the sanga breeds are of the taurine type and that several East-African zebu breeds are hybrids between taurine and zebu. These satellite RFLP, or SFLP, markers provide a fast method to screen the genetic makeup of African cattle.     

Genetic diversity,introgression and relationships among West/Central African cattle breeds

Genetic diversity, introgression and relationships were studied in 521 individuals from 9 African Bos indicus and 3 Bos taurus cattle breeds in Cameroon and Nigeria using genotype information on 28 markers (16 microsatellite, 7 milk protein and 5 blood protein markers). The genotypes of 13 of the 16 microsatellite markers studied on three European (German Angus, German Simmental and German Yellow) and two Indian (Nelore and Ongole) breeds were used to assess the relationships between them and the African breeds. Diversity levels at microsatellite loci were higher in the zebu than in the taurine breeds and were generally similar for protein loci in the breeds in each group. Microsatellite allelic distribution displayed groups of alleles specific to the Indian zebu, African taurine and European taurine. The level of the Indian zebu genetic admixture proportions in the African zebus was higher than the African taurine and European taurine admixture proportions, and ranged from 58.1% to 74.0%. The African taurine breed, Muturu was free of Indian zebu genes while its counter Namchi was highly introgressed (30.2%). Phylogenic reconstruction and principal component analysis indicate close relationships among the zebu breeds in Cameroon and Nigeria and a large genetic divergence between the main cattle groups – African taurine, European taurine and Indian zebu, and a central position for the African zebus. The study presents the first comprehensive information on the hybrid composition of the individual cattle breeds of Cameroon and Nigeria and the genetic relationships existing among them and other breeds outside of Africa. Strong evidence supporting separate domestication events for the Bos species is also provided.     

Investigation of X- and Y-specific single nucleotide polymorphisms in taurine (Bos taurus) and indicine (Bos indicus) cattle

Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossbreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle breeds (four Sanga breeds, including Raya Azebu, Danakil, Caprivi, Nguni; and two Zebu breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX ) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY ) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X-chromosome individuals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle breeds.     

Polymorphisms in Blood Proteins of Bos indicus and Bos taurus Cattle Breeds of Cameroon and Nigeria, and Description of New Albumin Variants

Polymorphisms in the five blood protein loci albumin (ALB), carbonic anhydrase (CA II), vitamin D binding protein (GC), haemoglobin (HBB), and transferrin (TF) were investigated in 520 individuals from 12 cattle populations (Bos indicus and Bos taurus) in Cameroon and Nigeria by isoelectric focusing with carrier ampholytes in ultrathin polyacrylamide gels (PAG-IEF) and by linear gradient polyacrylamide gel electrophoresis (PAGE). While all loci in nine populations were polymorphic with up to six alleles at the ALB and TF loci: the Namchi population showed monomorphism at the CA II locus and Muturu at the ALB, CA II, and HBB loci. There was a clear distinction between Bos indicus and Bos taurus breeds at the ALB locus with ALBB predominating in indicine and ALBA predominating in taurtine breeds. CA IIS, GCA, and HBBA were the most commonly occurring alleles in all populations. Two variants not described before were demonstrated by PAG-IEF at the ALB locus and named ALBJ and ALBK. Mean effective number of alleles as measure of intrabreed diversity was higher in zebu populations (2.040-2.288) as compared to taurine breeds (1.349-1.836). Significant deviations from Hardy-Weinberg equilibrium occurred in some populations at the HBB and TF loci. More haplotypes of ALB/GC occurred in the zebu than taurine breeds. ALBAGCA predominated in the taurine populations and ALBBGCA in the indicine populations. Influence of zebu genes on the Namchi and N'Dama taurine breeds was detected at the ALB, CA II, HBB, and TF loci, and estimated at 61.5% and 5.7%, respectively. The high resolution of PAG-IEF in screening for polymorphisms within diversity studies was demonstrated.     

Male-mediated introgression of Bos indicus genes into Argentine and Bolivian Creole cattle breeds

The geographic distribution and frequency of Bos taurus and Bos indicus Y chromosome haplotypes amongst Argentine and Bolivian Creole cattle breeds were studied, using cytogenetic and molecular genetic techniques. A complete correspondence between Y chromosome morphology and the haplotype of the Y-linked microsatellite marker INRA 124 was found in all males examined. The taurine and indicine haplotypes were detected in 85.7 and 14.3% of the males studied, respectively, although these frequencies varied amongst the different breeds examined. The geographic distribution of this polymorphism suggests a pattern of zebu introgression in South America. The highest frequencies of the Zebu Y-chromosome are found in Brazilian populations (43-90%), in the eastern part of the continent, while it is absent in the southernmost breeds from Uruguay and Argentina. Bolivian breeds, at the centre of the continent, exhibit intermediate values (17-41%). This east/west and north/south gradient of male Zebu introgression could be explained by historical events and environmental factors.     

Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle

In order to clarify the origin and genetic diversity of cattle in North Eastern Asia, this study examined mitochondrial displacement loop sequence variation and frequencies of Bos taurus and Bos indicus Y chromosome haplotypes in Japanese, Mongolian, and Korean native cattle. In mitochondrial analyses, 20% of Mongolian cattle carried B. indicus mitochondrial haplotypes, but Japanese and Korean cattle carried only B. taurus haplotypes. In contrast, all samples revealed B. taurus Y chromosome haplotypes. This may be due to the import of zebu and other cattle during the Mongol Empire era with subsequent crossing with native taurine cattle. B. taurus mtDNA sequences fall into several geographically distributed haplogroups and one of these, termed here T4, is described in each of the test samples, but has not been observed in Near Eastern, European or African cattle. This may have been locally domesticated from an East Eurasian strain of Bos primigenius.     

Taurine and zebu admixture in Near Eastern cattle: a comparison of mitochondrial, autosomal and Y-chromosomal data

Eight Bos taurus cattle breeds from the Near East region were screened with a Bos indicus (zebu)-diagnostic Y-specific microsatellite (INRA124) to estimate the proportion of zebu Y chromosomes in each population. This value was compared with previously published values for zebu introgression for both the mitochondrial and autosomal gene pools of the same breeds. All breeds revealed considerable levels of introgression from B. indicus cattle when the autosomal data were taken into consideration; this was particularly apparent in cattle populations from Iraq in the east, and declined in the populations further west towards Anatolia. This non-random pattern of introgression and admixture is suggestive of the introduction of zebu cattle from the region corresponding to present-day Iran and northern Pakistan. In addition, the maternal and paternal markers demonstrate that the movement of cattle into and within the Near East was complex.     

Origin and phylogeographical structure of Chinese cattle

Complete mitochondrial D-loop sequences of 231 samples were used to explore the origin and genetic diversity of Chinese cattle. Phylogenetical analysis of these sequences revealed both Bos taurus and Bos indicus mitochondrial types in Chinese cattle. Four of the previously identified mitochondrial DNA lineages (T1–T4) were identified in the Bos taurus type, including lineage T1, which was found for the first time in Chinese cattle. Two lineages (I1 and I2) were identified in the Bos indicus type. Our results support the suggestion that the Yunnan-Guizhou Plateau is the domestication site of Chinese zebu. We also found evidence that Tibetan cattle originated from taurine and zebu cattle. The distribution pattern of Chinese cattle breeds was closely related to the geographical and climatic background. It was possible to divide Chinese cattle in this study into two major groups: northern and southern cattle.     

Polymorphisms of two Y chromosome microsatellites in Chinese cattle

Two Y chromosome specific microsatellites UMN2404 and UMN0103 were genotyped and assessed for polymorphisms in a total of 423 unrelated males from 25 indigenous Chinese cattle breeds. Consistently, both microsatellites displayed specific indicine and taurine alleles in each bull examined. The indicine and taurine alleles were detected in 248 males (58.6%), and 175 males (41.4%), respectively, although these frequencies varied amongst different breeds examined. The indicine alleles dominated in the southern group (92.4%), while the taurine alleles dominated in the northern group (95.5%). Hainan Island was possibly the site for the origin of Chinese zebu, and Tibetan cattle were probably independently domesticated from another strain of Bos primigenius. The geographical distribution of these frequencies reveals a pattern of male indicine introgression and a hybrid zone of indicine and taurine cattle in China. The declining south-to-north and east-to-west gradient of male indicine introgression in China could be explained by historical data, geographical segregation and temperature and weather conditions.     

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.     

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.     

Worldwide Patterns of Ancestry,Divergence, and Admixture in Domesticated Cattle

The domestication and development of cattle has considerably impacted human societies, but the histories of cattle breeds and populations have been poorly understood especially for African, Asian, and American breeds. Using genotypes from 43,043 autosomal single nucleotide polymorphism markers scored in 1,543 animals, we evaluate the population structure of 134 domesticated bovid breeds. Regardless of the analytical method or sample subset, the three major groups of Asian indicine, Eurasian taurine, and African taurine were consistently observed. Patterns of geographic dispersal resulting from co-migration with humans and exportation are recognizable in phylogenetic networks. All analytical methods reveal patterns of hybridization which occurred after divergence. Using 19 breeds, we map the cline of indicine introgression into Africa. We infer that African taurine possess a large portion of wild African auroch ancestry, causing their divergence from Eurasian taurine. We detect exportation patterns in Asia and identify a cline of Eurasian taurine/indicine hybridization in Asia. We also identify the influence of species other than Bos taurus taurus and B. t. indicus in the formation of Asian breeds. We detect the pronounced influence of Shorthorn cattle in the formation of European breeds. Iberian and Italian cattle possess introgression from African taurine. American Criollo cattle originate from Iberia, and not directly from Africa with African ancestry inherited via Iberian ancestors. Indicine introgression into American cattle occurred in the Americas, and not Europe. We argue that cattle migration, movement and trading followed by admixture have been important forces in shaping modern bovine genomic variation.     

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.     

婆罗门牛mtDNA D-loop变异及其遗传背景

对10头原种婆罗门牛mtDNAD-loop全序列912 bp测序,婆罗门牛遗传多样性丰富,检测到的9种单倍型兼有瘤牛(B.indicus)与普通牛(B.taurus)的遗传背景,核苷酸变异率为6.25 %,单倍型多态度为0.978±0.054 ,核苷酸多态度为0.014 30±0.008 68。所有单倍型聚为明显的两大分支,婆罗门牛的大部分单倍型为普通牛单倍型类群,并占绝对优势(90 %) ,仅Brah-6与亚洲瘤牛聚在一起,属于亚洲瘤牛线粒体单倍型,表明婆罗门牛的确是集亚洲瘤牛、欧洲普通牛等优良特性于一身(易产犊、产肉性能好、耐热与体表寄生虫等)的瘤牛品种之一。育种学家引种瘤牛的目的是改善当地牛的生产力与适应性,现代普通牛表现出明显又普遍的瘤牛渐渗现象。对现代的瘤牛品种而言,除亚洲瘤牛品种外,普通牛对其他瘤牛品种育成的贡献同样高。支持瘤牛(B.indicus)为独立驯化、起源于印度次大陆的假说。     

Association between Sscp Haplotypes at the Bovine Growth Hormone Gene and Milk Protein Percentage

The bovine Growth Hormone gene (bGH) is an attractive candidate gene for milk production in cattle. Single-strand conformation polymorphisms at bGH were identified and used to define haplotype configurations at this gene in the Israeli Holstein dairy cattle population (Bos taurus) and in the parent animals of the International Bovine Reference Family Panel (a collection of B. taurus and B. indicus crosses). B. taurus and B. indicus haplotypes at the bGH gene differed qualitatively, confirming the previously proposed long evolutionary separation of these cattle subraces. Only a small number of bGH haplotypes were present in the Israel Holstein population. One of the haplotypes, apparently of B. indicus origin, was found to have a highly significant positive effect on milk protein percentage. This illustrates the utility of the haplotype approach for uncovering candidate gene involvement in quantitative genetic variation in agricultural populations. The strong effect of an indicine haplotype in a taurine background raises the possibility that indicine alleles at other candidate genes may comprise a genetic resource for improvement of taurine populations. It is proposed that haplotype analysis may be a useful adjunct to measures of genetic distance for evaluating rare breeds with respect to gene conservation.     

中国17个黄牛品种mtDNA变异特征与多态性分析

中国黄牛品种资源丰富,尚有28个地方固有品种.为了进一步深入了解这些宝贵遗传资源,本研究通过mtDNA变异特征与多态性分析揭示这些来自中国不同地域地方黄牛的母系起源与分子系统学特征.在17个品种84个体的mtDNA D-loop全序列中,一共检测到了102个核苷酸替代突变位.由此定义的53个单倍型被类聚为2个明显的单倍群：普通牛和瘤牛.mtDNA D-loop全序列变异的第一个特征是转换发生的频率远高于颠换;第二个特征是缺失与替代突变共存;第三个特征是缺失突变率比较高.所有D-loop全序列的核苷酸多样性和单倍型多样性分别为0.026 78±0.000 50和0.919±0.027.普通牛D-loop单倍型在北方牛种群中占有优势(80%～100%),而瘤牛单倍型在南方牛种群中占有优势(42.9%～100%),2种不同单倍型在中原牛种群中的分布也存在差异.2种不同单倍型在中国不同地域17个黄牛品种中的差异性分布揭示出了瘤牛mtDNA基因在中国黄牛中自南而北、由高到低的流动模式,这种基因流动模式的形成可能是由历史事件、地理隔离以及气候环境差异等造成的.     

Importance of sperm genotype (indicus versus taurus) for fertility and embryonic development at elevated temperatures

Heat stress has negative effects on bovine reproduction, particularly for European breeds (Bos taurus taurus) that are less thermotolerant than zebu cattle (Bos taurus indicus). Here, the evidence that spermatozoa and oocyte both contribute to early embryonic resistance to heat shock is demonstrated. In addition, the use of reproductive biotechnologies to improve bovine thermotolerance, are outlined by comparing data from taurus, indicus and crossbred genotypes.     

DNA sequence of SSCP haplotypes at the bovine growth hormone (bGH) gene

Previous studies using SSCP and PCR-RFLP methodologies uncovered nine polymorphic sites within the bGH gene, defining eight intragenic haplotypes falling into two main groups. In the present study we report the DNA sequence of these eight haplotypes. A total of 1494 bp were sequenced uncovering a total of 12 sequence variants. Haplotypes within groups differed among themselves at one or two sites, compared across groups, haplotypes of the two groups differed consistently at six sites, each of which was monomorphic within the respective groups. This comes to 4 differentiating sites per kb, suggesting that the two haplotype groups began to diverge about 400,000 years ago. This corresponds approximately to the estimated time of divergence of the Bos taurus and Bos indicus lineages, raising the possibility, supported by other evidence, that the two haplotype classes represent taurine and indicine haplotypes, respectively. Nucleotide sequence divergence of taurine and indicine genomes of this magnitude has far reaching implications with respect to QTL mapping and marker assisted selection in breeds derived from taurine x indicine crosses.     

Mitochondrial DNA variation in cattle of South China: origin and introgression

Ten restriction endonucleases were used to investigate the mitochondrial DNA restriction fragment length polymorphism (mtDNA RFLP) of 11 native cattle breeds and one cultivated cattle breed in South China. Twenty-three restriction morphs were detected, which can be sorted into five haplotypes. A phylogenetic tree of the haplotypes was constructed by using the 'upgMa' method. Our study showed that haplotype I and II are identical to the zebu (Bos indicus) and taurine (Bos taurus) haplotypes, respectively. Zebu and taurine were the two major origins of cattle populations in South China, and the zebu probably had more influence on the native cattle population than taurine did. Haplotype III is identical to haplotype I of yak (Bos grunniens), which was only detected in the Diqing cattle breed. Haplotype IV was detected for the first time. This haplotype, found only in Dehong cattle, might be from an independent domestication event, probably from another Bos indicus population. Divergence of haplotypes I and IV occurred about 268,000-535,000 years ago, much earlier than the 10,000-year history of cattle husbandry. Our results also suggest a secondary introgession of mtDNA from yak to Diqing cattle.