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.     

Genetic diversity and admixture of indigenous cattle from North Ethiopia: implications of historical introgressions in the gateway region to Africa

Microsatellite variation was surveyed to determine the genetic diversity, population structure and admixture of seven North Ethiopian cattle breeds by combining multiple microsatellite data sets of Indian and West African zebu, and European, African and Near-Eastern taurine in genetic analyses. Based on allelic distribution, we identified four diagnostic alleles (HEL1-123 bp, CSSM66-201 bp, BM2113-150 bp and ILSTS6-285 bp) specific to the Near-Eastern taurine. Results of genetic relationship and population structure analyses confirmed the previously established marked genetic distinction between taurine and zebu, and indicated further divergence among the bio-geographical groupings of breeds such as North Ethiopian, Indian and West African zebu, and African, European and Near-Eastern taurine. Using the diagnostic alleles for bio-geographical groupings and a Bayesian method for population structure inference, we estimated the genetic influences of major historical introgressions in North Ethiopian cattle. The breeds have been heavily (>90%) influenced by zebu, followed by African, European and the Near-Eastern taurine. Overall, North Ethiopian cattle show a high level of within-population genetic variation (e.g. observed heterozygosity = 0.659-0.687), which is in the upper range of that reported for domestic cattle and indicates their potential for future breeding applications, even in a global context. Rather low but significant population differentiation (F(ST) = 1.1%, P < 0.05) was recorded as a result of multiple introgression events and strong genetic exchanges among the North Ethiopian breeds.     

Microsatellite DNA Variation and the Evolution, Domestication and Phylogeography of Taurine and Zebu Cattle (Bos Taurus and Bos Indicus)

Genetic variation at 20 microsatellite loci was surveyed to determine the evolutionary relationships and molecular biogeography of 20 different cattle populations from Africa, Europe and Asia. Phylogenetic reconstruction and multivariate analysis highlighted a marked distinction between humpless (taurine) and humped (zebu) cattle, providing strong support for a separate origin for domesticated zebu cattle. A molecular clock calculation using bison (Bison sp.) as an outgroup gave an estimated divergence time between the two subspecies of 610,000-850,000 years. Substantial differences in the distribution of alleles at 10 of these loci were observed between zebu and taurine cattle. These markers subsequently proved very useful for investigations of gene flow and admixture in African populations. When these data were considered in conjunction with previous mitochondrial and Y chromosomal studies, a distinctive male-mediated pattern of zebu genetic introgression was revealed. The introgression of zebu-specific alleles in African cattle afforded a high resolution perspective on the hybrid nature of African cattle populations and also suggested that certain West African populations of valuable disease-tolerant taurine cattle are under threat of genetic absorption by migrating zebu herds.     

Association studies in QTL regions linked to bovine trypanotolerance in a West African crossbred population

African animal trypanosomosis is a parasitic blood disease transmitted by tsetse flies and is widespread in sub-Saharan Africa. West African taurine breeds have the ability, known as trypanotolerance, to limit parasitaemia and anaemia and remain productive in enzootic areas. Several quantitative trait loci (QTL) underlying traits related to trypanotolerance have been identified in an experimentally infected F(2) population resulting from a cross between taurine and zebu cattle. Although this information is highly valuable, the QTL remain to be confirmed in populations subjected to natural conditions of infection, and the corresponding regions need to be refined. In our study, 360 West African cattle were phenotyped for the packed cell volume control under natural conditions of infection in south-western Burkina Faso. Phenotypes were assessed by analysing data from previous cattle monitored over 2 years in an area enzootic for trypanosomosis. We further genotyped for 64 microsatellite markers mapping within four previously reported QTL on BTA02, BTA04, BTA07 and BTA13. These data enabled us to estimate the heritability of the phenotype using the kinship matrix between individuals computed from genotyping data. Thus, depending on the estimators considered and the method used, the heritability of anaemia control ranged from 0.09 to 0.22. Finally, an analysis of association identified an allele of the MNB42 marker on BTA04 as being strongly associated with anaemia control, and a candidate gene, INHBA, as being close to that marker.     

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.     

Genome-wide genetic diversity,population structure and admixture analysis in African and Asian cattle breeds

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.     

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.     

Classification of the southern African sanga and East African shorthorned zebu

Humped African cattle, which are differentiated into zebu and sanga types, have traditionally been classified as Bos indicus . This paper discusses existing evidence and presents new evidence supporting the classification of southern African sangas as Bos taurus and East African zebus as ' taurindicus '. Classification is based on karyotype, frequencies of DNA markers and protein polymorphisms. The Boran, an East African zebu, has an acrocentric Y chromosome typical of Bos indicus . The southern African sanga breeds have a submetacentric Y chromosome typical of Bos taurus . Frequencies of four DNA markers support the hypothesis that the Tuli, a southern African sanga, had taurine ancestors and the Boran had both taurine and indicine ancestors. Frequencies for several protein polymorphisms strongly suggest that southern African sangas have more in common with taurine than with indicine breeds, while East African zebus are an admixture of African taurine and Asian indicine breeds.     

Admixture and diversity in West African cattle populations

We present a population genetic analysis of microsatellite variation in 16 West African cattle populations. West Africa represents a unique juxtaposition of different climatic and ecological zones in a relatively small geographical area. While more humid coastal regions are inhabited by the tsetse fly, a vector which spreads trypanosomiasis among cattle, the disease is not transmitted in the drier areas outside this zone. This is the most thorough study of genetic diversity in cattle within this area, which contains genetically important trypanotolerant Bos taurus breeds. Genetic relationships among the many breeds are examined and levels of diversity are assessed. Admixture levels were determined using a variety of methods. Ancestry informative or population-associated alleles (PAAs) were selected using populations from India, the Near East and Europe. Multivariate analysis, the admix program and model-based Bayesian admixture analysis approaches were also employed. These analyses reveal the direct impact of ecological factors and the profound effect of admixture on the cattle of this region. They also highlight the importance of efforts to prevent further dilution of African taurine breeds by B. indicus cattle.     

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.     

Genetic characterization of Argentine and Bolivian Creole cattle breeds assessed through microsatellites

In the present report, the polymorphisms from 9 microsatellites were used to assess genetic diversity and relationships in 4 Creole cattle breeds from Argentina and Bolivia, 4 European taurine breeds, and 2 American zebu populations. The Creole populations display a relatively high level of genetic variation as estimated by allelic diversity and heterozygosity, whereas the British breeds displayed reduced levels of genetic diversity. The analysis of molecular variance indicated that 7.8% of variance can be explained by differences among taurine and zebu breeds. Consistent with these results, the first principal component (PC), which comprised the 40% of the total variance, clearly distinguishes these 2 groups. In addition, all constructed phylogenetic trees cluster together Nelore and Brahman breeds with robust bootstrap values. Only 1% of variance was due to difference between American Creole and European taurine cattle. Although this secondary split was supported by the classical genetic distance and the second PC (15%), the topology of trees is not particularly robust. The presence of zebu-specific alleles in Creole cattle allowed estimating a moderate degree of zebu admixture. When these data were compared with mitochondrial and Y chromosomal studies, a clear pattern of male-mediated introgression was revealed. The results presented here contribute to the understanding of origin and history of the American Creole cattle.     

Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya

The Kenyan East African zebu cattle are valuable and widely used genetic resources. Previous studies using microsatellite loci revealed the complex history of these populations with the presence of taurine and zebu genetic backgrounds. Here, we estimate at genome-wide level the genetic composition and population structure of the East African Shorthorn Zebu (EASZ) of western Kenya. A total of 548 EASZ from 20 sub-locations were genotyped using the Illumina BovineSNP50 v. 1 beadchip. STRUCTURE analysis reveals admixture with Asian zebu, African and European taurine cattle. The EASZ were separated into three categories: substantial (⩾12.5%), moderate (1.56%<X<12.5%) and non-introgressed (⩽1.56%) according to the European taurine genetic proportion. The non-European taurine introgressed animals (n=425) show an unfluctuating zebu and taurine ancestry of 0.84±0.009 s.d. and 0.16±0.009 s.d., respectively, with significant differences in African taurine (AT) and Asian zebu backgrounds across chromosomes (P<0.0001). In contrast, no such differences are observed for the European taurine ancestry (P=0.1357). Excluding European introgressed animals, low and nonsignificant genetic differentiation and isolation by distance are observed among sub-locations (F_st=0.0033, P=0.09; r=0.155, P=0.07). Following a short population expansion, a major reduction in effective population size (N_e) is observed from approximately 240 years ago to present time. Our results support ancient zebu × AT admixture in the EASZ population, subsequently shaped by selection and/or genetic drift, followed by a more recent exotic European cattle introgression.     

Historical demographic profiles and genetic variation of the East African Butana and Kenana indigenous dairy zebu cattle

Butana and Kenana breeds from Sudan are part of the East African zebu Bos indicus type of cattle. Unlike other indigenous zebu cattle in Africa, they are unique due to their reputation for high milk production and are regarded as dairy cattle, the only ones of their kind on the African continent. In this study, we sequenced the complete mitochondrial DNA (mtDNA) D‐loop of 70 animals to understand the maternal genetic variation, demographic profiles and history of the two breeds in relation to the history of cattle pastoralism on the African continent. Only taurine mtDNA sequences were identified. We found very high mtDNA diversity but low level of maternal genetic structure within and between the two breeds. Bayesian coalescent‐based analysis revealed different historical and demographic profiles for the two breeds, with an earlier population expansion in the Butana vis a vis the Kenana. The maternal ancestral populations of the two breeds may have diverged prior to their introduction into the African continent, with first the arrival of the ancestral Butana population. We also reveal distinct demographic history between the two breeds with the Butana showing a decline in its effective population size (N_e) in the recent past ~590 years. Our results provide new insights on the early history of cattle pastoralism in Sudan indicative of a large ancient effective population size.     

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.     

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.     

Detection of selection signatures within candidate regions underlying trypanotolerance in outbred cattle populations

Breeding indigenous African taurine cattle tolerant to trypanosomosis is a straightforward approach to control costs generated by this disease. A recent study identified quantitative trait loci (QTL) underlying trypanotolerance traits in experimental crosses between tolerant N'Dama and susceptible Boran zebu cattle. As trypanotolerance is thought to result from local adaptation of indigenous cattle breeds, we propose an alternative and complementary approach to study the genetic architecture of this trait, based on the identification of selection signatures within QTL or candidate genes. A panel of 92 microsatellite markers was genotyped on 509 cattle belonging to four West African trypanotolerant taurine breeds and 10 trypanosusceptible European or African cattle breeds. Some of these markers were located within previously identified QTL regions or candidate genes, while others were chosen in regions assumed to be neutral. A detailed analysis of the genetic structure of these different breeds was carried out to confirm a priori grouping of populations based on previous data. Tests based on the comparison of the observed heterozygosities and variances in microsatellite allelic size among trypanotolerant and trypanosusceptible breeds led to the identification of two significantly less variable microsatellite markers. BM4440, one of these two outlier loci, is located within the confidence interval of a previously described QTL underlying a trypanotolerance-related trait.
Detection of selection signatures appears to be a straightforward approach for unravelling the molecular determinism of trypanosomosis pathogenesis. We expect that a whole genome approach will help confirm these results and achieve a higher resolving power.     

Analysis of mitochondrial DNA diversity in Burkina Faso populations confirms the maternal genetic homogeneity of the West African goat

To date, no comprehensive study has been performed on mitochondrial genetic diversity of the West African goat. Here, we analysed a 481-bp fragment of the HVI region of 111 goats representing four native West African populations, namely the three main Burkina Faso breeds, zoo-farm kept Dwarf goats and endangered Spanish goat breeds used as the outgroup. Analyses gave 83 different haplotypes with 102 variable sites. Most haplotypes (65) were unique. Only three haplotypes were shared between populations. Haplotypes were assigned to cluster A except for H45 (belonging to the Spanish Bermeya goat) which was assigned to cluster C. amova analysis showed that divergence between groups (Φ_CT) was not statistically significant regardless of whether the partition in two hierarchical levels that was fitted included Spanish samples or not. The West African goat scenario shown here is consistent with that previously reported for the species: haplogroup A is predominant and has a very high haplotype diversity regardless of the geographic area or sampled breed. The large phenotypic differences observable between the West African Dwarf and Sahelian long-legged goat populations are not detectable with mitochondrial markers. Moreover, a previously suggested introgression of Sahelian goat southwards because of desertification could not be assessed using mtDNA information.