African Taurine Research Articles

Temporal variation in body measurements in three Taurine cattle populations of Burkina Faso supports introgression of Zebu genes into West African Taurine cattle

A total of 769 adult females belonging to 3 taurine and one zebu cattle populations sampled in 3 provinces of Burkina Faso were assessed for 19 body measurements during two different years (2014 and 2018). The aim of this research was to identify temporal morphological variation in cattle bred in the humid southern zones to obtain empirical evidence supporting a possible introgression of zebu cattle genes into Gourounsi and Lobi taurine cattle breeds. Zebu cattle samples were used as out-group for both 2014 and 2018 subsets. Least square means of body measurements allowed to classify Burkina Faso taurine cattle into three subgroups according to body size (Gourounsi–Sanguié –GourS-, Gourounsi-Nahouri –GourN- and Lobi from the tallest to the smallest respectively). Principal Component Analysis suggested that in 2014, taurine populations were structured. Dispersion map constructed using the two first factors informed that the GourS population was well separated from both the Lobi and the GourN, which, in turn, overlapped. However, in 2018 a strong signal of homogenization was identified, with GourN partially overlapping the other two populations. Linear Discriminant Analysis suggested that about 20% of both GourS and GourN individuals were reciprocally misclassified. Clues for such increase have been pointed out by MANOVA analysis. Although on 2014, Lobi cattle was clearly smaller than Gourounsi and both GourS and GourN populations showed clear differences on body traits, on 2018 it could be assessed an increase in size in Lobi cattle and a strong homogenization signal within Gourounsi cattle. Zebu cattle gene flow southwards in Burkina Faso is likely to have caused these changes, suggesting a fast erosion of taurine cattle genetic background. 
 Keywords: Body traits, quantitative traits, Gourounsi cattle, Lobi, Burkina Faso.

The patterns of admixture, divergence, and ancestry of African cattle populations determined from genome-wide SNP data

BackgroundHumpless Bos taurus cattle are one of the earliest domestic cattle in Africa, followed by the arrival of humped Bos indicus cattle. The diverse indigenous cattle breeds of Africa are derived from these migrations, with most appearing to be hybrids between Bos taurus and Bos indicus. The present study examines the patterns of admixture, diversity, and relationships among African cattle breeds.MethodsData for ~ 40 k SNPs was obtained from previous projects for 4089 animals representing 35 African indigenous, 6 European Bos taurus, 4 Bos indicus, and 5 African crossbred cattle populations. Genetic diversity and population structure were assessed using principal component analyses (PCA), admixture analyses, and Wright’s F statistic. The linkage disequilibrium and effective population size (Ne) were estimated for the pure cattle populations.ResultsThe first two principal components differentiated Bos indicus from European Bos taurus, and African Bos taurus from other breeds. PCA and admixture analyses showed that, except for recently admixed cattle, all indigenous breeds are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. The African zebu breeds had highest proportions of Bos indicus ancestry ranging from 70 to 90% or 60 to 75%, depending on the admixture model. Other indigenous breeds that were not 100% African Bos taurus, ranged from 42 to 70% or 23 to 61% Bos indicus ancestry. The African Bos taurus populations showed substantial genetic diversity, and other indigenous breeds show evidence of having more than one African taurine ancestor. Ne estimates based on r2 and r2adj showed a decline in Ne from a large population at 2000 generations ago, which is surprising for the indigenous breeds given the expected increase in cattle populations over that period and the lack of structured breeding programs.ConclusionAfrican indigenous cattle breeds have a large genetic diversity and are either pure African Bos taurus or admixtures of African Bos taurus and Bos indicus. This provides a rich resource of potentially valuable genetic variation, particularly for adaptation traits, and to support conservation programs. It also provides challenges for the development of genomic assays and tools for use in African populations.

Inverted CD4+/CD8+ T cell ratio in Boran (Bos indicus) cattle

The CD4+/CD8+ ratio is used as a marker of the immune regulation of T cell balance. When the ratio in peripheral blood is less than 1, this is considered an indication of immune suppression in an individual. Previous work on bovine Peripheral Blood Mononuclear Cells (PBMC) has consistently reported a ratio ≥1 as seen in other mammalian hosts, i.e. higher circulating CD4+ cell numbers than CD8+ cell numbers. However, a consistent inverted CD4+/CD8+ ratio (<1) was observed in Boran cattle, an African Bos indicus breed. The T cell populations were characterized in Boran cattle (n = 52), revealing higher percentages of circulating CD8+ cells (31.9 % average) than CD4+ cells (19.1 % average), thus resulting in the inversion of the expected T cell homeostasis in these animals. The results show that this inversion is not an effect of age or relatedness of the cattle, rather, it was shared by almost all Boran cattle used in this study. Despite this inversion being a feature shared by both males and females, the female cattle had significantly higher CD4+/CD8+ ratios than the male Boran.This paper describes the characteristics of the T cell fractions in the study animals and compares the findings to those of other Boran cattle in Kenya, and four other cattle breeds representing African indicine, African taurine, Brazilian indicine and European taurine cattle. We demonstrate that the consistent observation of inverted CD4+/CD8+ cell ratio was restricted to the Boran.

The mosaic genome of indigenous African cattle as a unique genetic resource for African pastoralism

Cattle pastoralism plays a central role in human livelihood in Africa. However, the genetic history of its success remains unknown. Here, through whole-genome sequence analysis of 172 indigenous African cattle from 16 breeds representative of the main cattle groups, we identify a major taurine × indicine cattle admixture event dated to circa 750-1,050 yr ago, which has shaped the genome of today's cattle in the Horn of Africa. We identify 16 loci linked to African environmental adaptations across crossbred animals showing an excess of taurine or indicine ancestry. These include immune-, heat-tolerance- and reproduction-related genes. Moreover, we identify one highly divergent locus in African taurine cattle, which is putatively linked to trypanotolerance and present in crossbred cattle living in trypanosomosis-infested areas. Our findings indicate that a combination of past taurine and recent indicine admixture-derived genetic resources is at the root of the present success of African pastoralism.

Whole genome characterization of autochthonous Bos taurus brachyceros and introduced Bos indicus indicus cattle breeds in Cameroon regarding their adaptive phenotypic traits and pathogen resistance

Background African indigenous taurine cattle display unique adaptive traits shaped by husbandry management, regional climate and exposure to endemic pathogens. They are less productive with respect to milk and meat production which has been associated with amongst others, small size, traditional beliefs, husbandry practices, limited feed resources, disease burden and lack of sustained breeding for trait improvement. This resulted in the severe dwindling of their population size rendering them vulnerable to extinction.The Namchi taurine cattle breed is referred to as [Namchi (Doayo)] and shows resistance traits against trypanosome infection and exposure to tick infestation. Nonetheless, the historically later introduced Zebu cattle are the main cattle breeds in Africa today, even though they suffer more from locally prevailing pathogens.By using a whole genome sequencing approach, we sequenced with high depth for the first time the genomes of five cattle breeds from Cameroon in order to provide a valuable genetic resource for future African cattle breeding: the Namchi, an endangered trypano-tolerant taurine breed, the Kapsiki, an indigenous trypano-susceptible taurine breed, and three Zebu (Bos indicus indicus) breeds: Ngaoundere Gudali, White Fulani and Red Fulani.ResultsApproximately 167 Gigabases of raw sequencing data were generated for each breed and mapped to the cattle reference genomes ARS-UCD1.2 and UMD3.1.The coverage was 103 to 140-fold when aligning the reads to ARS-UCD1.2 with an average mapping rate of ~ 99%, and 22 to 30-fold when aligning the reads to UMD3.1 with an average mapping rate of ~ 64%. The single nucleotide polymorphisms (SNPs) obtained from analysis using the genome ARS-UCD1.2 were compared with reference genomes of European Bos taurus Holstein, the Asian Bos indicus Brahman, and the African trypanotolerant N’Dama breeds.A total of ~ 100 million (M) SNPs were identified and 7.7 M of those were breed-specific. An approximately 11.1 M constituted of small insertions and deletions. By using only breed-specific non-synonymous variants we identified genes as genetic signatures and associated Gene Ontology (GO) terms that could explain certain cattle-breed specific phenotypes such as increased tolerance against trypanosome parasites in the Namchi breed and heat tolerance in the Kapsiki breed. Phylogenetic analysis grouped, except for Namchi, the Bos taurus breeds Kapsiki, N’Dama and Holstein together while the B. indicus breeds White and Red Fulani, Gudali and Brahman clustered separately. The deviating result for Namchi indicates a hybrid status of the selected animal with a recent introgression of Zebu genes into its genome.ConclusionsThe findings provide the first comprehensive set of genome-wide variant data of the most important Cameroonian cattle breeds. The genomic data shall constitute a foundation for breed amelioration whilst exploiting the heritable traits and support conservation efforts for the endangered local cattle breeds.

A genetically unique Chinese cattle population shows evidence of common ancestry with wild species when analysed with a reduced ascertainment bias SNP panel.

In Hong Kong, there is a cattle population of ~1,200 individuals of uncertain origin and genetic diversity. This population shows heterogeneous morphology, both in body type and pigmentation. Once used as draught animals by the local farmers, they were abandoned around the 1970s due to changes in the economy, and since then have lived as feral populations. To explore the origins of these cattle, we analysed ~50k genotype data of 21 Hong Kong feral cattle, along with data from 703 individuals of 36 cattle populations of European, African taurine, and Asian origin, the wild x domestic hybrid gayal, plus two wild bovine species, gaur and banteng. To reduce the effect of ascertainment bias ~4k loci that are polymorphic in the two wild species were selected for further analysis. The stringent SNP selection we applied resulted in increased heterozygosity across all populations studies, compared with the full panel of SNP, thus reducing the impact of ascertainment bias and facilitating the comparison of divergent breeds of cattle. Our results showed that Hong Kong feral cattle have relatively high levels of genetic distinctiveness, possibly due to the low level of artificial selection, and a likely common ancestry with wild species. We found signs of a putative taurine introgression, probably dating to the import of north European breeds during the British colonialism of Hong Kong. We showed that Hong Kong feral cattle, are distinct from Bos taurus and Bos indicus breeds. Our results highlight the distinctiveness of Hong Kong feral cattle and stress the conservation value of this indigenous breed that is likely to harbour adaptive genetic variation, which is a fundamental livestock resource in the face of climate change and diversifying market demands.

Genome Sequence Analysis Reveals Selection Signatures in Endangered Trypanotolerant West African Muturu Cattle.

Like most West African Bos taurus, the shorthorn Muturu is under threat of replacement or crossbreeding with zebu. Their populations are now reduced to a few hundred breeding individuals and they are considered endangered. So far, the genetic variation and genetic basis of the trypanotolerant Muturu environmental adaptation have not been assessed. Here, we present genome-wide candidate positive selection signatures in Muturu following within-population iHS and between population Rsb signatures of selection analysis. We compared the results in Muturu with the ones obtained in N’Dama, a West African longhorn trypanotolerant taurine, and in two European taurine (Holstein and Jersey). The results reveal candidate signatures of selection regions in Muturu including genes linked to the innate (e.g., TRIM10, TRIM15, TRIM40, and TRIM26) and the adaptive (e.g., JSP.1, BOLA-DQA2, BOLA-DQA5, BOLA-DRB3, and BLA-DQB) immune responses. The most significant regions are identified on BTA 23 at the bovine major histocompatibility complex (MHC) (iHS analysis) and on BTA 12 at genes including a heat tolerance gene (INTS6) (Rsb analysis). Other candidate selected regions include genes related to growth traits/stature (e.g., GHR and GHRHR), coat color (e.g., MITF and KIT), feed efficiency (e.g., ZRANB3 and MAP3K5) and reproduction (e.g., RFX2, SRY, LAP3, and GPX5). Genes under common signatures of selection regions with N’Dama, including for adaptive immunity and heat tolerance, suggest shared mechanisms of adaptation to environmental challenges for these two West African taurine cattle. Interestingly, out of the 242,910 SNPs identified within the candidate selected regions in Muturu, 917 are missense SNPs (0.4%), with an unequal distribution across 273 genes. Fifteen genes including RBBP8, NID1, TEX15, LAMA3, TRIM40, and OR12D3 comprise 220 missense variants, each between 11 and 32. Our results, while providing insights into the candidate genes under selection in Muturu, are paving the way to the identification of genes and their polymorphisms linked to the unique tropical adaptive traits of the West Africa taurine, including trypanotolerance.

Consequences of breed formation on patterns of genomic diversity and differentiation: the case of highly diverse peripheral Iberian cattle

BackgroundIberian primitive breeds exhibit a remarkable phenotypic diversity over a very limited geographical space. While genomic data are accumulating for most commercial cattle, it is still lacking for these primitive breeds. Whole genome data is key to understand the consequences of historic breed formation and the putative role of earlier admixture events in the observed diversity patterns.ResultsWe sequenced 48 genomes belonging to eight Iberian native breeds and found that the individual breeds are genetically very distinct with FST values ranging from 4 to 16% and have levels of nucleotide diversity similar or larger than those of their European counterparts, namely Jersey and Holstein. All eight breeds display significant gene flow or admixture from African taurine cattle and include mtDNA and Y-chromosome haplotypes from multiple origins. Furthermore, we detected a very low differentiation of chromosome X relative to autosomes within all analyzed taurine breeds, potentially reflecting male-biased gene flow.ConclusionsOur results show that an overall complex history of admixture resulted in unexpectedly high levels of genomic diversity for breeds with seemingly limited geographic ranges that are distantly located from the main domestication center for taurine cattle in the Near East. This is likely to result from a combination of trading traditions and breeding practices in Mediterranean countries. We also found that the levels of differentiation of autosomes vs sex chromosomes across all studied taurine and indicine breeds are likely to have been affected by widespread breeding practices associated with male-biased gene flow.

Determinants of Crossbreeding Practices by Cattle Farmers in South Benin, West Africa: Implications for the Sustainable Use of the Indigenous Lagune Cattle Population

While it is widely acknowledged that the small-sized West African Shorthorn taurine Lagune cattle is being increasingly crossbred with and replaced by large-sized zebus, little is known about the factors that influence farmers&amp;rsquo; crossbreeding decisions and selection practices. But this information is necessary for the development of strategies towards a rationale use and conservation of this unique African genetic resource. To fill this knowledge gap, we conducted, between September and November 2016, a questionnaire survey in the belt of this breed in South Benin. One hundred seventy-three cattle farms were surveyed. The binomial logistic regression approach was used to predict the likelihood of a Lagune cattle farmer to be willing to introduce zebus in his herd. The herds were composed of either Lagune only (82.1%), zebu only (4.0%), crossbred Lagune x zebu (1.2%), Lagune and zebu (9.2%) or Lagune and crossbred Lagune x zebu (3.5%). The low productivity of the Lagune cattle and the market demand for large-sized animals were the main farmers&amp;rsquo; motivations for crossbreeding. Farmers raising large herds of Lagune cattle under control mating system were more likely to adopt crossbreeding. The risk of dilution of the Lagune breed could be reduced by increasing awareness among farmers, improving their technical skills in herd management and empowering them to develop legal institutions, by-laws and collective actions for sustainable breed management. Farmers who have already adopted crossbreeding should be provided with appropriate services and technical assistance, whereas breed conservation initiatives should mainly focus on small purebred herds kept under control mating.

A genomic map of climate adaptation in Mediterranean cattle breeds.

Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short-term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate subtypes. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g., NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied on standing genomic variation of taurine origin, or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support conservation of these populations.

Deciphering the patterns of genetic admixture and diversity in southern European cattle using genome-wide SNPs.

The divergence between indicine cattle (Bos indicus) and taurine cattle (Bos taurus) is estimated to have occurred approximately 250,000 years ago, but a small number of European cattle breeds still display shared ancestry with indicine cattle. Additionally, following the divergence of African and European taurine, the gene flow between African taurine and southern European cattle has also been proposed. However, the extent to which non‐European cattle ancestry is diffused across southern European cattle has not been investigated thoroughly. Also, in recent times, many local breeds have suffered severe reductions in effective population size. Therefore, in the present study, we investigated the pattern of genetic diversity in various European cattle based on single nucleotide polymorphisms (SNP) identified from whole‐genome sequencing data. Additionally, we also employed unlinked and phased SNP‐based approaches on high‐density SNP array data to characterize non‐European cattle ancestry in several southern European cattle breeds. Using heterozygosity‐based parameters, we concluded that, on average, nucleotide diversity is greater in southern European cattle than western European (British and commercial) cattle. However, an abundance of long runs of homozygosity (ROH) and the pattern of Linkage disequilibrium decay suggested recent bottlenecks in Maltese and Romagnola. High nucleotide diversity outside ROH indicated a highly diverse founder population for southern European and African taurine. We also show that Iberian cattle display shared ancestry with African cattle. Furthermore, we show that Podolica is an ancient cross‐bred between Indicine zebu and European taurine. Additionally, we also inferred similar ancestry profile of non‐European cattle ancestry in different Balkan and Italian cattle breeds which might be an indication of the common origin of indicine ancestry in these breeds. Finally, we discuss several plausible demographic scenarios which might account for the presence of non‐European cattle ancestry in these cattle breeds.

Genetic diversity and relationships among six local cattle populations in semi-arid areas assessed by a bovine medium-density single nucleotide polymorphism data

The local cattle populations belonging to the ‘Brune de l’Atlas’ cattle in Algeria and Morocco are potential resources in terms of genetic diversity and socioeconomic prevalence and their characterization is an essential step in any program designed to conserve genetic diversity. Our objectives were to assess the genetic diversity, the population structure and relationships among four Algerian cattle breeds, the Biskra, Cheurfa, Chelifienne and Guelmoise and of two Moroccan, the Oulmès-Zaër and Tidili by genotyping 50 309 single nucleotide polymorphism in 203 unrelated animals. A low population structure was observed across breeds with pairwise F ST values ranging from 0.008 to 0.043, suggesting a high level of gene flow. These data were combined with the available data on cattle populations representative of Europe (EUT), West African taurine (WAT) and zebu (ZEB). Principle Components Analysis was carried out which revealed that the Maghrebin populations are closer to the EUT/ZEB population than to the WAT. Structure analysis confirmed this mixed origin of the Maghrebin cattle populations. We also detected the influence of zebu breeds in Cheurfa and Guelmoise populations. This study provides the first information about genetic diversity within and between Algerian and Moroccan cattle populations and gives a detailed description of their genetic structure and relationships according to their historical origins. This study revealed that several combined effects contributed to shape the genetic diversity of the six Maghrebin populations studied: (i) gene flow among local breeds, (ii) the recent introgression of European breeds in local Algerian breeds and (iii) the traditional management systems. The results of this study will primarily assist policy makers and livestock keepers to make useful decisions for improvement of genetic resources while ensuring the preservation and conservation of local breeds in Algeria and Morocco.

Signatures of Selection in Admixed Dairy Cattle in Tanzania.

Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we evaluated 839 admixed crossbred cows sampled from two major dairy regions in Tanzania namely Rungwe and Lushoto districts, in order to understand their genetic architecture and detect genomic regions showing preferential selection. Animals were genotyped at 150,000 SNP loci using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array. Population structure analysis showed a large within-population genetic diversity in the study animals with a high degree of variation in admixture ranging between 7 and 100% taurine genes (dairyness) of mostly Holstein and Friesian ancestry. We explored evidence of selection signatures using three statistical methods (iHS, XP-EHH, and pcadapt). Selection signature analysis identified 108 candidate selection regions in the study population. Annotation of these regions yielded interesting genes potentially under strong positive selection including ABCG2, ABCC2, XKR4, LYN, TGS1, TOX, HERC6, KIT, PLAG1, CHCHD7, NCAPG, and LCORL that are involved in multiple biological pathways underlying production and adaptation processes. Several candidate selection regions showed an excess of African taurine ancestral allele dosage. Our results provide further useful insight into potential selective sweeps in the genome of admixed cattle with possible adaptive and productive importance. Further investigations will be necessary to better characterize these candidate regions with respect to their functional significance to tropical adaptations for dairy cattle.

Genomic signatures of adaptive introgression and environmental adaptation in the Sheko cattle of southwest Ethiopia.

Although classified as an African taurine breed, the genomes of Sheko cattle are an admixture of Asian zebu and African taurine ancestries. They populate the humid Bench Maji zone in Sheko and Bench districts in the south-western part of Ethiopia and are considered as a trypanotolerant breed with high potential for dairy production. Here, we investigate the genome of Sheko cattle for candidate signatures of adaptive introgression and positive selection using medium density genome-wide SNP data. Following locus-ancestry deviation analysis, 15 and 72 genome regions show substantial excess and deficiency in Asian zebu ancestry, respectively. Nine and 23 regions show candidate signatures of positive selection following extended haplotype homozygosity (EHH)-based analyses (iHS and Rsb), respectively. The results support natural selection before admixture for one iHS, one Rsb and three zebu ancestry-deficient regions. Genes and/or QTL associated with bovine immunity, fertility, heat tolerance, trypanotolerance and lactation are present within candidate selected regions. The identification of candidate regions under selection in Sheko cattle warrants further investigation of a larger sample size using full genome sequence data to better characterise the underlying haplotypes. The results can then support informative genomic breeding programmes to sustainably enhance livestock productivity in East African trypanosomosis infested areas.

Domestication of cattle: Two or three events?

Cattle have been invaluable for the transition of human society from nomadic hunter‐gatherers to sedentary farming communities throughout much of Europe, Asia and Africa since the earliest domestication of cattle more than 10,000 years ago. Although current understanding of relationships among ancestral populations remains limited, domestication of cattle is thought to have occurred on two or three occasions, giving rise to the taurine (Bos taurus) and indicine (Bos indicus) species that share the aurochs (Bos primigenius) as common ancestor ~250,000 years ago. Indicine and taurine cattle were domesticated in the Indus Valley and Fertile Crescent, respectively; however, an additional domestication event for taurine in the Western Desert of Egypt has also been proposed. We analysed medium density Illumina Bovine SNP array (~54,000 loci) data across 3,196 individuals, representing 180 taurine and indicine populations to investigate population structure within and between populations, and domestication and demographic dynamics using approximate Bayesian computation (ABC). Comparative analyses between scenarios modelling two and three domestication events consistently favour a model with only two episodes and suggest that the additional genetic variation component usually detected in African taurine cattle may be explained by hybridization with local aurochs in Africa after the domestication of taurine cattle in the Fertile Crescent. African indicine cattle exhibit high levels of shared genetic variation with Asian indicine cattle due to their recent divergence and with African taurine cattle through relatively recent gene flow. Scenarios with unidirectional or bidirectional migratory events between European taurine and Asian indicine cattle are also plausible, although further studies are needed to disentangle the complex human‐mediated dispersion patterns of domestic cattle. This study therefore helps to clarify the effect of past demographic history on the genetic variation of modern cattle, providing a basis for further analyses exploring alternative migratory routes for early domestic populations.

Genetic diversity and origin of Namchi cattle breed inferred by matrilineage analyses

In animal genetic studies, mitochondrial DNA (mtDNA) analysis offers a way to detect changes in populations over time along with their maternal origin and migration routes. To determine these patterns in Namchi cattle breeds of Cameroon, analyses of 17 sequences of a 336 base pair fragment of the mtDNA D-loop region from two populations (Namchi Poli and Namchi Ngaoundere) were conducted in conjunction with previously published sequences from African, European, Japanese and Chinese subjects. As expected for an African taurine breed, all individuals in the study were found to be members of haplogroup T1. Due to the size of fragment analyzed, only one sub-haplogroup (T1c)could be detected, at a rate of 5.88%.This suggested that The Namchi cattle breed originated most probably from south west Asia and migrated to Cameroon through the Ismuth of Suez to Egypt and through Arabia to Somalia and Ethiopia. A relatively high nucleotide diversity (π) was found in Namchi Poli population (0.03421±0.00582) while in Namchi Ngaoundere a value of 0.00980±0.00185 was obtained, for a total nucleotide diversity of 0.01387±0.00234. The high genetic diversity observed in Namchi cattle breed reflects not only the presence of sub-haplogroups T1 but also an introgression from hybridization. This study provides new information regarding the sub haplogroups of the Namchi cattle, their origin and migration routes and their genetic diversity which seems to have been affected by gene flow with zebus like White Fulani or Red Fulani. To facilitate the preservation and the conservation of the Namchi cattle breed in Cameroon, it is therefore important to adopt effective breeding management practices.

Morphological assessment of Niger Kuri cattle using multivariate methods

A total of 406 adult cows and 34 bulls belonging to the Niger Kuri cattle population were assessed for 16 body measurements and 11 qualitative traits to contribute to the characterization of this unique cattle breed. Body measurements included facial, horn, ear and rump lengths; facial, cranial, shoulder, pelvic and ischium widths; height at withers and at hips; muzzle circumference; heart girth; body and tail lengths; and thorax depth. Qualitative traits included cephalic profile, ear shape, muzzle pigmentation, eyelid pigmentation, hoof pigmentation, horn colour, dewlap size, backline profile, horn shape, spotting pattern, and coat colour pattern. Data were analysed jointly with 377 individuals from four other West African taurine cattle breeds (N’Dama, Lagunaire, Lobi and Somba) using multivariate statistical methods, including canonical and correspondence analyses. Among the breeds analysed, Kuri cattle had the highest mean values for all body measurements: height at withers and body length had mean values of 124.0 ± 0.4 and 146.8 ± 1.0 cm in Kuri cows, respectively, and 126.0 ± 2.2 and 155.7 ± 3.6 cm, respectively, in Kuri bulls. Canonical analysis allowed the construction of contour plots to illustrate the high differentiation between Kuri cattle and the other breeds, regardless of the sex of the individuals. Further, the Mahalanobis distance matrices showed that pairs involving Kuri cattle had the higher differentiation of these populations. Correspondence analysis carried out on these 11 qualitative traits allowed the researchers to ascertain a clear differentiation between the Kuri and the other taurine cattle breeds. The N’Dama, Lagunaire, Lobi, and Somba breeds did not show clear differentiation at qualitative-type trait level with 75% confidence regions computed for these four breeds being highly intermingled. In the current data, Kuri cattle had the highest frequency in qualitative features, such as concave cephalic profile, dropped ears, non-pigmented muzzle and grey-coloured horns, which are absent in West African taurine and zebu cattle breeds, according to the literature. The current evidence would suggest that unique Kuri cattle type features may result from breeding decisions rather than from zebu admixture. This work confirms that at type trait level Kuri cattle is a unique population within the West African taurine cattle group. The implementation of genetic analyses aiming at ascertaining the degree of uniqueness of the breed is advised. Keywords: Body measurements, Bos taurus , multivariate analyses, qualitative traits, West African cattle

Effect of genetic European taurine ancestry on milk yield of Ankole-Holstein crossbred dairy cattle in mixed smallholders system of Burundi highlands.

Different breeding systems associated with specific bovine genetic resources have coexisted in Burundi. To prepare for the development of a national action plan for the improvement of bovine genetic resources in Burundi, we aimed at performing genetic characterization of Ankole and Ankole×European crossbred individuals and assessing the effect of European ancestry on milk productivity of cows kept under the mixed crops livestock system. To that end, we genotyped 37 Ankole and 138 crossbred individuals on 42636 SNPs and combined these genotypes with those from 21 cattle breeds, representative of the bovine genetic diversity. We also measured milk yield not suckled and estimated suckled milk. Given the results, we confirmed the indicine×African taurine admixed origin of the Ankole in Burundi and showed that crossbred individuals present a high proportion of European ancestry (i.e. 57% on average). As the proportion of European ancestry increased, milk yield increased by 0.03±0.01l/day, at a lower extent than expected. We also observed that breeders were unable to correctly evaluate the European proportion in their livestock. Our results may provide useful information for objective dairy breeding in Burundi. As an example, an ex-situ conservation program of Ankole within the framework of value chains is proposed as an accompanying strategy to improve the sustainability of the crossbreeding program.

Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu.

The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to fine map 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.

Differences in genetic structure assessed using Y-chromosome and mitochondrial DNA markers do not shape the contributions to diversity in African sires.

Up to 173 African sires belonging to 11 different subpopulations representative of four cattle groups were analysed for six Y-specific microsatellite loci and a mitochondrial DNA fragment. Differences in Y-chromosome and mtDNA haplotype structuring were assessed. In addition, the effect of such structuring on contributions to total genetic diversity was assessed. Thirty-five Y-chromosome and 71 mtDNA haplotypes were identified. Most Y-chromosomes analysed (73.4%) were of zebu origin (11 haplotypes). Twenty-two Y-haplotypes (44 samples) belonged to the African taurine subfamily Y2a. All mtDNA haplotypes belonged to the "African" taurine T1 haplogroup with 16 samples and nine haplotypes belonging to a recently identified subhaplogroup (T1e). Median-joining networks showed that Y-chromosome phylogenies were highly reticulated with clear separation between zebu and taurine clusters. Mitochondrial haplotypes showed a clear star-like shape with small number of mutations separating haplotypes. Mitochondrial-based FST -statistics computed between cattle groups tended to be statistically non-significant (p>.05). Most FST values computed among groups and subpopulations using Y-chromosome markers were statistically significant. AMOVA confirmed that divergence between cattle groups was only significant for Y-chromosome markers (ΦCT =0.209). At the mitochondrial level, African sires resembled an undifferentiated population with individuals explaining 94.3% of the total variance. Whatever the markers considered, the highest contributions to total Nei's gene diversity and allelic richness were found in West African cattle. Genetic structuring had no effect on patterns of contributions to diversity.