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In the context of global changes, preserving local livestock genetic resources is primordial to keep traits and alleles that will be important in the future. To characterize this population, we performed qualitative and quantitative phenotypic description of 400 cattle . We also explored genetic diversity by genotyping 150 individuals with the Illumina 54K SNP chip and by comparing these genotyping data to a panel of breeds belonging to the main groups of cattle populations (i.e. European taurine, African taurine, zebu and hybrid) available on Widde plateform (1,2,3). At last, we estimated recent inbreeding level(4). Using phenotypic data, we were able to define the descriptive profile of the population of Mayotte. Qualitative phenotypes were heterogenous with several patterns of fur, horns and humps. Regarding morphological traits, Zebu of Mayotte presented small size as exemplified by the mean withers height (i.e 106 cm). Exploratory genomic analyses of its genetic structure revealed that this population resulted from admixture between zebu (with an indicine proportion of 96%) and African taurine and was genetically close to Zebu of Madagascar. Both breeds harbored the highest indicine ascendance compared to other African cattle breeds. A weak European taurine ancestry (i.e. less than 5%) was detected in few individuals, indicating that this breed was still relatively well preserved from crossing with exotic (European taurine) cattle breeds. The estimation of recent inbreeding for this population indicates a favorable inbreeding situation for conservation perspectives of Mahorais Zebu. However, lack of control of artificial insemination and recent import of European cows could have an impact on cattle genetic diversity in Mayotte Island. This must be taken account in future conservation projects. A report of these results was presented to the French Ministry of Agriculture, and leaded to the official recognition of this breed.

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Knowledge about the origin and evolutionary history of the bison has been improved recently owing to several genomic and paleogenomic studies published in the last two years, which elucidated large parts of the evolution of bison populations during the Upper Pleistocene and Holocene in Eurasia. The produced data, however, were interpreted in contradicting manners. Here, we have gathered, reanalyzed and compared previously published or unpublished morphometric and genetic data that have not yet been integrated and that we synthesize in a unified framework. In particular, we re-estimate dates of divergence of mitogenome lineages based on an extended dataset comprising 81 complete ancient bison mitogenomes and we revisit putative gene flow between the Bos and Bison genera based on comparative analyses of ancient and modern bison genomes, thereby questioning published conclusions. Morphometric analyses taking into account sexual dimorphism invalidate a previous claim that Bison schoetensacki was present in France during the Late Pleistocene. Both morphometric and genome analyses reveal that Eurasian bison belonging to different Bison priscus and Bison bonasus lineages maintained parallel evolutionary paths with gene flow during a long period of incomplete speciation that ceased only upon the migration of B. priscus to the American continent establishing the American bison lineage. Our nuclear genome analysis of the evolutionary history of B. bonasus allows us to reject the previous hypothesis that it is a hybrid of B. priscus and Bos primigenius. Based on present-day behavioral studies of European and American bison, we propose that apparently conflicting lines of evidence can be reconciled by positing that female bison drove the specialization of bison populations to different ecological niches while male bison drove regular homogenizing genetic exchanges between populations.

National audience; Animal African Trypanosomosis (AAT) is a vector-borne disease caused by blood protozoan parasites of the Trypanosoma genus. It represents a major constraint to the development of cattle breeding in the humid and sub-humid zones of Africa because of the high morbidity and mortality it causes. Zebu breeds and European taurine breeds are very susceptible to AAT and they usually die in the absence treatment. On the contrary, some taurine breeds in West Africa have the capacity to tolerate the disease and are called trypanotolerant. The trypanotolerant phenotype is known to be polygenic and multifactorial, but up to now, its mechanisms remain unknown. In order to decipher the molecular bases of trypanotolerance, we chose to analyse the genes expression of blood cells of susceptible and tolerant cattle during an experimental infection, performed in Burkina Faso, in 40 cattle from five West African breeds with T. congolense. mRNA were extracted from blood, comprising bovine leukocytes and parasites, before and during the infection and were sequenced using a Illumina highSeq2000. We mapped the reads on the bovine and trypanosome genomes, counted the reads on the annotated genes and performed a differential expression analysis. The genes identified as differentially expressed during the infection were then analysed using the Ingenuity Pathway Analysis software in order to identify enriched functional patterns. The functional analyses highlighted upstream regulators and canonical pathways associated with the immune response, the cell proliferation and signaling. Very fine differences in the modulation of the response between trypanotolerant and susceptible cattle were observed.

Medium density genotyping data (50K SNP) of 174 individuals from 9 Burundi cattle populations (see README_DATA.txt).

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In recent decades, changes in climate have caused impacts on natural and human systems. Mediterranean countries will be particularly affected by this phenomenon, with growing temperatures and reduced rainfall. Understanding how species and ecosystems respond to climate change has become a crucial focus in biodiversity conservation and management. The genome-wide SNP panels allows providing background information on genome structure in domestic animals, opening new perspectives to livestock genetics. The International Project GALIMED "Genetic Adaptation of Bovine Livestock and production systems in MEDiterranean region", develops an integrated approach that combines the analysis of SNP markers, bioclimatic variables and farming system information to identify genotypes and breeding practices able to respond to climate change. Italian and Corsican local breeds are part of this project. The aim of the study is to identify genomic regions related to adaptation to climate change in these local breeds. Individuals of Cinisara (71), Modicana (72), Maremmana (25), Piemontese (21), Romagnola (21), Sarda (30), Sardo-Modicana (28) and Corse (31) breeds were genotyped using Bovine SNP 50k. Farming systems data were collected by interviewing breeders. Geographic coordinates and 19 bioclimatic variables were also available. Principal Components Analysis (PCA) was performed on SNPs data and climatic variables. Co-inertia (CIA) analysis was realized to detect a possible common structure between such different information. After edits, 43,625 SNPs were retained. The PC1 on individual genotypes differentiates Modicana from other breeds, and shows that Sardo-Modicana is close to Modicana, but is clearly admixed to another breed. The PC2 differentiates Cinisara from a cluster "Romagnola/Maremmana" and shows a large variability of the Modicana breed. The CIA coefficient between molecular data and both geographic and climatic information is equal to 0.38, (P-value=0.001), suggesting evidence of genetic adaptation to different climatic pressures. Further analyses are on going to identify the genetic regions with a potential adaptive role. The results will provide a solid scientific foundation to reconsider objectives and selection criteria and to improve farming practices to prepare livestock to new environmental conditions.

Cattle breeds may be broadly divided between temperate taurine breeds, from European origins, African taurine breeds, and Indian zebu breeds, and various admixed populations. A little number of these breeds has a worldwide distribution, while many of them have evolved in restrained areas and remain at a local or a regional level. Tropical countries are rich of a wide diversity of original cattle breeds, whose characteristics remain mostly undescribed. These characteristics are the results of various forces, such as the genetic background of the ancestral populations, the influence of agroecological environment in which they have evolved, and the livestock keeper preferences and practices. Tropical cattle breeds have therefore developed specific attributes and functions, to adapt to a wide range of environmental constraints and production systems. Such characteristics are the ability to tolerate high ambient temperature, with a reduced effect on their production skills, resistance to internal or external parasites and infectious diseases, valorization of rough diets, tolerance to harsh conditions and ability to recuperate during more favorable seasons, and working ability. These characteristics may be in the future of great utility to face the deleterious effects of climate change. The physiological traits involved in these characteristics are complex and their genetic basis has not yet been unraveled. However some studies of selection signatures identification give some insights on the genetic background of some adaptation traits of local tropical cattle breeds that could be useful in the future to face the direct and indirect effects of climatic change on livestock production systems. (Texte intégral)

Plot of the individuals according to their coordinates on the first two principal components of the principal component analysis including 31,477 SNPs genotyped on 2270 individuals from 49 cattle populations. This dataset contains 7 new individuals from two populations i.e. Montbéliard (A_221) and Tarentaise (A_125). The individuals which belong to the three main cattle population groups (European taurine, African taurine and Zebu) are indicated on the plot. (PDF 157 kb)

T According to IPCC, Mediterranean countries will be particularly affected by global warming, with growing temperatures, reduced rainfall during summer months and recurrent heat waves and droughts; this climate is estimated to move inland. In this context, local Mediterranean cattle breeds, genetically selected to adapt to this harsh environment and breed with specific practices are valuable genetic resources.

Cattle breeds may be broadly divided between temperate taurine breeds, from European origins, African taurine breeds, and Indian zebu breeds, and various admixed populations. A little number of these breeds has a world-wide distribution, while many of them have evolved in restrained area and remain at a local or a regional level. Tropical countries are rich of a wide diversity of original cattle breeds, which characteristics remain mostly undescribed. These characteristics are the results of various forces, like the genetic background of the ancestral populations, the influence of agro ecological environment in which they have evolved, and the livestock keeper preferences and practices. Tropical cattle breeds have therefore develop specific attributes and functions, to adapt to a wide range of environmental constraints and production systems. Such characteristics are the ability to tolerate high ambient temperature, with a reduce effect on their production skills, resistance to internal or external parasites and infectious diseases, valorisation of rough diets, tolerance to harsh conditions and ability to recuperate in more favourable seasons, and working ability. These characteristics may be in the future of a great utility to face the deleterious effects of climate change. The physiological traits involved in these characteristics are complex and their genetic basis has not yet been unraveled. However some studies of selection signatures identification give some insights on the genetic background of some adaptation traits of local tropical cattle breeds that could be useful in the future to face the direct and indirect effects of climatic change on livestock production systems.

Sample BSON documents illustrating variant and genotyping data storage. The two typical kinds of database records, i.e. Variant document and VariantRunData document, contain variant-level information and run-level genotyping data, respectively. Because storage is made in such a way that dictionary keys are repeated for each record, we defined them as short as two characters in order to keep disk space usage reasonable. Flexibility is illustrated by the use of lists and dictionaries, which can grow without the need to redefine a fixed model. (PDF 160 kb)

According to IPCC, Mediterranean countries will be particularly affected by global warming, with rising temperatures, reduced rainfall during summer months and recurrent heat waves and droughts; this climate is estimated to move inland. In this context, local Mediterranean cattle breeds, genetically selected to adapt to this harsh environment and breed with specific practices are valuable genetic resources. In order to identify genotypes and breeding practices capable of coping with the environmental challenge induced by climate change, we propose an integrative approach combining genetic analysis of cattle populations, climate conditions and livestock systems. For this purpose, 21 breeds from three southern (Algeria, Egypt and Morocco), two eastern (Cyprus and Greece) and three northern (France, Italy and Spain) Mediterranean countries were genotyped at 41187 SNPs. These data were combined to those available on breeds from neighbouring areas (Massif Central, Alps). Bioclimatic data (annual trends, seasonality, extreme factors) was obtained from WorldClim, a database for ecological modelling. Meanwhile, we have characterized the breeding systems of these local breeds thanks to questionnaires proposed to experts, completed by several extensive case studies. Model-based clustered methods and Principal Component Analysis were first performed to address the overall structuration of populations. Then a redundancy analysis was performed to describe how geographical and bioclimatic features shape the genetic variation among breeds. Breeds are clearly differentiated according to geography and climate (temperature, rainfall). Finally, genomic regions that contribute the most to the genetic variation associated to climate are identified. The main features of breeding practices in Mediterranean environment are also determined as well as the main animal traits that breeders associate to breeds' adaptation. This work was supported by the INRA Metaprogram ACCAF (GALIMED project). (Texte intégral)

Ce numéro d’Innovations Agronomiques comprend les articles correspondant aux présentations du colloque « La diversité génétique, ressource pour l’agriculture de demain » qui s’est tenu à Paris le 18 juin 2013; The origin of the currently observed cattle species diversity is intimately related to human population history since first domestication events. While new genomic tools (medium to high density SNP chips, next generation sequencing) provide insights into this complex history through the genetic characterisation of cattle breeds, they also allow identifying footprints left in their genome by human (artificial selection pressures) and more generally by environmental constraints (natural selection pressures). [br/]After a brief report on current knowledge of possible origins of cattle diversity, based on the characterization of cattle breeds neutral genetic diversity, we illustrate, in this article, studies of natural and artificial selection footprints in bovine genome from analyses carried out in African and New World tropical cattle breeds and in high-producing dairy cattle.; L’origine de la grande diversité actuelle de l'espèce bovine est intimement liée à l’histoire des peuplements humains depuis les premiers événements de domestication. Si les nouveaux outils génomiques (puces de génotypage de SNP à moyenne et haute densité, séquençage à haut-débit) aident à retracer cette histoire complexe, à travers la caractérisation génétique fine des races actuelles, ils permettent également d'identifier dans le génome de ces races les empreintes laissées par les contraintes exercées par l'homme (pressions de sélection artificielle) et plus généralement par l'environnement (pressions de sélection naturelle). [br/]Après un bref état des lieux des connaissances actuelles sur les origines probables de la diversité observée dans l'espèce bovine, présentant la caractérisation de la diversité génétique neutre des races bovines, nous proposons d'illustrer dans cet article l’étude des traces de sélections naturelle et artificielle dans le génome à partir d'exemple de travaux menés sur les races bovines tropicales africaines et du nouveau monde, et sur les races laitières hautes productrices françaises.