Insights into the Genetic History of French Cattle from Dense SNP Data on 47 Worldwide Breeds

BACKGROUND: Modern cattle originate from populations of the wild extinct aurochs through a few domestication events which occurred about 8,000 years ago. Newly domesticated populations subsequently spread worldwide following breeder migration routes. The resulting complex historical origins associated with both natural and artificial selection have led to the differentiation of numerous different cattle breeds displaying a broad phenotypic variety over a short period of time. METHODOLOGY/PRINCIPAL FINDINGS: This study gives a detailed assessment of cattle genetic diversity based on 1,121 individuals sampled in 47 populations from different parts of the world (with a special focus on French cattle) genotyped for 44,706 autosomal SNPs. The analyzed data set consisted of new genotypes for 296 individuals representing 14 French cattle breeds which were combined to those available from three previously published studies. After characterizing SNP polymorphism in the different populations, we performed a detailed analysis of genetic structure at both the individual and population levels. We further searched for spatial patterns of genetic diversity among 23 European populations, most of them being of French origin, under the recently developed spatial Principal Component analysis framework. CONCLUSIONS/SIGNIFICANCE: Overall, such high throughput genotyping data confirmed a clear partitioning of the cattle genetic diversity into distinct breeds. In addition, patterns of differentiation among the three main groups of populations--the African taurine, the European taurine and zebus--may provide some additional support for three distinct domestication centres. Finally, among the European cattle breeds investigated, spatial patterns of genetic diversity were found in good agreement with the two main migration routes towards France, initially postulated based on archeological evidence

Consensus genetic structuring and typological value of markers using multiple co-inertia analysis

Working with weakly congruent markers means that consensus genetic structuring of populations requires methods explicitly devoted to this purpose. The method, which is presented here, belongs to the multivariate analyses. This method consists of different steps. First, single-marker analyses were performed using a version of principal component analysis, which is designed for allelic frequencies (%PCA). Drawing confidence ellipses around the population positions enhances %PCA plots. Second, a multiple co-inertia analysis (MCOA) was performed, which reveals the common features of single-marker analyses, builds a reference structure and makes it possible to compare single-marker structures with this reference through graphical tools. Finally, a typological value is provided for each marker. The typological value measures the efficiency of a marker to structure populations in the same way as other markers. In this study, we evaluate the interest and the efficiency of this method applied to a European and African bovine microsatellite data set. The typological value differs among markers, indicating that some markers are more efficient in displaying a consensus typology than others. Moreover, efficient markers in one collection of populations do not remain efficient in others. The number of markers used in a study is not a sufficient criterion to judge its reliability. "Quantity is not quality"

WIDDE: a Web-Interfaced next generation database for genetic diversity exploration, with a first application in cattle

Background The advent and democratization of next generation sequencing and genotyping technologies lead to a huge amount of data for the characterization of population genetic diversity in model and non model-species. However, efficient storage, management, cross-analyzing and exploration of such dense genotyping datasets remain challenging. This is particularly true for the bovine species where many SNP datasets have been generated in various cattle populations with different genotyping tools. Description We developed WIDDE, a Web-Interfaced Next Generation Database that stands as a generic tool applicable to a wide range of species and marker types (http://widde.toulouse.inra.fr). As a first illustration, we hereby describe its first version dedicated to cattle biodiversity, which includes a large and evolving cattle genotyping dataset for over 750,000 SNPs available on 129 (89 public) different cattle populations representative of the world-wide bovine genetic diversity and on 7 outgroup bovid species. This version proposes an optional marker and individual filtering step, an export of genotyping data in different popular formats, and an exploration of genetic diversity through a principal component analysis. Users can also explore their own genotyping data together with data from WIDDE, assign their samples to WIDDE populations based on distance assignment method and supervised clustering, and estimate their ancestry composition relative to the populations represented in the database. Conclusion The cattle version of WIDDE represents to our knowledge the first database dedicated to cattle biodiversity and SNP genotyping data that will be very useful for researchers interested in this field. As a generic tool applicable to a wide range of marker types, WIDDE is overall intended to the genetic diversity exploration of any species and will be extended to other species shortly. The structure makes it easy to include additional output formats and new tools dedicated to genetic diversity exploration. (Résumé d'auteur

Genomic Adaptation of Local Cattle Breeds in the Alpine Massif

Understanding adaptive ability of livestock is a key factor in the context of global climate change and become a crucial focus in conservation and management for a sustainable farming in a changing environment. One way to better understand adaptation abilities is to identify genes underlying adaptation phenotypes. This goal can be achieved by genetically characterising livestock species and detecting footprints of selection in the animal genome. The recent availability of genome-wide SNP panels allows providing background information concerning genome structure in domestic animals, opening new perspectives to livestock genetics. In order to investigate the genetic regions with a potential adaptive role, we investigate 24 cattle breeds, (high productive specialised breeds and several autochthonous populations) reared in six different neighbouring nations from East to West Alpine Massif. Several analyses have been performed to detect footprints of selection and genomic regions associated with climate variables. More precisely, using breed GPS coordinates, 4 climatic variables (annual mean temperature, annual precipitation, annual mean radiation, and annual mean moisture index) were extracted from the Climond database. In order to identify footprints of selection, a whole genome scan for adaptive differentiation were performed using Bovine 50K SNP chip genotyping data with the XtX model implemented in the BAYPASS software. In addition, across-population whole genome scans for association with the population-specific climatic variables were performed using the AUX model. Footprints of selection were detected on BTA6 and BTA18 pointing out several candidate genes (i.e. LCORL, PDGFRA, KDR and SPG7); moreover different genomic regions (on BTA 6, 10, 19 and 20) were associated with annual mean radiation. Ongoing analyses will specify candidate regions and genes involved in local adaptation in the Alpine massif

Relations génétiques entre populations de taurins ou zébus d'Afrique de l'Ouest et taurins européens

Le polymorphisme de 16 systèmes génétiques, les 11 systèmes de groupes sanguins connus chez les bovins (A, B, C, F, J, L, M, S, Z, R’, T’) et cinq locus de protéines sanguines (albumine et transferrine sériques, hémoglobine, purine nucléoside phosphorylase et phosphoglucomutase érythrocytaires), a été analysé dans dix populations de taurins ou de zébus de l’Afrique de l’Ouest et traité par des méthodes de classification et par analyse factorielle des correspondances pour tenter de préciser les relations de parenté existant entre ces populations. Douze systèmes génétiques (groupes sanguins et transferrine) étant communs à cette étude et au travail antérieur sur les races françaises, les données des deux sources ont été regroupées et analysées par les mêmes méthodes. Ces analyses séparent clairement les zébus (Bos indicus) des taurins (Bos taurus), ainsi que les taurins africains des taurins européens. L’analyse factorielle des correspondances fait ressortir le rôle discriminant d’allèles propres aux zébus (TƒF, Aﺎs) ou plus fréquents chez ceux-ci (HbB) et celui d’allèles paraissant largement spécifiques des bovins africains (F-, C-, CC1-). En revanche, les outils utilisés ne permettent de séparer d’une manière robuste, ni les populations taurines de l’ensemble Ouest africain, ni les races bovines européennes.The polymorphism of 16 genetic systems, the 11 known blood group systems in cattle (A, B, C, F, J, L, M, S, Z, R', T’) and five blood protein loci (serum albumin and transferrin, erythrocyte haemoglobin, purine nucleoside phosphorylase and phosphoglucomutase) - has been analysed in ten West-African taurine and indicine populations, and submitted to classification methods and correspondence analysis in an attempt to clarify the genetic relationships between these populations. Since 12 loci are common to this study and an earlier one concerning French breeds, the data of both studies have been pooled and analysed by the same methods. The results show a clear separation between zebus (Bos indicus) and taurines (Bos taurus), as well as between African and European taurines. The correspondence analysis highlights the discriminant effect of alleles specific to Zebu (TƒF , Aﺎs) or more frequent in Zebu than in taurines (HbB) and that of alleles mainly found in African cattle (F-, C-, CC1-). On the other hand, the methods used could not clearly separate the West-African taurine populations or the European cattle breeds

A whole genome Bayesian scan for adaptive genetic divergence in West African cattle

BACKGROUND: The recent settlement of cattle in West Africa after several waves of migration from remote centres of domestication has imposed dramatic changes in their environmental conditions, in particular through exposure to new pathogens. West African cattle populations thus represent an appealing model to unravel the genome response to adaptation to tropical conditions. The purpose of this study was to identify footprints of adaptive selection at the whole genome level in a newly collected data set comprising 36,320 SNPs genotyped in 9 West African cattle populations. RESULTS: After a detailed analysis of population structure, we performed a scan for SNP differentiation via a previously proposed Bayesian procedure including extensions to improve the detection of loci under selection. Based on these results we identified 53 genomic regions and 42 strong candidate genes. Their physiological functions were mainly related to immune response (MHC region which was found under strong balancing selection, CD79A, CXCR4, DLK1, RFX3, SEMA4A, TICAM1 and TRIM21), nervous system (NEUROD6, OLFM2, MAGI1, SEMA4A and HTR4) and skin and hair properties (EDNRB, TRSP1 and KRTAP8-1). CONCLUSIONS: The main possible underlying selective pressures may be related to climatic conditions but also to the host response to pathogens such as Trypanosoma(sp). Overall, these results might open the way towards the identification of important variants involved in adaptation to tropical conditions and in particular to resistance to tropical infectious diseases

Genetic analysis of Thai cattle reveals a Southeast Asian indicine ancestry

Cattle commonly raised in Thailand have characteristics of [i]Bos indicus[/i] (zebu). We do not know when or how cattle domestication in Thailand occurred, and so questions remain regarding their origins and relationships to other breeds. We obtained genome-wide SNP genotypic data of 28 bovine individuals sampled from four regions: North (Kho-Khaolampoon), Northeast (Kho-Isaan), Central (Kho-Lan) and South (Kho-Chon) Thailand. These regional varieties have distinctive traits suggestive of breed-like genetic variations. From these data, we confirmed that all four Thai varieties are [i]Bos indicus[/i] and that they are distinct from other indicine breeds. Among these Thai cattle, a distinctive ancestry pattern is apparent, which is the purest within Kho-Chon individuals. This ancestral component is only present outside of Thailand among other indicine breeds in Southeast Asia. From this pattern, we conclude that a unique [i]Bos indicus[/i] ancestor originated in Southeast Asia, and native Kho-Chon Thai cattle retain the signal of this ancestry with limited admixture of other bovine ancestors

Impact of strong selection for the PrP major gene on genetic variability of four French sheep breeds (Open Access publication)

Effective selection on the PrP gene has been implemented since October 2001 in all French sheep breeds. After four years, the ARR "resistant" allele frequency increased by about 35% in young males. The aim of this study was to evaluate the impact of this strong selection on genetic variability. It is focussed on four French sheep breeds and based on the comparison of two groups of 94 animals within each breed: the first group of animals was born before the selection began, and the second, 3–4 years later. Genetic variability was assessed using genealogical and molecular data (29 microsatellite markers). The expected loss of genetic variability on the PrP gene was confirmed. Moreover, among the five markers located in the PrP region, only the three closest ones were affected. The evolution of the number of alleles, heterozygote deficiency within population, expected heterozygosity and the Reynolds distances agreed with the criteria from pedigree and pointed out that neutral genetic variability was not much affected. This trend depended on breed, i.e. on their initial states (population size, PrP frequencies) and on the selection strategies for improving scrapie resistance while carrying out selection for production traits