Diversité du génome entier et dynamique démographique de la race ovine D'man

D’man est une race ovine importante au Maroc présentant des traits reproductifs exceptionnels. Cependant, sa structure génétique et son état de consanguinité sont peu connus. Cette étude caractérise la diversité de D’man et sa dynamique démographique en utilisant les données génomiques de 30 moutons échantillonnés dans trois régions administratives (Drâa-Tafilalet, Sous-Massa et Guelmim-Ouednoun) pour inférer les paramètres de diversité génétique neutre. De plus, trois approches complémentaires ont été utilisées pour inférer la structure de la population: sNMF pour calculer les coefficients d'admixture individuels, Treemix pour générer un arbre de vraisemblance maximale et des événements de migration, et une analyse en composantes principales. Les résultats ont montré que la race D’man présentait un faible niveau d'hétérozygotie observée, un coefficient de consanguinité élevé et une valeur élevée de diversité nucléotidique par rapport à d'autres races locales. Ces valeurs étaient comparables dans les trois régions et peuvent s'expliquer par l'isolement de cette race et ses systèmes d'élevage typiques. Une certaine structuration géographique a été observée liée aux vallées dont les individus sont originaires. Bien qu'il y ait eu un niveau important de flux génétique, la race s'est révélée bien homogénéisée. L'arbre de vraisemblance maximale a révélé l'existence de deux sous-populations génétiquement distinctes lorsque chaque région administrative était traitée comme un groupe unique, indiquant la présence de deux lignées principales. La race D’man présente donc une diversité génétique remarquable, mais aussi une consanguinité considérable, à prendre en compte pour des programmes d'élevage et de conservation efficaces

Genomic Uniqueness of Local Sheep Breeds From Morocco

International audienceSheep farming is a major source of meat in Morocco and plays a key role in the country’s agriculture. This study aims at characterizing the whole-genome diversity and demographic history of the main Moroccan sheep breeds, as well as to identify selection signatures within and between breeds. Whole genome data from 87 individuals representing the five predominant local breeds were used to estimate their level of neutral genetic diversity and to infer the variation of their effective population size over time. In addition, we used two methods to detect selection signatures: either for detecting selective sweeps within each breed separately or by detecting differentially selected regions by contrasting different breeds. We identified hundreds of genomic regions putatively under selection, which related to several biological terms involved in local adaptation or the expression of zootechnical performances such as Growth, UV protection, Cell maturation or Feeding behavior. The results of this study revealed selection signatures in genes that have an important role in traits of interest and increased our understanding of how genetic diversity is distributed in these local breeds. Thus, Moroccan local sheep breeds exhibit both a high genetic diversity and a large set of adaptive variations, and therefore, represent a valuable genetic resource for the conservation of sheep in the context of climate change

Algerian goat genotypes (.map file)

Genotypes obtained with the Illumina GoatSNP50K Genotyping BeadChip (markers files by chromosomes) for four Algerian goat breeds in a Plink format

Data from: Genetic homogeneity of North-African goats

North Africa represents a rich and early reservoir of goat genetic diversity, from which the main African breeds have been derived. In this study, the genetic diversity of four indigenous Algerian goat breeds (i.e., Arabia, Makatia, M’Zabite and Kabyle, with n = 12 for each breed) has been investigated for the first time by genome-wide SNP genotyping; moreover in a broader context, genetic structuration of Algerian and Moroccan goats was explored (via FST, MDS, STRUCTURE, FineSTRUCTURE, BAPS, sPCA and DAPC analyses). At national level, the study revealed high level of genetic diversity and a significant phenomenon of admixture affecting all the Algerian breeds. At broader scale, clear global genetic homogeneity appeared considering both Algerian and Moroccan stocks. Indeed, genetic structuration was almost nonexistent among Arabia (from Algeria), Draa, Black and Nord (from Morocco), while the ancestral Kabyle and M’Zabite breeds, reared by Berber peoples, showed genetic distinctness. The study highlighted the threat to the Maghrebin stock, probably induced by unsupervised cross-breeding practices which have intensified in recent centuries. Moreover, it underlined the necessity to deepen our understanding of the genetic resources represented by the resilient North-African goat stock

Genetic homogeneity of North-African goats.

North Africa represents a rich and early reservoir of goat genetic diversity, from which the main African breeds have been derived. In this study, the genetic diversity of four indigenous Algerian goat breeds (i.e., Arabia, Makatia, M'Zabite and Kabyle, with n = 12 for each breed) has been investigated for the first time by genome-wide SNP genotyping; moreover in a broader context, genetic structuration of Algerian and Moroccan goats was explored (via FST, MDS, STRUCTURE, FineSTRUCTURE, BAPS, sPCA and DAPC analyses). At national level, the study revealed high level of genetic diversity and a significant phenomenon of admixture affecting all the Algerian breeds. At broader scale, clear global genetic homogeneity appeared considering both Algerian and Moroccan stocks. Indeed, genetic structuration was almost nonexistent among Arabia (from Algeria), Draa, Black and Nord (from Morocco), while the ancestral Kabyle and M'Zabite breeds, reared by Berber peoples, showed genetic distinctness. The study highlighted the threat to the Maghrebin stock, probably induced by unsupervised cross-breeding practices which have intensified in recent centuries. Moreover, it underlined the necessity to deepen our understanding of the genetic resources represented by the resilient North-African goat stock

Genetic homogenization of indigenous sheep breeds in Northwest Africa

Northwest-African sheep represent an ideal case-study for assessing the potential impact of genetic homogenization as a threat to the future of traditional breeds that are adapted to local conditions. We studied ten Algerian and Moroccan breeds of sheep, including three transboundary breeds, distributed over a large part of the Maghreb region, which represents a geographically and historically coherent unit. Our analysis of the dataset that involved carrying out Genome-wide SNP genotyping, revealed a high level of homogenization (ADMIXTURE, NetView, fineSTRUCTURE and IBD segments analyses), in such a way that some breeds from different origins appeared genetically undistinguished: by grouping the eight most admixed populations, we obtained a mean global FST value of 0.0024. The sPCA analysis revealed that the major part of Morocco and the Northern part of Algeria were affected by the phenomenon, including most of the breeds considered. Unsupervised cross-breeding with the popular Ouled-Djellal breed was identified as a proximate cause of this homogenization. The issue of transboundary breeds was investigated, and the Hamra breed in particular was examined via ROH fragments analysis. Genetic diversity was considered in the light of historical archives and anthropological works. All of these elements taken together suggest that homogenization as a factor affecting the Maghrebin sheep stock, has been particularly significant over the last few decades, although this process probably started much earlier. In particular, we have identified the policies set by the French administration during the colonial period of the region's history as a causal factor that probably contributed significantly to this process. The genetic homogenization that we have observed calls into question the integrity of the farm animal genomic resources represented by these local breeds, whose conservation is of critical importance to the future of the livestock sector