Genetic homogenization of indigenous sheep breeds in Northwest Africa

Abstract

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 F ST 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.

The origin of sheep settlement in Western Mediterranean

“…In contrast, the two southern ones, Blanche de Montagne and D'man had strong and recent links with Sardi and Timahdite breeds. The strong proportion of connections between the D'man and the other breeds were also found from the study based on SNPs over Northwest African sheep breeds 12 . It can be assumed that the D'man and the Blanche de Montagne, being small sized breeds 10 , were crossed with the biggest Sardi and Timahdite individuals to increase their meat production.…”

“…At the national level, characterization work on sheep breeds has been based on morphological characters 10 and blood protein polymorphism 11 . Recently, a study based on SNPs markers highlighted the differentiation between most of Moroccan and Algerian breeds, with a special focus on inter-population exchanges 12 . However, the information about the link between Moroccan and European breeds is still lacking.…”

Genome-wide insights on gastrointestinal nematode resistance in autochthonous Tunisian sheep

“…The lack of genetic differentiation and structure was also reported between prolific and non-prolific cohorts of Bonga sheep from Ethiopia 41 and in the Brazilian Santa Inês breed which shows variability in resistance to GIN infection 19 . The absence of genetic stratification appears to be a characteristic of sheep from the Maghreb as it has also been observed in sheep populations from Algeria 42 and Morocco 43 implicating extensive intermixing and cross-mating. There are four possible explanations for the lack of genomic stratification corresponding to infection status.…”

Inference of Breed Structure in Farm Animals: Empirical Comparison between SNP and Microsatellite Performance

“…Cattle genotypes [29] were obtained using the Illumina BovineSNP50v1 BeadChip. Algerian sheep genotypes [30,31] were obtained using the Illumina OvineSNP50K BeadChip. French sheep population genotypes [32] were obtained using the Illumina Ovine HD SNP chip; for the purpose of the study, a subset of SNPs was extracted using the OvineSNP50K BeadChip coordinates.…”