Inferring the population structure of the Maghreb sheep breeds using a medium‐density SNP chip

Abstract

North Africa has a great diversity of indigenous sheep breeds whose origin is linked to its environmental characteristics and to certain historical events that took place in the region. To date, few genome-wide studies have been conducted to investigate the population structure of North African indigenous sheep. The objective of the present study was to provide a detailed assessment of the genetic structure and admixture patterns of six Maghreb sheep populations using the Illumina 50K Ovine BeadChip and comparisons with 22 global populations of sheep and mouflon. Regardless of the method of analysis used, patterns of multiple hybridization events were observed within all North African populations, leading to a heterogeneous genetic architecture that varies according to the breed. The Barbarine population showed the lowest genetic heterogeneity and major southwest Asian ancestry, providing additional support to the Asian origin of the North African fat-tailed sheep. All other breeds presented substantial Merino introgression ranging from 15% for D'man to 31% for Black Thibar. We highlighted several signals of ancestral introgression between North African and southern European sheep. In addition, we identified two opposite gradients of ancestry, southwest Asian and central European, occurring between North Africa and central Europe. Our results provide further evidence of the weak global population structure of sheep resulting from high levels of gene flow among breeds occurring worldwide. At the regional level, signs of recent admixture among North African populations, resulting in a change of the original genomic architecture of minority breeds, were also detected.

Genetic Variability and Population Structure of the Tunisian Sicilo-Sarde Dairy Sheep Breed Inferred from Microsatellites Analysis

“…The present-day sheep are the miscegenation result of these three ancestral gene pools, as depicted in Figure 5 b,c and as revealed by Ben Sassi-Zaidy et al [ 19 ], who studied the genetic structure of Tunisian native meat sheep using microsatellite markers. Ben Jemaa et al [ 46 ], inferring the population structure of some Mediterranean sheep using SNP markers, proved the ancestral relationship between the dairy Sicilo-Sarde breed, and the Italian Sarda and Comisana breeds and revealed the existence of three ancestral gene pool clusters in the genetic structure of the Sicilo-Sarde and other Mediterranean sheep. Furthermore, with SNP markers, Ciani et al [ 47 ] revealed the genetic differentiation of the two insular Sicilian and Sardinian Italian sheep from continental sheep populations, demonstrating the influence of the isolation of these breeds in preserving the ancestral genetic patterns, which reflect the historic maritime waves of sheep introduction to the Mediterranean area.…”

How have sheep breeds differentiated from each other in Morocco? Genetic structure and geographical distribution patterns

“…In addition, using single nucleotide polymorphisms, Belabdi et al [ 21 ] revealed a high level of homogenization, such that some breeds with different origins appeared to be genetically undistinguishable. In addition, Ben Jemaa et al [ 22 ] reported a pattern of multiple hybridization events within all North African sheep populations. Several investigations of the genetic structuration of goat breeds in North Africa resulted in similar results.…”

Food securers or invasive aliens? Trends and consequences of non-native livestock introgression in developing countries

“…Genomics may offer a solution to inconsistencies in definition of breed type, which could consequently improve the inferences if our study were to be repeated in the future. Depending on species, breeds and locations, extent of influence from exotic (generally of European descent) breeds due to recent admixture has been found to range from negligible to predominant in local populations ( Leroy et al, 2012 ; Murray et al, 2013 ; Buzanskas et al, 2017 ; Selepe et al, 2018 ; Ben Jemaa et al, 2019 ; Zhang et al, 2019 ). Although incomparably more precise to assess genetic origins of individuals than other sources of information, molecular approaches are currently limited in their coverage of livestock populations.…”