Genome‐wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds

Abstract

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north-south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long-lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds.

Genome-wide analysis highlights genetic dilution in Algerian sheep

“…SNPs data from Algerian breeds were merged with available data from world-wide breeds (Kijas et al, 2012) and Italian breeds (Ciani et al, 2014), producing a data set composed of 1625 individuals (a minimum of 3 and a maximum of 20 individuals per breed were considered) from 92 populations (see Supplementary Table S1). A NeighborNet graph, considering all the breeds (except the American breeds BCS, GCN and STE, as they were shown to not cluster with the other American breeds; Kijas et al, 2012) was constructed from a matrix of Reynolds' distances using Splitstree (Huson, 1998).…”

“…The genotypes from additional 15 Italian breeds (Ciani et al, 2014) were also included in order to account for possible gene flow between Mediterranean countries. The data set consisted of ∼ 20 animals per breed, chosen according to their geographic origin, history, census, morphology and production purpose.…”

“…Two groups were detected: (1) Ouled-Djellal, Rembi and Berber showed very low values of pair-wise F ST (o0.004), and not significantly different from zero (Po0.001) for Ouled-Djellal/ Rembi and Rembi/Berber; and (2) the other breeds showed values of F ST ranging from 0.028 (Rembi/Barbarine) to 0.109 (Hamra/Tazegzawt) (Table 1). A total of 4460 pair-wise F ST values were calculated considering all together, in the same data set, Algerian breeds, HapMap breeds (Kijas et al, 2012) and Italian breeds (Ciani et al, 2014); the following five lowest pair-wise F ST values were observed: Rembi/Ouled-Djellal (0.000); Rembi/Berber (0.002); Ouled-Djellal/ Berber (0.004); Australian Merino/Australian Industry Merino (0.004); and Australian Poll Merino/Australian Industry Merino (0.009). All other pair-wise F ST values were 40.01 (data not shown).…”

“…A NeighborNet graph, using the Reynolds' distance and considering Algerian breeds, a subset of breeds from the Sheep HapMap project (see Materials and methods) (Kijas et al, 2012) and Italian breeds (Ciani et al, 2014), was built ( Figure 5). Algerian breeds appeared as being at the crossroad of Africa and Europe (Italian breeds, particularly Bagnolese and Laticauda, and, to a lesser extent, with breeds from the Sicily island in Southern Italy: Comisana, Leccese, Valle del Belice and Pinzirita), and also very close to samples from Americas.…”

“…The aims of the study were: (1) to provide a comprehensive view of the genetic diversity of Algerian sheep by furthering the investigations began by Gaouar et al (2015), using a more powerful tool and a wider breed repertoire, also including three breeds (Berber, Barbarine and Tazegzawt) considered here for the first time from a genetic point of view; and (2) to bring new information to the history of the sheep domestication by exploring the relationships of Algerian sheep in an international context (by comparison with world-wide panel of sheep breeds genotyped by the sheep HapMap Project (Kijas et al, 2012) and Italian breeds provided by the BiOvIta Consortium (Ciani et al, 2014)). …”