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

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.

A first comparative map of copy number variations in the sheep genome.

We carried out a cross species cattle-sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle and goat genomes indicated that overlaps between sheep and both other species CNVRs are highly significant (P<0.0001), suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVRs include genes with important biological functions. Further studies are needed to evaluate their functional relevance.

Effect of dietary energy content on the intramuscular fat depots and triglyceride composition of river buffalo meat.

The production of river buffalo meat in Italy has long been under discussion due to poor acceptance by consumers. In order to understand whether dietary energy content may affect the organoleptic characteristics of buffalo meat, two groups of river buffalo calves were fed on two diets, with high (H) and low (L) energy contents. The animals were slaughtered at 4-monthly intervals starting from 6 months old (10, 14 and 18 months) and five muscles were dissected on the half-carcass: Caput longum tricipitis brachii (CloTB), Gluteobiceps (Gb), Semitendinosus (St), Semimembranosus (Sm) and Longissimus dorsi (LD). The results showed that from 6 to 10 months of age the meat lipid content decreases and protein content increases for both diets. The lipid content increases slowly with both diets from 10 to 14 months. In the last experimental period (from 14 to 18 months) an increase in the percentage of lipids with diet H and a decrease with diet L was observed. At all slaughtering ages the meat from the animals fed on diet H had a higher energy content. The different energy content of the two diets did not significantly influence the composition of triglycerides only formed by SFA and triglycerides with a higher degree of unsaturation. The triglycerides with an unsaturated fatty acid in position sn 2 did not show the same behaviour in relation to age and diet. The energy content of the feed did influence the unsaturated fatty acid composition: MUFA increased with an increased energy level of the diet, while PUFA increased with a reduction in the energy level of the diet. The muscle LD showed a significantly higher (P<0.05) content of SFA and lower (P<0.05) of MUFA and PUFA than the other muscles. On the basis of our results, the better TAG's composition is found in the meat of animals fed on diet H and slaughtered at 4 months of age.