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Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY and DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes, Y1A, Y1B, Y2A and Y2B, with a marked geographical partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and seven wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during migrations into northern Europe, eastern and southern Asia, and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographical range.

Stearoyl-coenzyme A desaturase (SCD) catalyses the synthesis of monounsaturated fatty acids, by introducing a cis double bond at the delta 9–10 position. The study investigated the effects of a polymorphism at the ovine SCD gene and its interaction with the inclusion of fresh forage in the diet on cheese fatty acid (FA) composition in Valle del Belice ewes. A region of 527 bp of the ovine SCD gene including the partial sequence of the promoter, the complete sequence of the 5’ UTR and exon 1 and the partial sequence of intron 1 were analyzed in order to identify the g.87C > A SNP located in the promoter region. A feeding trial was carried out using 16 Valle del Belice ewes selected on the basis of their genotype (6 CC and 10 AC). Each genetic group was fed, according to a latin square experimental design, with diets based on conserved or fresh forage, consisted of sulla hay (SH) or sulla green forage (SGF), integrated with 1 kg/d of concentrate feed. Cheese made from individual milk was analyzed for FA composition. The SCD genotype had no effect on cheese monounsaturated and polyunsaturated FA, whereas significantly influenced the desaturation activity, as demonstrated by the higher desaturation indices in the CC ewes compared to AC ewes (C14 index: 0.021 vs. 0.017; C18 index: 0.71 vs. 0.68; trans-vaccenic index: 0.38 vs. 0.32; p < .05). This result seems consistent with the possible role of this polymorphism on the enzyme desaturase synthesis and its activity in the mammary gland. However, this does not appear to be supported by the levels of monounsaturated FA or conjugated linoleic acid (CLA, C18:2c9t11) which were not affected by the g.87C > A polymorphism. The SGF diet significantly increased trans vaccenic, linoleic and CLA acids of cheese, compared to the SH diet (respectively: 2.30 vs. 1.31; 2.53 vs. 2.25; 1.00 vs. 0.80; p < .05). No significant interaction resulted, thus the effect of SCD genotype on desaturation indices was evident regardless of the diet. The results obtained, while showing an effect of SCD polymorphism on the level of desaturation, do not allow to highlight a role of the more favourable CC genotype in further improving the acidic composition of the cheese in health terms due to the presence of green forage in the diet. However, the genetic polymorphism of sheep SCD and its interaction with diet should be further investigated, given the lack of information on this species.

Growth hormone, a polypeptide encoded by the GH gene, is a member of the somatotropin/prolactin family of hormones, which plays an important role on milk production and metabolism. In bovine, a single nucleotide polymorphism (SNP) in exon 5 changes leucine to valine (CTG to GTG) in the mature GH molecule. The purpose of this study was to evaluate, in Modicana and Cinisara cows, the effects of genetic polymorphism at GH locus and its interaction with feeding system on milk traits. A total of 97 individual Modicana blood samples were collected, 65 from a semi extensive and 32 from an extensive farm. A total of 58 Cinisara individual milk samples were collected, 32 from 7 extensive farms and 26 from 6 semi-extensive farms. In the extensive farms the cows were fed exclusively with pasture; in the semi-extensive farms cows were fed with pasture, hay and concentrate. DNA was extracted from Modicana white blood cells and from Cinisara milk somatic cells. Bovine Growth Hormone (bGH) was analyzed at the 5th exon according to Komisarek et al (2011). In Modicana farms, monthly, individual milk yield was recorded and individual milk samples collected. In Cinisara farms milk production was recorded once, the day of samples collection. Fat and protein were determined (Combi-foss 6000, Foss Electric, Hillerød, Denmark). In Modicana, milk yield, fat and protein were analysed using the GLM procedure for repeated measures of SPSS (SPSS for Windows, SPSS Inc., Chicago IL, USA). In Cinisara, milk yield, fat and protein were analysed using the univariate GLM procedure of SPSS. The analyses included main effects of GH genotype, feeding system and the interaction genotype × feeding system. Three genotypes were found:: LL (236, 132, 36bp), LV (236, 185, 132, 51, 36 bp) and VV (185, 132, 51, 36 bp). Genotype frequencies, respectively in Modicana and Cinisara breeds were: LL, 0.61 and 0.34; LV, 0.37 and 0.57; VV, 0.02 and 0.09. Milk production and gross composition were not influenzed by GH genotype (respectively in Modicana and Cinisara: milk yield, LL 9.06 and 12.3, LV 9.24 and 11.4, VV 7.61 and 8.33; fat, LL 4.08 and 3.32, LV 3.91 and 3.13, VV 4.04 and 3.62; protein, LL 3.67 and 3.51, LV 3.66 and 3.56, VV 3.64 and 3.71). These results are in line with different authors. The higher energy level of the diets offered in the semi extensive farms did not interfere with GH genotype effect on milk traits: no significant interaction was found between genotype and feeding system.

The Italian Goat Consortium (IGC), joined the effort of many Universities and Research Institutes, in a comprehensive study of the Italian goat population genetic makeup using a medium density (54K) SNPs chip. Currently IGC has geno- typed more than 1,000 animals from more than 30 goat breeds and populations from all Italian geographical and agro- ecological areas of goat rearing. The aim of this work is to obtain a clear picture of the Italian caprine biodiversity, to reconstruct the ancestry, to disentangle the genetic background and to assess the relationships among and within the investigated breeds. To date, the IGC dataset includes about 50 million genotypes. The data were quality checked by excluding markers and individuals on the basis of missing genotypes, minor allele frequency and close individual relatedness. Genetic relationships among and within breeds was investigated by Multi-Dimensional Scaling and Principal Component Analysis. Population structure, ancestry models and admixture were estimated by ADMIXTURE and fastSTRUCTURE software. Finally, phylogenic trees were recon- structed with PHYLIP software suite starting from shared-allele identity by state, and Reynolds distance matrices, while past migration events were modeled with TreeMix software. The results confirmed high levels of genetic polymorphism and confirmed the North-South geographical pattern of diver- sity, previously reported on a smaller sample of Italian goat breeds. The analysis also revealed a pivotal role of Central Italy in connecting the genetic resources of the northern and southern areas of the country, and confirms the genetic isola- tion of insular breeds. Moreover, some breeds show clearly distinctive and homogeneous gene pools, whereas other breeds present complex and, in some cases, dishomogeneous genetic background. Even if "A breed is a group of domestic animals, termed such by common consent of the breeders" (Lush J.L., 1994), genomic tools are useful in understanding the genetic back- ground of populations and in defining their relationships or uniqueness. These tools can complement the traditional ones in providing farmers and their associations a powerful aid for a more conscious management of goat populations and their biodiversity.

Genetic characterization is a fundamental prerequisite for managing animal genetic resources. Nowadays high-throughput commercial SNP platforms allow the genetic characterization of intra and inter-breeds diversity. The Illumina porcine SNP60 genotyping BeadChip was recently used for the genetic analysis of the autochthonous Nero Siciliano black pig, reared in the natural park of the Nebrodi Mountains. The comparison of 92 individuals well distributed in 22 farms with cosmopolitan breeds suggested the uniqueness of this breed. Moreover 100 randomly chosen SNP seemed enough to distinguish the investigated breeds, offering a useful tool for the traceability of typical products. Since cytogenetic investigation suggested a possible cross with wild boar in at least one Nero Siciliano pig, showing a rob(15;17), we compared the 92 individuals with 88 wild boars from a recent study on Northwest European breeds. The genetic structure of this dataset (180 individuals) was investigated by a Bayesian clustering approach with the ADMIXTURE software, which highlighted a low level of admixture between the wild boar and the domestic pig in almost all samples (81 out of 92 pigs). This admixture could be derived both from SNP recently introgressed or from common ancestors. In particular two Nero Siciliano pigs showed a higher proportion of admixture. Analyses are in progress to assess the origin of the introgression in these two subjects.

The Italian Goat Consortium was established from the Innovagen Project to join local efforts and resources for the genomic characterisation of Italian goat breeds. Thirteen Italian goat breeds (Valdostana, Saanen, Orobica, Bionda dell'Adamello, Val Passiria, Grigia Ciociara, Teramana, Nicastrese, Aspromontana, Girgentana, Argentata dell'Etna, Sarda and Maltese - the latter sampled in Sardinia and Sicily) for a total of 350 animals (15-32 per breed) were analysed using a medium density SNP array. Data editing was based on the following thresholds: MAF 5%; Missing animal >5%; HW within breed FDR >20%. After filtering, a total of 51,136 SNPs were retained, showing that the adopted SNP chip is highly informative for the characterization of Italian goat breeds. Population structure and breed distinctiveness were investigated with the software Admixture, that revealed the best fitting solution at K=11 partitions. The software also highlighted variable levels of admixture and an early differentiation of Val Passiria, Orobica, Valdostana, Teramana, Girgentana and Sarda breeds. Within MDS plot, some breeds are clearly appreciable as distinct: Girgentana, Teramana, Orobica and Maltese. PCA analysis revealed a gradient of diversity North (from alpine breeds) - South (to Sicilian breeds) and East (from Val Passiria breed) - West (to Valdostana breed) in the Alps. The calculation of Fis index indicated little or no inbreeding, while LD analysis in Chromosome 6 showed levels of disequilibrium much lower than cattle at short physical distance.

Publication of the LACTIMED project (ANIMA / CIHEAM-IAMM / Slow Food / ASTER) with the University of Catania, the University of Palermo and the CRPA; To encourage integrated development of dairy chain in Sicily, Italy, Lactimed carried out a diagnosis to help local authorities and support structures adopt a strategy for promoting the typical dairy products of their territory. This diagnosis report includes an overview of the dairy chain, the analysis of the results of field survey with producers, the identification of typical dairy products with their production specifications and information on the domestic market.

Publication du projet européen LACTIMED (ANIMA / CIHEAM-IAMM / Slow Food / ASTER) avec l'Université de Catane, l'Université de Palerme et le CRPA; Lactimed a réalisé un diagnostic de la filière laitière de Sicile (Italie) afin d’aider les autorités locales et les structures d’appui à adopter une stratégie pour la valorisation des produits laitiers typiques de leur territoire. Ce rapport de diagnostic inclut un état des lieux de la filière, l’analyse des résultats d’enquêtes de terrain menées auprès des producteurs, l’identification de produits laitiers typiques avec leur cahier des charges de production et des informations sur le marché domestique.

Pubblicazione del progetto LACTIMED (ANIMA / CIHEAM-IAMM / Slow Food / ASTER) con la Università di Catania, la Università di Palermo e il CRPA; Al fi ne di incoraggiare uno sviluppo integrato della fi liera lattiero-casearia siciliana, il progetto Lactimed si fonda su un’analisi della fi liera e sullo studio delle opportunità di sbocco sui mercati nazionali e internazionali, aiutando innanzi tutto le autorità locali e le strutture di supporto ad adottare una strategia per la valorizzazione delle produzioni lattiero casearie tipiche locali.

Background SNP data of goats of three Mediterranean countries were used for population studies and reconstruction of geographical patterning. 496 individuals belonging to Italian, Albanian and Greek breeds were genotyped to assess the basic population parameters. Results A total of 26 SNPs were used, for a total of 12,896 genotypes assayed. Statistical analysis revealed that breeds are not so similar in terms of genetic variability, as reported in studies performed using different markers. The Mantel test showed a strongly significant correlation between genetic and geographic distance. Also, PCA analysis revealed that breeds are grouped according to geographical origin, with the exception of the Greek Skopelos breed. Conclusion Our data point out that the use of SNP markers to analyze a wider breed sample could help in understanding the recent evolutionary history of domestic goats. We found correlation between genetic diversity and geographic distance. Also PCA analysis shows that the breeds are well differentiated, with good correspondence to geographical locations, thus confirming the correlation between geographical and genetic distances. This suggests that migration history of the species played a pivotal role in the present-day structure of the breeds and a scenario in which coastal routes were easier for migrating in comparison with inland routes. A westward coastal route to Italy through Greece could have led to gene flow along the Northern Mediterranean.