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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.

[Background]: Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra., [Findings]: A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin., [Conclusions]: We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies., We are grateful to France Génomique “Call for high impact projects” (ANR‐10‐INBS‐09‐08) for selecting our project and providing us the resources to sequence 400 goats. We would like to mention that APIS-GENE funded some WGS sequences through ACTIVEGOAT & CAPRISNP projects. We thank the Occitanie region and the Animal Genetics Division of the French National Institute for Agriculture, Food and Environment (INRAE-GA) for financing the PhD of ET. We thank the Ministère de l'Enseignement supérieur, de la Recherche et de l'Innovation for financing LD. We thank André Eggen (Illumina) for providing chips to genotype 192 animals. We thank the Animal Genetics Division of the French National Institute for Agriculture, Food and Environment (INRAE-GA) for funding VarGoats2 grant, which allowed DNA extraction and genotyping of 384 animals and CRB-Anim, Grant Agreement ANR-11-INBS-0003, (https://crb-anim.fr/) for funding French local breeds sampling. We thank the Italian Goat and Sheep Breeders Association (AssoNaPa) for supporting in sampling. Whole-genome sequencing libraries for the African goats were prepared and sequenced by Edinburgh Genomics and funded via Biotechnology and Biological Sciences Research Council research grant (BBS/OS/GC/000012F) ‘Reference genome and population sequencing of African goats’ awarded to The Roslin Institute. USDA-ARS with funding from USAID funded the collection of samples from Uganda, Tanzania, Malawi, Mozambique and Zimbabwe. EC and MS were partially supported by the Bill & Melinda Gates Foundation and with UK aid from the UK Government’s Department for International Development (Grant Agreement OPP1127286) under the auspices of the Centre for Tropical Livestock Genetics and Health (CTLGH), established jointly by the University of Edinburgh, SRUC (Scotland’s Rural College), and the International Livestock Research Institute. The findings and conclusions contained within are those of the authors and do not necessarily reflect positions or policies of the Bill & Melinda Gates Foundation nor the UK Government.

Despite the growing diffusion of cosmopolite specialized breeds, several autochthonous cattle breeds and populations are still bred in Italy. The aim of this study was to provide a high-resolution picture of the genome-wide diversity and population structure of Italian local cattle breeds using medium-density genome-wide SNP markers. After data editing, the dataset included 800 samples from 32 breeds that were genotyped for 31 013 SNPs. For several breeds we observed a low level of polymorphism and genetic diversity, that together with the small effective population sizes confirmed threat of extinction. According to the runs of homozygosity analysis, evidence of recent inbreeding was strong in some breeds. Low pair-wise genetic differentiation values, shared ancestry, admixture events, and reticulations observed on the phylogenetic tree between some breeds, all suggest high levels of gene flow. Clear clusters and relationships between breeds that originated from the same region or area were detected. However, in spite the complex admixture history of most breeds, many of the local Italian cattle breeds have retained unique identities and are differentiated breeds, and this can be due to differences in the origin, differences in climate, genetic isolation and inbreeding. This study represents the first exhaustive analysis of Italian cattle diversity. The results largely agreed with the breeding history of the Italian cattle breeds. The population structure and the low genetic diversity presented here for several breeds should be useful in creating conservation strategies. If reproductive isolation within groups of the same herd and area is maintained in subsequent generations, the short-term rate of inbreeding will increase dangerously, resulting in a decrease in the effective population size and seriously damaging the breeds future. Thus, efforts should be made to improve genetic diversity in these breeds. In particular, mating decisions will play an important role in limiting inbreeding and will increase the size of these local breeds.

Analysis of genomic data is increasingly becoming part of the livestock industry and is an invaluable resource for effective management of breeding programs in small populations. The recent availability of genome-wide SNP panels allows providing background information concerning genome structure in domestic animals, opening new perspectives to livestock genetics. BOVITA was established to join local efforts and resources for the genomic characterization of Italian local cattle breeds. Despite the growing diffusion of some cosmopolite specialized breeds, several autochthonous breeds are still bred in Italy. The main aim of the BOVITA is to investigate the genomic structure of Italian local cattle breeds, to provide information on their genetic status that will be useful for the management of the genetic variability, as a contribution to biodiversity conservation and prioritization actions. A total of about 800 animals (20-32 per breed) belonging to thirty Italian cattle breeds (Agerolese, Barà-Pustertaler, Burlina, Cabannina, Calvana, Chianina, Cinisara, Garfagnina, Italian Brown, Italian Holstein, Italian Simmental, Marchigiana, Maremmana, Modenese, Modicana, Mucca Pisana, Pezzata Rossa d’Oropa, Piedmontese, Pinzgau, Podolica, Pontremolese, Pustertaler, Reggiana, Rendena, Romagnola, Rossa Siciliana, Sarda, Sardo-Bruna, Sardo-Modicana and Ottonese-Varzese) and two cosmopolitan breeds (Charolaise and Limousine) genotyped with the Illumina BovineSNP50 v2 BeadChip array were collected for the analysis. The genotypes of several breeds were detected in the frame of the project, whereas for some breeds these data are derived by previous studies. The dataset will be analyzed to: study several aspects of population genetic diversity, multi-dimensional scaling plot, population structure, linkage disequilibrium, and runs of homozygosity. In addition, comparative analysis of conserved haplotypes will be conducted to identify genomic segments under selection pressure. Such information also provides important insights into the mechanisms of evolution and is useful for the annotation of significant functional genomics regions. Data analysis will also be useful to select SNPs suitable for parentage test and breed genetic traceability. The analysis of the data will pinpoint the genetic distinctiveness of Italian breeds. Moreover, the obtained results contribute to a better characterization of history and genetic structure of Italian cattle breeds.

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.

Pig from Casertana and Siciliana breeds are two endangered breeds raised in the southern-Italy (Campania and Sicily regions, respectively) and characterized to have a black skin. Special projects are trying to save and characterize both of them by using several approaches. In this study we report the preliminary results we obtained after a cytogenetic investigation we performed by using both C- and R-banding techniques and the sister chromatid exchange (SCE) test to verify their chromosome stability under the environmental conditions. Fifty-two pigs from Casertana breed and 19 pigs from Siciliana breed were investigated. All animals from both breeds showed a normal karyotype, with the exception of two male pig from Siciliana breed which were found heterozygous carrier of rob(15;17) (2n=37, XY), probably being hybrids with the wild pig (2n=36) present in the Nebrodi mountains where this breed is raised in Sicily. SCE-test applied on 42 pigs from Casertana breed (22 males and 20 females) and 19 pigs from Siciliana breed (8 males and 11 females) revealed no statistical differences between the SCE-mean number in Casertana pig (7.13±3.20) than that (6.87±3.12) achieved in Siciliana pig. Statistical differences were found between males (7.26±3.38) and females (6.59±2.90) of Siciliana pig breed, as well as between females of Casertana (7.24±3.26) and Siciliana (6.59±2.90) breeds, while no statistical differences were found between males of the breeds, as well as between males and females of Casertana breed.

The αs2 casein, encoded by the CSN1S2 gene, is one of the three Calcium sensitive caseins present in the milk of ruminants of zootechnical interest and in the milk of Equidae species (horse and donkey). In the present study, we cloned, sequenced and analysed two different donkey CSN1S2 cDNAs that we called CSN1S2 I and CSN1S2 II. The first, which spans over a fragment of 1016 nt, is constituted by 19 exons and encodes for a predicted protein (called αs2-I) of 221 aminoacids; the second, of which we determined the entire sequence (16 exons), encodes for a predicted peptide (called αs2-II) of 168 aminoacids. Alternative splicing and genetic markers are reported for both genes.

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.

To quantify radiation treatments for bone metastases from breast cancer in three Sicilian provinces (Messina, Catania, Ragusa) with respect to the general population and the incidence and prevalence of breast cancer in this macro-area in a 8-year period.All bone metastasis patients treated using radiotherapy in 8 radiation departments operating in the provinces of Messina, Catania and Ragusa were collected. Among these, metastases from breast carcinoma were analyzed according to year of irradiation. An analysis of breast cancer incidence and prevalence with respect to inhabitants in this macro-area was conducted using literature and census data.From January 2004 to December 2011, irradiation was delivered in 4419 bone metastasis patients. Among these, 1617 had a primary breast cancer with a median treatment per year of 206.5 (range, 164-251); 211 patients were treated in 2004 and 206 in 2011. In 2004, there were 1,048,957 female residents in the three provinces and 1,065,422 in 2011. The reported breast cancer incidence and prevalence in Sicily was respectively 100.79/100,000 and 908.54/100,000 in 2004 and 108.41/100,000 and 1091.29/100,000 in 2010.There has been an increase in both incidence and prevalence of breast cancer in Sicily. Nevertheless, it seems that there was no increment in skeletal-related events requiring irradiation in such patients in eastern Sicily radiation departments.

Analysis of the goat beta-lactoglobulin gene evidenced three differences, two in the 7th exon (a G--A transition in position 83 and a 10 nucleotides, 5'-AGGCCCCTCC-3', insertion/deletion rearrangement phenomenon located downstream nucleotide 104) and one in the 6th intron (an A--G transition located 7 nucleotides upstream the 7th exon). In order to identify carriers of the two exonic mutations, a PCR-RFLP method of analysis has been set up. The frequency of the insertion in a local goat population reared in province of Naples and in Girgentana goats reared in Basilicata and Sicilia was 0.09 and 0.01 respectively

Chantier qualité GA Liste des auteurs de l'European Cattle Genetic Consortium, classés par pays : Austria: R. Baumung, S. Manatrinon, BOKU University, Vienna; Belgium: G. Mommens, University of Ghent, Merelbeke; Denmark: L.-E. Holm, Aarhus University, Tjele; K.B. Withen, B.V. Pedersen, P. Gravlund, University of Copenhagen, Copenhagen; Estonia: H. Viinalass, Estonian University of Life Sciences, Tartu; Finland: J. Kantanen, I. Tapio, M.H. Li, MTT, Jokioinen; France: K. Moazami-Goudarzi, M. Gautier, Denis Laloë, INRA, Jouy-en-Josas; A. Oulmouden, H. Levéziel, INRA, Limoges; P. Taberlet, Université Joseph Fourier et CNRS, Grenoble; Germany: B. Harlizius, School of Veterinary Medicine, Hannover; H. Simianer, H. Täubert, Georg-August-Universität, Göttingen; G. Erhardt, O. Jann, C. Weimann, E.-M. Prinzenberg, Justus-Liebig Universität, Giessen; I. Medugorac, A. Medugorac, M. Förster, Ludwig-Maximilians Universität, Munich; H.M. Mix, Naturschutz International, Grünheide; C. Looft, E. Kalm, Christian-Albrechts-Universität, Kiel; Ireland: D.G. Bradley, C.J. Edwards, D.E. MacHugh, A.R. Freeman, Trinity College, Dublin; Italy: P. Ajmone Marsan, R. Negrini, Università Cattolica del S. Cuore, Piacenza; M. Longeri, G. Ceriotti, M. Zanotti, Università degli Studi di Milano; D. Marletta, A. Criscione, Universita degli Studi di Catania, Catania; A. Valentini, C. Marchitelli, L. Pariset, M.C. Savarese, Università della Tuscia, Viterbo; F. Pilla, Università del Molise, Campobasso; Latvia: Z. Grislis, Latvia University of Agriculture, Jelgava; Lithuania: I. Miceikienė, Lithuanian Veterinary Academy, Kaunas; Netherlands: I.J. Nijman, Utrecht University; W. van Haeringen, L. van de Goor, Van Haeringen Laboratory, Wageningen; Norway: I. Olsaker, Norwegian School of Veterinary Science, Oslo; Portugal: C. Ginja, L.T.Gama, Instituto Nacional de Recursos Biológicos—INIA, Lisbon University, Lisboa; L.T. Gama, Instituto Nacional de Recursos Biológicos-INIA, I.P., Vale de Santarem; J.C. Mateus, Universidade de Trás-os-Montes e Alto Douro, Vila Real; A. Beja-Pereira, N. Ferrand, Oporto University; Russia: Z. Ivanova, R. Popov, I. Ammosov, Yakutian Research Institute of Agricultural Sciences, Yakutsk, Sakha; T. Kiselyova, All-Russian Research Institute for Farm Animals and Breeding, St. Petersburgh-Pushkin; N. Marzanov, All-Russian Research Institute of Animal Husbandry, Dubrovitsy; Serbia: S. Stojanovic, Ministry of Agriculture and Water Management, Belgrade; Slovenia: M. Simčič, P. Dovč, D.Kompan, University of Ljubljana, Domzale; Spain: S. Dunner, Universidad Complutense de Madrid; C. Rodellar, I. Martín-Burriel, Veterinary Faculty, Zaragoza; A. Sánchez, J. Piedrafita, Universitat Autònoma de Barcelona; P.J. Azor, J.V. Delgado, A. Martínez-Martínez, A. Molina, E. Rodero, University of Córdoba; Switzerland: G. Dolf, University of Berne; UK: J.L. Williams, P. Wiener, Roslin Institute; M.W. Bruford, T.C. Bray, Cardiff University, Cardiff; L. Alderson, Countrywide Livestock Ltd, Shrewsbury; USA: M.C.T. Penedo. University of California, Davis, CA; International audience; Classification of cattle breeds contributes to our understanding of the history of cattle and is essential for an effective conservation of genetic diversity. Here we review the various classifications over the last two centuries and compare the most recent classifications with genetic data. The classifications devised during the 19th to the late 20th century were in line with the Linnaean taxonomy and emphasized cranial or horn morphology. Subsequent classifications were based on coat color, geographic origin or molecular markers. Several theories were developed that linked breed characteristics either to a supposed ancestral aurochs subspecies or to a presumed ethnic origin. Most of the older classifications have now been discarded, but have introduced several Latin terms that are still in use. The most consistent classification was proposed in 1995 by Felius and emphasizes the geographic origin of breeds. This is largely in agreement with the breed clusters indicated by a biochemical and molecular genetic analysis, which reflect either groups of breeds with a common geographic origin or single breeds that have expanded by export and/or crossbreeding. We propose that this information is also relevant for managing the genetic diversity of cattle.