Search

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.

Congenital hypotrichosis in mammalian species consists of partial or complete absence of a hair coat at birth. Affected individuals having a partial hair coat at birth may loose it subsequently.The aim of this paper was to physically map the ovine hr gene using fluorescence in situ hybridization (FISH).A preliminary study on an internet data bank (http://www.informatics.jax.org) showed that the regions of the hr gene on murine chromosome 14 and human chromosome 8 present homology with ovine chromosome 2.

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.

Purpose of this investigation was to deter- mine the nature of a visible spotting defect on the slice of dry-cured ham and assess environ- mental and genetic causes of this frequent problem. A group of 233 pigs from commercial cross-breeding lines, progeny of ten boars and forty seven sows, was raised in a single herd to obtain the Italian Heavy Pig, typically slaugh- tered at 160±10 kg live weight and older than 9 months of age. A quality evaluation of their right dry-cured hams, seasoned according to the Parma P.D.O. protocol, was undertaken. Each ham was cross-sectioned to obtain a slice of Semimembranosus, Semitendinosus and Biceps Femoris muscles. The focused pheno- type was the presence/absence of brownish spots in these muscles, which represent a remarkable meat defect with strong impact on the final sale price. Environmental and man- agement factors were considered in order to evaluate variability related to the phenotype. Animals were raised on two different flooring types (concrete and slatted floor) and a Vitamin C diet was also supplemented in the last 45 days before slaughtering to half of the animals. While the pre-planned environmental effects did not show any significant contribution to the total variability of the phenotype, the genetic analysis showed a near to zero value for heri- tability with a consistent 0.32 repeatability. The proportion of the total phenotypic variance was explained by an important dominance genetic component (0.26) indicating that the techno- logical seasoning process may play a secondary role on the expression of this phenotype.