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The domestication of taurine cattle initiated ~10 000 years ago in the Near East from a wild aurochs (Bos primigenius) population followed by their dispersal through migration of agriculturalists to Europe. Although gene flow from wild aurochs still present at the time of this early dispersion is still debated, some of the extant primitive cattle populations are believed to possess the aurochs-like primitive features. In this study, we use genome-wide single nucleotide polymorphisms to assess relationship, admixture patterns and demographic history of an ancient aurochs sample and European cattle populations, several of which have primitive features and are suitable for extensive management. The principal component analysis, the model-based clustering and a distance-based network analysis support previous works suggesting different histories for north-western and southern European cattle. Population admixture analysis indicates a zebu gene flow in the Balkan and Italian Podolic cattle populations. Our analysis supports the previous report of gene flow between British and Irish primitive cattle populations and local aurochs. In addition, we show evidence of aurochs gene flow in the Iberian cattle populations indicating wide geographical distribution of the aurochs. Runs of homozygosity (ROH) reveal that demographic processes like genetic isolation and breed formation have contributed to genomic variations of European cattle populations. The ROH also indicate recent inbreeding in southern European cattle populations. We conclude that in addition to factors such as ancient human migrations, isolation by distance and cross-breeding, gene flow between domestic and wild-cattle populations also has shaped genomic composition of European cattle populations.Heredity advance online publication, 28 September 2016; doi:10.1038/hdy.2016.79.

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.

The identification of the breed of origin of cattle derived products has recently assumed particular relevance since the increasing interest in marketing mono-breed labelled cheese and beef. These products are usually sold at a higher price creating financial incentives to substituting them with lower value products coming from undifferentiated or common breeds or crossbred animals. Frauds can damage these valuable niche markets that, indirectly, may help to preserve genetic diversity through the economic incentive on raising local breeds, derived by the high value products, that are usually less productive. DNA analysis can help to identify fraudulent behaviour as we already demonstrated for Parmigiano Reggiano cheese produced from only Reggiana cattle milk. In this study we used Illumina BovineSNP50 BeadChip genotyping data from different cattle breeds to identify single nucleotide polymorphisms (SNPs) that could be useful for breed authentication of dairy and beef products. The dataset was made of genotyping data obtained from the chip v.1 or v.2 analysed on 749 Italian Brown, 2093 Italian Friesian, 479 Italian Simmental, 410 Marchigiana, 71 Cinisara and 72 Modicana cattle. About 51,000 SNPs were retained for further analyses after filtering according to a few parameters (Hardy-Weinberg equilibrium ≥0.0001; call rate ≥0.90). A quite high number of SNPs presented fixed alleles in one breed that had minor allele frequency (MAF) >0.30-0.40 in the other breeds. This was true for all breed combinations. These SNPs were indicated as highly informative for authentication purposes. Using the selected panel of SNPs, Principal Component Analysis (PCA) was able to discriminate investigated breeds. These results may represent a starting point to develop targeted DNA based tests for authentication of mono-breed cattle products.

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.

Recent studies have shown that copy number variants (CNVs) are important sources of variability of mammalian genomes. We applied a cross species array comparative genome hybridization (aCGH) experiment using as reference the cattle genome to investigate, for the first time, variability in the sheep and goat genomes derived from copy number variation and identified 431 and 358 CNVs, respectively. A comparison of these results to those obtained in other mammals for similar experiments is reported. The identified CNVs could be important in determining phenotypic and production differences between and within breeds. Further studies will be carried out to evaluate the identified CNVs from both functional and evolutionary points of view.

Fatty acid profile of lipids in animal origin products (AOP) for human food regimen plays an important role for its effects on consumer health. Over time ‘lard’ has played an useful function in the composition of a ration for human diets. A revaluation of biochemical effects of ‘lard ', as a source of biomolecules with nutritional and extranutritional properties, is in progress. The Autochthonous Genetic Types, especially ancient types (AAGT), can be considered in future a particularly useful source of this AOP. 'Casertana' pig, known since ancient times, deserves AAGT title. The study was carried out on 'fresh lard' taken at the level of 4th ÷ 6th lumbar vertebra from 50 ‘Casertana’ pigs (21 castrated males and 29 females) bred at Experimental Station of ConSDABI (Circello, Benevento). The acidic fraction was extracted by Folch method and analyzed, as methyl esteres, by gas-chromatography. The acidic fraction considered consists of: palmitic, palmitoleic, margaric, eptadecenoic, stearic, oleic, C18:1 cis,12, linoleic, γ-linolenic and linolenic fatty acid and CLA, the more representative is C18:2 cis9, trans11 and the other 6 isomers were detected in traces. The effect of sex, year and month of slaughtering (covariates), age and refrigerated carcass weight was always significant (P

The purpose of the work was to detect the milk yield and milk composition in Autochthonous Italian Grey Cattle (ex Podolian) machine milked. The ‘Podolian’ breed derived from Bos primigenius primigenius (Aurochs) of the Near East with possible introgression from indigenous Aurochsen of Middle Southern Italy. Milk production was detected in a population of 97 cows of 'Masseria Colombo' farm. The milking technique adopted contemplates that, for around 8 months, after the machine milking of the morning, the calf remains with its mother for about 7-8 h. Therefore, the milk yield is referred to a single milking\day. The first recording data was carried out in May 2010 and the last one in January 2011. The attitude to machine milking was good. As expected, the individual milk yield, on average, increased with the parity order reaching in the third order: kg 213 ± 50 at 30 days, kg 421 ± 94 at 2 months, kg 609 ± 116 at 3 months and kg 1,215 ± 186 at 7 months (P

The aim of the research was to investigate colour characteristics of ‘soppressata’ stored for 45 and 90 days under vacuum and under perirenal fat. The products were obtained from 20 pigs (10 castrated males and 10 entire females) belonging to AAGT ‘Casertana’, reared in multiple boxes at ConSDABI experimental farm. For each ‘soppressata’ the colorimetric profile was determined on 7÷8 samples by using spectrophotometer (U3000, Hitachi) equipped with integrated sphere. The results showed that: (i) castrated males furnish product with higher redness value (a*) and a lower hue value at 45 days if stored under perirenal fat, while the females showed higher yellowness value (b*) when stored under vacuum; (ii) at 90 days of storage the differences in the colour characteristics are confirmed.

Sensory characteristics of two products: ‘prosciutto’ (dry cured ham) and ‘fiocco’, seasoned for 24 and 12 months respectively, obtained from castrated males and entire females of pig AAGT ‘Casertana’ were investigated. On 18 hams and 20 ‘fiocco’, at the end of the ripening period, colour profile (L*, a*, b*) with spectrophotometer (U3000) and rheological traits of single muscle with TPA and compression test were detected. The results showed values of redness and yellowness significantly lower in ‘fiocco’ in comparison with ‘prosciutto’, which provides better rheological characteristics due to the longer seasoning period, hence to the higher proteolysis and lipolysis. Females furnished both products with better traits in comparison with castrated males (P

The study was carried out on some typical traditional products obtained from Casertana pig, an autochthonous genetic type mostly reared in Campania in order to point out possible differences between genders during the ripening period. The products (Capocollo, Fiocco, Lardo, Pancetta arrotolata, Pancetta tesa, Prosciutto, Salsiccia, Sopressata) were obtained from 35 castrated males and 22 entire females. The pigs were reared in multiple boxes and slaughtered at 160 kg of live weight. The difference in ripening loss percentage between genders in salsiccia was not significant whereas the percentage loss of fiocco, pancetta and prosciutto was higher in castrated males at any time considered. Such difference could be due to different texture of adipose tissue as well as to a higher intramuscular fat content in females.

The aim of the research was to evaluate rheological characteristics of dry cured ham of some Italian autochthonous genetic types of pig. In 108 dry cured hams obtained from Calabrese, Casertana, Cinta Senese and Nero Siciliano rheological traits were determined on Biceps femoris, Semimembranosus and Semitendinosus muscle using a Texturometer. Curing process was performed in Parma (64 hams) and in Morcone (Benevento) (44 hams). Data was analysed using time as covariate and AGT, sex, curing plant, muscle as fixed factors .

The research was carried out on 15 castrated males and 10 females of Casertana pig slaughtered at a live weight ranging from 130 to 250 kg. Rheological and colorimetric characteristics were determined on the muscles Caput longum tricipitis brachii (CL), longissimus dorsi (LD), psoas maior (PM) anconeus (PA), supraspinatus (SS) after storage at -20 °C for 120 d. Statistical analysis considered live weight as covariate and sex, muscle and interaction as fixed factor (GLM procedure, SAS). Results showed that females have darker meat than castrated males. LD muscle showed the lowest value of a* and b* and was chracacterized by the greater lightness with the lowest chroma and the highest hue value. On the other hand, PA was the darkest muscle and showed the worst rheological traits. PM exhibited the lowest hardness and chewiness value. Sex did not significantly affect rheological characteristics.

The work identified the most hydrolysed myofibrillar proteins and polypeptide components of Fiocco, a traditional italian product from pork leg, after 12 months of seasoning.

Colour parameters were detected on Biceps Femoris (BF), Semitendinosus (St) and Semimembranosus (Sm) muscles and fat from dry cured hams of Calabrese, Casertana, Cinta senese and Siciliano autochthonous genetic types. With increase of the maturation period the reflectance percentage and lightness decreased and the yellow index increased. The reflectance percentage was higher for ham obtained from Casertana, especially in the 660-780 nm range, in comparison with that obtained from Siciliano, Cinta senese and Calabrese. Casertana ham showed a higher lightness (L*), hence it is ‘lighter’. Moreover, Casertana gave ham with a lower red index (a*) than Cinta Senese. Calabrese and Casertana gave ham whose fat shows a higher reflectance percentage from 360 to 600 nm in comparison with Siciliano.

Weight loss was monitored, from preparation to maturation, on the following typified traditional products: ‘capocollo del Sannio’, ‘fiocco del Sannio’, ‘prosciutto stagionato del Sannio’, ‘salame Napoli’, ‘salsiccia del Sannio’, ‘soppressata del Sannio’ obtained from 12 pigs belonging to ‘Casertana’ genetic type. Furthermore on the last three products some quality traits were also determined. ‘Salsiccia del Sannio’ showed the highest weight loss during the first 15 days of the maturation process whereas the ‘soppressata del Sannio’ showed a decrease in weight especially in the following 15 days. The weight loss was more gradual and lower for ‘Capocollo del Sannio’ and ‘fiocco del Sannio’. The ‘soppressata del Sannio’ had higher values of hardness, cohesiveness, springiness and chewiness, whereas the salsiccia had the lowest values.

The research aimed to assess the effect of breed, sex, age at slaughter, rearing system and electrical stimulation on some colorimetric characteristics measured on the muscles Longissimus dorsi (LD), Gluteobiceps (Gb), Semimembranosus (Sm) and Rectus femoris (RF) of lambs belonging to the genetic types Gentile di Puglia (GP), Ile de France (IF) and the cross-breeds F1, F2 and F3. The IF lambs provided meat with the highest value of hue and lightness and the lowest chroma and redness. The F1 lambs showed the highest values of redness while the F2 crossbreed significantly differed from the other three genetic types only in pH, which was always the lowest. The F3 crossbreed revealed similar behaviour to the other genetic types, except for the pH which was always higher than in GP, F1 and F2. The differences between sexes were restricted to L* and pH values, being higher in the male. The lambs slaughtered at 56 days showed high a* values, while b* and hue were on average higher in younger lambs (35 days). The lambs reared with maternal milk in comparison with the artificially reared ones provided meat with the highest a* chroma and b* and the lowest hue values. Electrical stimulation of the carcass seems to have produced the same effects as the usual ageing time in cold store. The RF muscle provided the brightest meat; Sm showed the highest values of b* and chroma; LD provided the “darkest” meat and the lowest values of b* and hue; Gb produced a lower a* value than muscles LD, RF and Sm.

Chemical composition and lactodynamometric characteristics were studied in milk obtained from Agerolese, Burlina, Bianca Val Padana, Marchigiana, Varzese-Ottonese, Piemontese and Reggiana bovine genetic types. ‘Caciocavallo’ cheese yields were detected at 48 hour and 30, 60, 90, 180 and 360 days of maturation. Marchigiana shows a higher protein and lactose percentage than the other genetic types. Agerolese milk tends to have a better coagulation aptitude in comparison to Burlina. Caciocavallo yield was of about 9% for Burlina, Agerolese and Reggiana, reaching values of 7.2-7.5% in the other genetic types. Burlina, Agerolese and Reggiana had a higher loss during ripening at 30, 60, 90 and 180 days in comparison with the other genetic types that have the highest weight loss at 360 days of maturation. This research highlights the importance of genetic type for obtaining diversifie products.

Rheological parameters were studied on ‘caciocavallo’ cheese, obtained from Agerolese, Burlina, Bianca Val Padana, Marchigiana, Ottonese, Piemontese and Reggiana bovine genetic types, at 30, 60, 90 and 180 days of maturation. Marchigiana ‘caciocavallo’ was characterized by higher hardness and springiness than the other genetic types; hence requiring more chewing effort. As the maturation period increased from 30 to 180 days, hardness and chewiness increased because of higher firmness. The results suggest that it is possible to produce caciocavallo with diversified rheological traits depending on breed, genetic type and maturation period.