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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.

In recent years consumers prefer genuine, tasty, protein-rich, low in fat and cholesterol products. The Cinisara cow is a dairy Sicilian autochthonous breed, reared in the western part of the isle according to the traditional livestock system, based on grazing natural pastures. The meat of Cinisara cattle could be used to obtain also processed products, among which salami and bresaola, as commercial alternatives to fresh meat, in order to increase the economic profitability of farms. The aim of this research was to produce bresaola and salami with meat from adult cows (AC) and grazing (GB) or housed (HB) young bulls of Cinisara breed, evaluating their physico-chemical and sensory traits. In the last 3 months, all animals were fed with hay ad libitum and concentrate; moreover AC and GB were continuously grazing pasture until slaughtering. After a week maturation phase in cold room, the carcasses were dissected to separate semimembranosus (SM), semitendinosus (ST) and biceps brachii (BB) muscles for bresaola production, and using the rest of meat for salami production. The muscles, after removing fat and external tendons, were salted in 2 steps for a total of 14 days at 4°C. After they were placed to drain for 8 days at 4°C and subsequently stuffed into natural casing and transferred to drying cells. For the preparation of the salami, the meat of the three animal categories was minced separately and added with 20% of lard from pigs of “Nero dei Nebrodi” breed cut into cubes, and a mixture of salt and spices. Each mixture was separately stuffed into natural casings of straight type (35 cm in length and 7 cm in diameter). During the phases of dripping, fermentation and maturation, the salami and bresaola were stored in rooms with controlled temperature and relative humidity for 45 and 35 days, respectively. The fat content (% DM) was higher in AC both for bresaola (9.68 vs 4.78 in HB and 3.52 in GB; P≤0.001) and salami (41.46 vs 36.96 in HB and 32.62 in GB; P≤0.01) due to the higher fat content of meat. Also the total fatty acid (FA) content (%DM) was higher in AC both for bresaola (8.90 vs 4.37 in HB and 3.13 in GB; P≤0.001) and salami (37.20 vs 33.47 in HB and 29.62 in GB; P≤0.01). The content in saturated, monounsaturated (MUFA) and polyunsaturated (PUFA) FA (% on total FA) of bresaola showed differences between animals (45.24, 42.51 and 10.79 in AC; 41.73, 23.33 and 34.80 in GB; 45.20, 32.32 and 21.72 in HB; P≤0.001), in accordance with the different fat content and the proportions of FA which, as is known, vary with the age of the animal and its diet. In bresaola, oleic acid (% on total FA) was equal to 32.25 in AC, 23.70 in HB and 15.45 in GB, (P≤0.01), due to the different distribution and location of MUFA and PUFA in animal tissues. In salami, the differences between the animals were minor, although significant, probably due to the lower lipid contribution of meat compared to the lard added. The evaluation of the sensory analysis of ripened salami showed a better overall acceptability for AC, with higher scores for color uniformity, fat/lean connection, flavor intensity and chewiness. A good general acceptability emerged also for bresaola, even if those of AC were less appreciated for chewiness and tenderness. ST bresaola showed higher colorimetric parameters, higher fat and MUFA percentages, while those obtained from grazing animals (AC and GB) showed higher shear force at Warner-Bratzler test. In both products the volatile organic compounds were higher in AC than in GB and HB which had a similar content. From multivariate statistical approaches, a good discrimination was obtained among animal categories for both bresaola and salami. The results evidenced the possibility to obtain bresaola and salami with appreciable sensory properties for consumers from different animal categories and muscle cuts, thus to improve the economic performance of autochthonous cattle.

The current availability of very large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers particularly suitable for the detection of genomic regions where a reduction in heterozygosity occurred and offers new opportunities to improve the accuracy of inbreeding (F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and the distribution of ROH in medium-density SNP genotypes (~ 50 000) in order to characterize autozygosity in 512 individuals of Valle del Belice sheep and identify the regions of the genome with high ROH frequencies. A total of 11 629 ROH were identified. All individuals displayed at least one ROH > 1 Mb. The mean value of FROH>1Mb was 0.084±0.061. ROH that were shorter than 10 Mb predominated. The highest coverage of chromosome (OAR) by ROH was observed on OAR24, whereas the lowest one was observed on OAR1. A typical pattern was observed for the number of ROH per OAR with higher values in the first three chromosomes. There was a considerable difference among animals for the number of ROH segments and the length of the genome covered by ROH. The genomic regions most commonly associated with ROH were identified by selecting the top 1% of the SNPs most commonly observed in ROH within breed. A total of 239 SNPs were considered as candidate SNPs and we identified 107 potential candidate genes that may be under directional selection. Six genomic regions located on six chromosomes (OAR2, OAR3, OAR4, OAR10, OAR11 and OAR23), corresponding to ROH island, presented hotspot of autozygosity. According to KEGG database, a majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. The ROH islands spanned several candidate genes which influence traits that are associated with adaptability and with the regulation of immune responses (NPAS2, PDCL3, SERPINF1 and SERPINF2) and we did not identified candidate genes with important influence on milk production traits in sheep. The Valle del Belice breed is subjected to limited breeding selection programs for milk production traits, but shows excellent adaptability to the local environments. Therefore, these results suggest at least a partial role of natural selection in shaping the genome of Valle del Belice sheep breed.

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.

Il brevetto consiste in un metodo per l’autenticazione e la tracciabilità genetica delle produzioni lattiero-casearie mono-razza su base molecolare con approccio statistico-probabilistico. Il metodo si basa sull’impiego di tecniche di analisi ad elevata processività (in particolare SNPs genotyping su Bead Chip Illumina) su pool di DNA e sull’applicazione di metodi computazionali innovativi. Il metodo è già stato validato su produzioni lattiero-casearie ovine quali la Vastedda della Valle del Belice (DOP), sia su prodotti lattiero caseari a DOP ottenuti in laboratorio, che su prodotti a DOP reperibili sul mercato. Il metodo può comunque essere esteso, su richiesta, a qualsiasi altro prodotto lattiero-caseario mono-razza. Le possibili applicazioni del brevetto riguardano sia la certificazione e quindi l’autenticazione di tutte le produzioni lattiero-casearie iscritte nel Registro delle denominazioni di origine protette e delle indicazioni geografiche protette per le quali si richiede la verifica dell’origine della materia prima, sia per la certificazione e l’autenticazione di tutte le produzioni lattiero-casearie, tipiche e non, per le quali si ritiene commercialmente utile la verifica del legame razza-prodotto. Il metodo consente di certificare/verificare la conformità della materia prima (il latte) utilizzata per la produzione del prodotto lattiero-caseario, per i prodotti che devono essere ottenuti esclusivamente con il latte proveniente da una determinata razza.

In livestock, single nucleotide polymorphism genotyping arrays have been used to differentiate breeds and populations for several downstream applications, including breed allocation of individuals, breeds of origin of crossbred animals, authentication of mono breed products, comparative analyses of selection signatures among several other uses. We already tested a combination of principal component analysis (PCA), used as preselection method, and random forest (RF) used as classification method to assign cosmopolitan Italian breeds with no or very low error rate. In this work, we increased the number of breeds and approaches, to have a more comprehensive view of the strategies available and the applicability to local Italian breeds. The most common cosmopolitan dairy or dual purpose breeds (Holstein, Brown, Simmental) and 3 local breeds subjected to limited or no breeding programs (Reggiana, Modicana and Cinisara) were analyzed comparing several methods of SNPs pre-selection (Delta, Fst and PCA) in addition to RF classifications. From these classifications, two panels of 96 and 48 SNPs that contained the most discriminant SNPs were created for each pre-selection method. The results showed that the 96-SNP panels were generally more able to discriminate all breeds, while for the 48- SNP panels the error rate increased mainly for autochthonous breeds, particularly for Cinisara. This was probably a consequence of limited selection pressure, admixed origin, and ascertain bias on the construction of the SNP chip that was not designed considering these breeds. Several selected SNPs are located nearby genes affecting breed-specific traits (e.g. coat color and stature) or associated to production traits. The 96-SNP panel obtained after a preselection chromosome by chromosome, and used in the previous work with cosmopolitan breeds only, could identify informative SNPs that were particularly useful for the assignment of minor breeds. This panel reached the lowest value of out of bag (OOB) error in the RF test even in the Cinisara, whose value was quite high in all other panels. Moreover, this panel contained also the lowest number of SNPs in linkage disequilibrium. Our results showed the usefulness and power of the combination of PCA pre-selection and RF also for the discrimination of local cattle 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.

In goats, classical genetic studies reported a large number of alleles at the Agouti locus with effects on coat color and pattern distribution. From these early studies, the dominant A(Wt) (white/tan) allele was suggested to cause the white color of the Saanen breed. Here, we sequenced the coding region of the goat ASIP gene in 6 goat breeds (Girgentana, Maltese, Derivata di Siria, Murciano-Granadina, Camosciata delle Alpi, and Saanen), with different coat colors and patterns. Five single nucleotide polymorphisms (SNPs) were identified, 3 of which caused missense mutations in conserved positions of the cysteine-rich carboxy-terminal domain of the protein (p.Ala96Gly, p.Cys126Gly, and p.Val128Gly). Allele and genotype frequencies suggested that these mutations are not associated or not completely associated with coat color in the investigated goat breeds. Moreover, genotyping and sequencing results, deviation from Hardy-Weinberg equilibrium, as well as allele copy number evaluation from semiquantitative fluorescent multiplex PCR, indicated the presence of copy number variation (CNV) in all investigated breeds. To confirm the presence of CNV and evaluate its extension, we applied a bovine-goat cross-species array comparative genome hybridization (aCGH) experiment using a custom tiling array based on bovine chromosome 13. aCGH results obtained for 8 goat DNA samples confirmed the presence of CNV affecting a region of less that 100 kb including the ASIP and AHCY genes. In Girgentana and Saanen breeds, this CNV might cause the A(Wt) allele, as already suggested for a similar structural mutation in sheep affecting the ASIP and AHCY genes, providing evidence for a recurrent interspecies CNV. However, other mechanisms may also be involved in determining coat color in these 2 breeds.

Background Somatic cell score (SCS) has been promoted as a selection criterion to improve mastitis resistance. However, SCS from healthy and infected animals may be considered as separate traits. Moreover, imperfect sensitivity and specificity could influence animals' classification and impact on estimated variance components. This study was aimed at: (1) estimating the heritability of bacteria negative SCS, bacteria positive SCS, and infection status, (2) estimating phenotypic and genetic correlations between bacteria negative and bacteria positive SCS, and the genetic correlation between bacteria negative SCS and infection status, and (3) evaluating the impact of imperfect diagnosis of infection on variance component estimates. Methods Data on SCS and udder infection status for 1,120 ewes were collected from four Valle del Belice flocks. The pedigree file included 1,603 animals. The SCS dataset was split according to whether animals were infected or not at the time of sampling. A repeatability test-day animal model was used to estimate genetic parameters for SCS traits and the heritability of infection status. The genetic correlation between bacteria negative SCS and infection status was estimated using an MCMC threshold model, implemented by Gibbs Sampling. Results The heritability was 0.10 for bacteria negative SCS, 0.03 for bacteria positive SCS, and 0.09 for infection status, on the liability scale. The genetic correlation between bacteria negative and bacteria positive SCS was 0.62, suggesting that they may be genetically different traits. The genetic correlation between bacteria negative SCS and infection status was 0.51. We demonstrate that imperfect diagnosis of infection leads to underestimation of differences between bacteria negative and bacteria positive SCS, and we derive formulae to predict impacts on estimated genetic parameters. Conclusions The results suggest that bacteria negative and bacteria positive SCS are genetically different traits. A positive genetic correlation between bacteria negative SCS and liability to infection was found, suggesting that the approach of selecting animals for decreased SCS should help to reduce mastitis prevalence. However, the results show that imperfect diagnosis of infection has an impact on estimated genetic parameters, which may reduce the efficiency of selection strategies aiming at distinguishing between bacteria negative and bacteria positive SCS.

Nowadays in dairy sheep, test-day records are collected monthly under an alternate morning/evening system. This alternate system was implemented because of the steady increase in recording cost per sheep observed in the last few decades. Furthermore, additional modifications to the testing schemes have been proposed to reduce the costs of milk recording. In dairy sheep, the cost for milk recording is indeed too high compared both with individual outputs and with other dairy species. Therefore, the purposes of the present study were: i) to compare estimated breeding values (EBVs) for milk yield using different simplified testing schemes with a test-day sire model; ii) to evaluate the effect of different testing schemes on the ranking of top rams; and iii) to evaluate the effect of different testing schemes on the genetic progress, based on sire selection. A total of 28,304 test-day records from 4,968 lactations of 2,429 Valle del Belice ewes, collected in 15 flocks between 1994 and 2006, were used for the analysis. To have the same ewes through different testing schemes, it was requested that a ewe have at least six test-day records included in the dataset. The pedigree file included a total of 206 sires. The response variable was the daily milk production. Four different recording schemes were used to estimate breeding values and to make comparisons. The reference scheme considered all data obtained from ewes in the present recording system in which ewes in lactation were tested every month. Three alternative schemes that used less information were considered. A random regression sire model that used a Legendre function of days in milk was fitted. EBVs obtained with alternative recording schemes and under different intensities of selection showed different degrees of Spearman correlation with EBVs obtained using the monthly recording scheme. These correlations ranged from 0.68 to 0.98. The consequence of moving the test-day schedule to one of these schemes will produce a decrease in genetic response to selection due to the associated loss of intensity and accuracy. Consequently, before given any recommendation in this regard, further research should be done to better elucidate the consequences of a change in the scheme of test-day collection.

A total of 19.207 test-days, collected on 4 farms from 1999-2006 and belonging to 1109 Valle del Belice dairy sheep were analyzed with a repeatability model. After strict outlier analysis 17.747 records were retained. Animals were reared in an extensive system resulting in large environmental influences. However, significant genetic variation was detected in production traits (milk production mean=1336 stdg=93 g/d, fat+protein 167 stdg=12 g/d). Heritability was only 3% while the interaction year by month of test-day explained 27% of the variation. A protein and DNA analysis program was initiated in order to facilitate selection to maintain these flocks under these conditions. In total 427 animals were typed for the -lactoglobulin locus. Using the recorded pedigree this genotype information was spread over the entire population. The trend in frequency for the AA genotype was significantly negative (p-value=.0057), as were trends in milk yield and lactation length. Possibly farmers have a preference for the BB animals. Relations with production traits were indicative for this trend, but not significant. A possible explanation is the relevant, but non significant difference in length of the lactation between AA and BB animals.

La filogenesi della razza Girgentana ancora oggi rimane più o meno sconosciuta sebbene l’ipotesi più valida sembrerebbe quella che la ricollega alla capra Falconeri o Markor (Himalaya). La consistenza numerica della razza nell’ultimi anni ha subito una notevole contrazione, tanto da potersi annoverare tra le razze in via di estinzione. Il latte della capra Girgentana era utilizzato solo per il consumo diretto. Quando è entrato in vigore il regolamento che vietava la vendita del latte al dettaglio, il valore zoo-economico della razza Girgentana è diminuito notevolmente, contribuendo alla contrazione numerica della razza nell’ultimo ventennio. La rivalutazione della razza sarebbe di fondamentale importanza, infatti è stato evidenziato che il latte della capra Girgentana presenta delle varianti proteiche rare, che potrebbero assumere un ruolo non indifferente nell’alimentazione umana. Le proteine del latte maggiormente presenti sono le caseine alphaS1 (CSN1S1), beta (CSN2), alphaS2 (CSN1S2) e kappa (CSN3). In diverse razze caprine, i loci caseinici sono altamente polimorfici, e alcune varianti genetiche hanno un effetto sulla produzione di latte. Lo scopo di questo lavoro è stato quello di stimare la variabilità dei loci caseinici nella razza Girgentana e di determinare se esiste una correlazione tra i polimorfismi dell’alphaS1-caseina a livello molecolare e l’isoelettrofocalizzazione (IEF), che determina l’espressione della proteina stessa. Sebbene l’IEF sia una tecnica rapida e poco costosa non permette di distinguere tutti gli alleli presenti a questo locus. Alleli col medesimo punto isoelettrico (pI) si sovrappongono. È possibile, ad ogni modo, suddividere gli individui in gruppi in base al contenuto in alphaS1-caseina: contenuto alto, contenuto medio e contenuto basso. Sono stati genotipizzati 40 individui (20 capre e 20 becchi) per 9 SNPs ed una delezione (esone 9) al locus CSN1S1, 7 SNPs al locus CSN2, 3 SNPs al locus CSN1S2 e 13 SNPs al locus CSN3. I genotipi all’esone 9 sono risultati in accordo con i risultati all’IEF; gli individui omozigoti per la delezione hanno un livello molto basso di S1-caseina, gli individui eterozigoti hanno un livello intermedio di espressione proteica, mentre gli individui omozigoti per la non-delezione mostrano una completa epressione della proteina. Per ogni gene sono stati costruiti gli aplotipi delle genotipizzazioni effettuate tramite SNPs. Sono stati trovati solo un numero limitato di aplotipi all’interno di ogni locus. Sei aplotipi per i loci CSN1S1 e CSN2, 3 per CSN1S2 e 7 per CSN3. Il numero limitato di aplotipi dimostra uno stretto linkage disequilibrium (LD) tra gli SNPs all’interno di ciascun locus.

“Rossa Siciliana” is a dairy cattle population traditionally linked to cheese production protein polymorphisms from 62 individual milk samples from 19 farms were analyzed by isoelectrofocusing. High variability was found at the CNS1S1, CSN2, CSN3, LGB and LALBA loci, while the CNS1S2 locus was monomorphic for the A allele. The casein haplotype frequencies and the occurrence of the linkage disequilibrium, taking into account the association among loci were investigated. The population was not in Hardy-Weinberg equilibrium (Chi-square=19.0, p-value=0.0407), probably due to genetic drift. Frequencies of the three allele detected at CSN1S1 locus were B (0.734), C (0.258) and D (0.008). high frequencies were found for CSN2*A2 (0.573) and CSN3*B (0.637). Whey protein showed high frequencies for LALBA*B (0.903) and LGB*B (0.815). Strong linkage disequilibrium was detected for the polymorphic casein loci CSN1S1-CSN2-CSN3. Out of the 27 possible combination from the 3x3x3 alleles considered, only four haplotypes had a frequency above 0.10. the most frequent haplotype frequency was BA2B (0.236) followed by CA2B (0.214), BA1A (0.168), BA1B (0.131), and BA2A (0.094). the CSN1S1*B variant showed an allele frequency of 0.734 and occurred in almost all haplotype combinations.

The “Rossa Siciliana” is an autochthonous small Sicilian dairy cattle population, accounting for 5-7,000 individuals.This breed is characterized by high ability to live on poor pasture lands, moderate milk production, and traditionally linked to cheese production. Aim of this work was to investigate milk protein polymorphisms in this population. A total of 62 individual milk samples were collected from 19 extensive farms spread in the “Parco dei Nebrodi” area (Messina). All samples were analyzed by isoelectrofocusing (IEF) with pH range 2.5-6. High variability was found at the CSN1S1, CSN2, CSN3, LGB and LALBA loci, while the CSN1S2 locus was monomorphic for the A allele. The allele frequencies and the Hardy-Weinberg equilibrium were estimated using the GENEPOP software, further the casein haplotype frequencies and the occurrence of the linkage disequilibrium were computed with the EH software, taking into account the association among loci. Joint analysis at all loci showed that the population is not in Hardy-Weinberg equilibrium (Chi-square=19.0, pvalue=0.0407), probably due to genetic drift. Of the three alleles detected at CSN1S1 locus, CSN1S1*B and CSN1S1*C had high frequencies (0.734 and 0.258 respectively), as reported for most breeds. The CSN1S1*D allele was detected with a low frequency (0.008). High frequencies were found for CSN2*A2 (0.573) and CSN3*B (0.637). High frequencies were observed for LALBA*B (0.903) and LGB*B (0.815). Strong linkage disequilibrium was detected for the polymorphic casein loci CSN1S1-CSN2-CSN3. For the casein haplotype only the hypothesis of association among loci was considered. Out of the 27 expected, only four haplotypes had a frequency higher than 0.10. The most frequent haplotype was BA2B (0.236), followed by CA2B (0.214), BA1A (0.168), BA1B (0.131), and BA2A (0.094). The high frequency of BA2B haplotype and the possible relation with production traits are under investigation.