The objectives of this study were to determine genetic variation and to analyze population structure of 6 Italian local chicken breeds involved in a conservation program. Twenty microsatellite markers were investigated in 337 birds belonging to 6 breeds: Ermellinata di Rovigo, Robusta Maculata, Robusta Lionata, Pépoi, Padovana, and Polverara; a commercial layer cross was used as reference. One hundred twelve alleles were detected in the overall population, with a mean number of 5.6 ± 2.1 alleles per locus. For the local breeds, the observed and expected heterozygosity ranged from a minimum of 0.240 to a maximum of 0.413 and from 0.243 to 0.463 for the Pépoi and Polverara breeds, respectively. Deviation from Hardy-Weinberg equilibrium was observed in 5 breeds and in the commercial cross. The overall population heterozygote deficiency was 0.427, the average inbreeding coefficient was 0.097, and the heterozygote deficiency due to breed subdivisions was 0.437. Reynolds’ distances were used to draw an unrooted neighbor-joining tree, which topology gave information on the genetic origin of these breeds and confirmed their known history. The estimated molecular kinship within a breed ranged from 0.559 to 0.769, evidencing high coancestry. Structure analysis was performed to detect the presence of population substructures. Inferred clusters corresponded to the different breeds, without presence of admixture. The exception was the Polverara breed, for which a more complex genetic structure was found. The results supported the decision of safeguarding these breeds as an important reservoir of genetic diversity and confirmed the usefulness of microsatellite markers to characterize and to monitor genetic variability in local chicken breeds.

1. An experiment involving 60 male chickens reared in an organic production system was carried out in order to investigate carcase characteristics and qualitative meat traits of three slow-growing Italian local breeds of chicken (Ermellinata, Padovana and Pepoi). 2. Chicks were randomly selected at hatch, raised together under the same conditions, slaughtered at 190 d of age, dissected for carcase traits, and meat (breast and thigh) stored for subsequent analysis of quality parameters. 3. Ermellinata (EA) chickens were significantly different from Padovana (PA) and Pepoi (PI) chickens for live, carcase and thigh weights. Breeds were also different for breast muscle protein content (EA PI and PA), shear force (PA EA and PI) and cooking loss (PI PA and EA) values. 4. The CIE system values of lightness (L*), redness (a*), and yellowness (b*) evidenced a distinctive darker meat and lighter skin colour of PA breast meat. 5. Polyunsaturated fatty acids composition of breast meat was similar among the analysed breeds. EA had significantly higher saturated but significantly lower monounsaturated fatty acid contents than the other two breeds.

In Italy more than fifty different local breeds of chicken (Gallus gallus L.) are known to have been present in the past. The overall situation is now critical since most of these breeds are becoming extinct or threatened and only a few are subject of conservation plans. The use of molecular markers for the analysis of chicken populations could help in characterizing their genetic variation and preserving them from genetic erosion. valuable and irreplaceable sources of chicken germplasm from indigenous populations of the veneto region were analyzed by means of DNA fingerprinting with molecular markers designed on interspersed mini- and microsatellite repeats. The identification of either among-breed discriminant or breed-specific markers was based on the S-SAP and M-AFLP systems derived from the AFLP technology. Genomic DNA fingerprints were generated in 84 individuals belonging to six local breeds (Ermellinata, Padovana, Pépoi, Polverara, Robusta Lionata and Robusta Maculata) and one commercial line used as reference standard. A number of variation statistics were computed to assess the genetic variability within and relatedness among breeds: the effective number of alleles per locus (n(e)= 1.570), total and single-breed genetic diversity (H(T)= 0.366 and H(S)= 0.209, respectively) and the fixation index (G(ST)= 0.429). The mean genetic similarity coefficients within and between local breeds were 0.769 and 0.628, respectively. Markers useful for the genetic traceability of breeds revealed significant sequence similarities with either genic or intergenic regions of known chromosome position. Sequence tagged site primers were designed for the most discriminant markers in order to develop multiplex non-radioactive genomic PCR assays. Analysis of the population structure along with individual assignment tests successfully identified all breed clusters and subclusters. The vast majority of animals were correctly allocated to their breed of origin, demonstrating the suitability and reliability of the chosen AFLP-derived marker systems for detecting population structure and tracing individual breeds. The local breeds have been preliminarily identified according to sequence-specific SNPs and haplotypes and the polymorphism information content of genomic AFLP-derived markers is reported and critically discussed.

The genetic variability and presence of population substructures in 4 native Northern Italian sheep breeds, Alpagota, Brogna, Foza, and Lamon, undergoing in situ conservation, and 1 widespread Italian breed, Bergamasca, were studied by investigating 19 microsatellite markers. The breeds showed considerable genetic variability in terms of number of alleles and heterozygosity, with the exception of Alpagota, which was the least variable (0.607). Nevertheless, a significant deficit of heterozygotes was observed in each breed due to rather increased levels of inbreeding or to the presence of population substructures, probably caused by increased genetic variation in the founder populations. The analyses evidenced clear genetic differentiation (F(ST) = 0.085), reduced levels of admixture, and presence of private alleles among the breeds, confirming their genetic uniqueness. In particular, according to Reynolds genetic distances, Alpagota was the most differentiated, perhaps because it had been bred mostly in a rather isolated area. Loss of any of the investigated breeds would result in a loss of genetic diversity ranging from 0.5 to 1.6% of the total observed gene diversity. Results supported the decision to safeguard these breeds as important reservoirs of genetic diversity and suggested breeding and mating practices to maintain variability and to overcome within-breed substructures.

The assessment of a method able to assign individuals to the breed of origin is needed to certify origin and quality of livestock products. A set of 21 microsatellites was tested for breed identification in four native Italian beef breeds: Chianina, Marchigiana, Romagnola, and Piemontese. Two statistical approaches, based on maximum likelihood and on a Bayesian method, were evaluated. Different marker sets, chosen in order of the highest gene diversity and FST estimates were also tested. The Bayesian method performed better, achieving a correct assignment rate of about 90% even with six microsatellites. The marker sets with the highest gene diversity were shown to perform best. Considering a threshold probability of 90%, only 52.5% of the genotypes were correctly allocated. Such results are mainly due to the low genetic differentiation estimates among breeds (FST=0.049). These findings suggest that markers with high gene diversity and the presence of private alleles should be investigated and the Bayesian method used.

The aim of this study was to analyze, through the use of microsatellite molecular markers, the genetic diversity and variability of nine Alpine sheep breeds reared in Italy (Bergamasca, Biellese, Schwarzbraunes Bergschaf, Tiroler Bergschaf, and Schnalserschaf), Germany (Brillenschaf and Weisses Bergschaf) and Slovenia (Bovška and Jezerzkǒ-Solčavska), and one Italian crossbreed population. Allelic richness was rather high in each breed highlighting a considerable genetic diversity. However, the study evidenced a significant departure from Hardy–Weinberg equilibrium in all analyzed breeds caused by a heterozygote deficiency. Such lack seems to be caused both to the presence of population substructure within breed and to a rather high level of inbreeding. The genetic differentiation among breed was rather low (FST = 0.057) but significant. The clustering analysis performed with STRUCTURE detected the presence of eight clusters; Schwarzbraunes Bergschaf and Tiroler Bergschaf were grouped together and Biellese and Bergamasca as well, evidencing a high similarity of their genetic make up. Reynolds’ genetic distance estimates confirmed the close relationship between these pairs of breeds. Moreover, Bovška, Jezerzkǒ-Solčavska and Brillenschaf resulted rather similar as expected according to their region of origin and to their common ancestors. Molecular coancestry confirmed as well such findings, suggesting that the studied breeds had origin from different ancestral populations. Concluding, microsatellite resulted a useful tool to investigate breed variability and to characterize Alpine sheep breeds. Obtained findings suggest the need to set up a conservation plan aiming to safeguard and increase the genetic variability of the studied breeds compromised by the high level of inbreeding. Microsatellites genotyping could help to monitor breed variability and to organize matings.

In Italy, more than 75% of milk is used for cheese making. For this reason, milk composition and coagulation traits and cheese quality represent the most important tools for the economic development of the dairy sector. In particular, cheese quality varies in relation to cheese-making technology and breed of cow. The aim of this study was to investigate the effect of 3 types of milk, originating from Holstein-Friesian (HF), Brown Swiss (BS), and mixed of both breeds, on vat milk characteristics, cheese yield, and quality in 3 different typical Italian cheese-making conditions (Casolet, Vezzena, and Grana Trentino). One hundred forty-four cows (66 HF and 78 BS) were involved, and a total of 24 vats of milk were evaluated. At maturity, 30, 21, and 16 wheels of Casolet, Vezzena, and Grana Trentino cheese were analyzed. Brown Swiss cows yielded 9% less milk per day than HF cows, but milk showed greater contents of protein, casein, titratable acidity, and better rennet coagulation time and curd firmness than HF milk. The chemical composition and cholesterol content of the 3 types of cheese were similar between breeds, whereas the cheese made with BS milk showed greater contents of monounsaturated and polyunsaturated fatty acids. Cheese made with BS milk had greater b* (yellow component) than HF. Cheese yield, recorded at different ripening times, demonstrated that BS milk yielded more cheese than HF. Mixed milk showed values, on average, intermediate to HF and BS milk characteristics, and this trend was confirmed in cheese yield at different ripening times.

Traceability systems have become necessary, especially for beef products, to protect consumers’ health. Aims of this study were to validate and to test a set of 12 microsatellite (STR) markers for the assessment of a genetic traceability system in six cattle breeds. The probability to find, by chance, two individuals sharing the same profile at the studied loci, was computed considering different number of STR, pooling the alleles in each breed, in the total population and in the dairy and beef population separately. Best results were then obtained considering match probabilities per breed. In this study, genotyping the five most polymorphic loci, the probability of finding two identical animals was approximately five in one million. Match probability values increased when the pooled marker sets were used, but were still satisfactory; moreover, use of the pooled marker sets will reduce the cost of analyses.

The present study was a contribution on the genetic characterization of the Burlina local cattle breed, and an approach to understanding the relationships between Burlina, Holstein Friesian and Brown Swiss which represent the majority of the dairy cattle reared nowadays in North-East Italy. The obtained results helped to clarify the genetic diversity and distinctiveness of Burlina population. In particular, the low genetic distance between Burlina and Holstein Friesian and the assignment of a moderate percentage of Burlina animals to Holstein Friesian suggested that crosses between them took place in the past, while crosses with Brown Swiss seemed to be less frequent. However, analyses of marker genotypes, showed a cluster with only Burlina individuals, which demonstrates the genetic distinctness of this breed. The Burlina breed showed the highest variability among the analysed breeds and its inbreeding coefficient was low. The data contribute to the feasibility of a conservation and selection programme for this breed and the results are useful for the implementation of a conservation strategy that should aim to conserve animals where the contribution from foreign breeds is as small as possible.

This study aimed to estimate genetic parameters for body condition score (BCS), calving interval (CI), somatic cell score (SCS), yield, and linear type traits for the Italian Brown Swiss cattle population. A total of 32,359 records of first-parity lactating cows were collected from 2002 to 2004 in 4,885 dairy herds. The pedigree file included 96,661 animals. Multiple-trait animal models were analyzed using REML to estimate (co)variance components without repeated observations on traits. The estimated heritability was 0.15 for BCS, 0.05 for CI, and 0.06 for SCS, and ranged from 0.09 to 0.14 for test-day yield traits and from 0.07 to 0.32 for linear type traits. The genetic correlations of CI with yield and most linear type traits were positive, whereas the correlation between CI and BCS was negative (-0.35). For type traits, BCS showed, in general, a moderately negative genetic correlation except for strength, pastern, and heel height. The genetic correlation of CI or BCS with SCS was moderately low but favorable (0.19 and -0.26, respectively). The estimated correlations indicated that selection for greater yield and type traits can exert unfavorable effects on the reproductive ability of cows. To counterbalance these effects and to carry out early prediction of breeding values of bulls for fertility, inclusion of BCS in the breeding program is advisable.

A SNPs (Single Nucleotide Polymorphism) based analysis was developed to differentiate four economically important species belonging to the Gadiformes order: Pacific cod Gadus macrocephalus, Atlantic cod Gadus morhua, Haddock Melanogrammus aeglefinus and Ling Molva molva. A 430bp fragment of the 16s rRNA gene was amplified using interspecific conserved primer and sequenced. The sequences were aligned and analyzed for the presence of SNPs; three SNPs (MerSNP1, MerSNP7 and MerSNP9) were identified and selected to allow discrimination between the four species. Aplotypes were TCC, CCC, CAT and CAC for Pacific cod, Atlantic cod, Haddock and Ling respectively. Confirmation of results was achieved by sequencing 16s rRNA gene fragments of 16 G. morhua, 7 G. macrocephalus, 15 M. aeglefinus and 5 M. molva samples collected at different fish catching campaign. Nucleotide sequence of 16s rRNA mitochondial gene has been shown to be a useful tool to allow rapid reliable and fully automatable for discrimination of 4 economically important species in fisheries industry.

Genetic relationships among Veneto native breeds of chickens were studied on the basis of microsatellites polymorphisms. A total of 100 DNA samples from 2 local chicken breeds (45 Robusta Lionata and 43 Robusta Maculata) and a commercial broiler line (12 Golden Comet) were analyzed using 19 microsatellite markers. The average number of alleles per locus was 4.05 and the expected heterozigosity resulted lower for the local breeds than the broiler line. The Robusta Lionata breed and the broiler line showed a significant deficit and excess of heterozygotes, respectively, deviating from Hardy-Weinberg equilibrium. Nei's standard genetic distances corrected for bias due to sampling of individuals (Da), based on allele frequencies, were calculated among breeds. The local breeds resulted very similar confirming the same genetic origin. The results suggested that microsatellite markers are a useful tool for studying the genetic diversity among local chicken breeds.

Traceability is the ability to maintain the identification of animal, or animal products, all along the production chain. It represents an essential tool to safeguard public and animal health and to valorize typical production systems. European food legislation is particularly strict and traceability systems, based on product labeling, have become mandatory in all European countries. However, the implementation of this system does not ensure consumers against fraud. Paper documents can be counterfeit so researchers have focused on the study of genetic traceability systems based on products identification through DNA analysis. In fact DNA is inalterable, detectable in every cell, resistant to heat treatments, and allows for individual, breed or species identification. Even if results are promising, these techniques are too expensive to be converted in routine tests but they could be a trusted tool for verification of suspected fraud. The present review proposes a synthesis of the major advances made in individual, breed, and species genetic identification in the last years, focusing on advantages and disadvantages and on their real future applications for animal productions.

Genetic variation in four indigenous chicken breeds from the Veneto region of Italy was assessed using amplified fragment length polymorphism (AFLP) markers. A total of 99 individuals were analysed using three AFLP primer combinations that produced 70 polymorphisms. Four indigenous Veneto chicken breeds (Ermellinata, Padovana, Pépoi and Robusta) and a reference broiler line were included in the analysis. Breed-specific markers were identified in each breed. The expected heterozygosity did not differ significantly among the indigenous Veneto chicken breeds and the broiler line. The coefficient of gene variation (Gst) value across loci indicated that almost half of the total variability was observed among breeds. Nei's standard genetic distance between pairs of breeds showed that the distance between the broiler line and the Pépoi breed was greater than the distances between the broiler line and the other three chicken breeds. Cluster analysis based on standard genetic distances between breeds indicated that the Padovana and Pépoi breeds were closely related. Factorial analysis based on a binary matrix of the AFLP data showed a clear distinction of all breeds.

Genetic diversity in two ancient indigenous chicken breeds of the Veneto region was assessed using Amplified Fragment Length Polymorphism (AFLP) markers. A total of 63 individuals were analysed using three selected AFLP primer combinations that produced 66 clear polymorphisms. The breeds analyzed were the Padovana and the Polverara (two ancient breeds) and a reference broiler line. The expected heterozygosity (Het) did not differ significantly among breeds. The variability at AFLP loci was largely maintained across breeds, as indicated by the coefficient of genetic differentiation (Gst) value. The lowest genetic distance is found between the Padovana and Polverara breeds suggesting that they could be genetically close.

A recent Italian poultry study (Zanon et al., 2001) showed, in the last decades, the presence of 90 poultry breeds (53 of them are chicken’s), they represent a historical and cultural patrimony, and a genetic source of biodiversity.