Genetic, phenotypic and proteomic characterisation of local chicken breeds

In common domestic species for which varieties, strains or breeds are in danger of extinction, the population levels at which action needs to be taken are object of research in many countries. Different approaches have been developed and exploited to understand the different aspects that contribute to breed differentiation and to study the typical products that originate from them. The thesis is made up of three contributes. The objectives of the first one were to determine genetic variation and to analyze population structure in six Italian local chicken breeds involved in a conservation program. Twenty microsatellite markers were investigated in 337 animals belonging to six breeds: Ermellinata di Rovigo, Robusta Maculata, Robusta Lionata, Pepoi, 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 plus or minus 2.1 alleles per locus. For the local breeds, the observed and expected heterozigosity 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 has been observed in five breeds and in the commercial cross. The overall population heterozygote deficiency FIT, resulted 0.427, the average FIS 0.097, while FST was 0.437, indicating a high heterozygote deficiency mainly due to breed subdivisions. 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 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. Exception was the Polverara, for which a more complex genetic structure was found. Obtained results confirmed the usefulness of molecular markers, as microsatellites, to characterize local breeds and to monitor genetic diversity in livestock conservation schemes. The objective of the second contribute was to describe carcass characteristics and qualitative meat traits of three local chicken breeds showing, at maturity, light, medium-light, and medium live weights. By the fact, those breeds could permit to extend and diversify consumer's offer to fit all the local demands in typical diversified poultry products. The experiment involved 60 male chickens reared in an organic production system where housing was an indoor pen with access to a grass paddock was carried out in order to investigate carcass characteristics and qualitative meat traits of three slow-growing Italian local breeds of chicken (Ermellinata, Padovana, and Pépoi). Chicks were randomly selected at hatch, raised together under the same conditions, slaughtered at 190 days of age, dissected for carcass traits and meat was stored for subsequent analysis of breast and thigh meat quality. Ermellinata chickens were consistently heavier than Padovana and Pépoi chickens for live, carcass, thigh weight and there were differences among breeds for protein percentage (Ermellinata > Pépoi and Padovana), shear force (Padovana Padovana and Ermellinata). The CIE system values of lightness (L*), redness (a*), and yellowness (b*) evidenced a distinctive darker and lighter colour of Padovana for meat and skin, respectively. Fatty acid composition of breast was similar among the studied breeds, while saturated and monounsaturated fatty acids contents of Ermellinata were higher and lower, respectively than the other breeds. Aim of the third study was to apply a proteomic approach for characterization of local chicken breeds. The experiment involved a total of 29 males of Pépoi, Padovana, and Ermellinata local chicken breeds. Samples were taken from breast muscle (Pectoralis superficialis). Sarcoplasmic protein fractions of breast muscle were analysed by bidimensional electrophoresis. Image analysis followed by statistical analysis enabled to differentiate groups of individuals on the similarities of protein expression. Individuals were distinguished into clusters and groups, corresponding to the breed of origin. SAM analysis enabled identification of the most relevant spots; 10 of these were identified by Mass Spectrometry revealing preliminary evidences on the mechanics of the breed differentiation process. Results evidenced a possible utilisation of proteomic approach in the field of breed characterization studies as an alternative to genomic analyses performed using molecular markers, both for breed and product traceability purposes