D. Bigi

ANALYSIS OF EXPRESSED SEQUENCE TAGS OF PORCINE SKELETAL MUSCLE

Porcine skeletal muscle genes play a major role in determining muscle growth and meat quality. Therefore, to progress towards a better understanding of the genetic factors influencing these traits, the first step is to characterize the genes expressed in skeletal muscle tissue in pig. To this aim, we constructed a porcine biceps femoris muscle cDNA library and sequenced 111 randomly isolated clones. By FASTA analysis, we identified 72 unique clones: 47 showed homology to previously identified genes in human or other mammals, 20 matched uncharacterized expressed sequence tags (ESTs), two showed no significant matches to sequences already present in DNA databases, and three other clones containing only repetitive elements were excluded from further analysis. Mitochondrial genes (16.2%), myosin heavy chain genes (9%) and the actin alpha skeletal muscle gene (9%) were the most abundant transcripts. Among the 47 identified genes several muscle-specific or predominant sequences expressed in skeletal muscle were found. The sequences of the clones matching uncharacterized human, mouse or porcine ESTs were tested by GRAIL in order to identify putative coding regions. The results of our analysis allowed the establishment of a first list of genes expressed in porcine skeletal muscle.

Multilocus detection of wolf x dog hybridization in Italy, and guidelines for marker selection

Hybridization and introgression can impact the evolution of natural populations. Several wild canid species hybridize in nature, sometimes originating new taxa. However, hybridization with free-ranging dogs is threatening the genetic integrity of grey wolf populations (Canis lupus), or even the survival of endangered species (e.g., the Ethiopian wolf C. simensis). Efficient molecular tools to assess hybridization rates are essential in wolf conservation strategies. We evaluated the power of biparental and uniparental markers (39 autosomal and 4 Y-linked microsatellites, a melanistic deletion at the β-defensin CBD103 gene, the hypervariable domain of the mtDNA control-region) to identify the multilocus admixture patterns in wolf x dog hybrids. We used empirical data from 2 hybrid groups with different histories: 30 presumptive natural hybrids from Italy and 73 Czechoslovakian wolfdogs of known hybrid origin, as well as simulated data. We assessed the efficiency of various marker combinations and reference samples in admixture analyses using 69 dogs of different breeds and 99 wolves from Italy, Balkans and Carpathian Mountains. Results confirmed the occurrence of hybrids in Italy, some of them showing anomalous phenotypic traits and exogenous mtDNA or Y-chromosome introgression. Hybridization was mostly attributable to village dogs and not strictly patrilineal. The melanistic β-defensin deletion was found only in Italian dogs and in putative hybrids. The 24 most divergent microsatellites (largest wolf-dog FST values) were equally or more informative than the entire panel of 39 loci. A smaller panel of 12 microsatellites increased risks to identify false admixed individuals. The frequency of F1 and F2 was lower than backcrosses or introgressed individuals, suggesting hybridization already occurred some generations in the past, during early phases of wolf expansion from their historical core areas. Empirical and simulated data indicated the identification of the past generation backcrosses is always uncertain, and a larger number of ancestry-informative markers is needed.

Genetic characterization of four native Italian shepherd dog breeds and analysis of their relationship to cosmopolitan dog breeds using microsatellite markers

Very little research into genetic diversity of Italian native dog breeds has been carried out so far. In this study we aimed to estimate and compare the genetic diversity of four native Italian shepherd dog breeds: the Maremma, Bergamasco, Lupino del Gigante and Oropa shepherds. Therefore, some cosmopolitan dog breeds, which have been widely raised in Italy for a long time past, have also been considered to check possible influence of these dog populations on the Italian autochthonous breeds considered here. A total of 212 individuals, belonging to 10 different dog breeds, were sampled and genotyped using 18 autosomal microsatellite loci. We analyzed the genetic diversity of these breeds, within breed diversity, breed relationship and population structure. The 10 breeds considered in this study were clearly genetically differentiated from each other, regardless of current population sizes and the onset of separate breeding history. The level of genetic diversity explained 20% of the total genetic variation. The level of H E found here is in agreement with that found by other studies. The native Italian breeds showed generally higher genetic diversity compared with the long established, well-defined cosmopolitan dog breeds. As the Border Collie seems closer to the Italian breeds than the other cosmopolitan shepherd dogs considered here, a possible utilization of this breed to improve working performance in Italian traditional working shepherd dogs cannot be ignored. The data and information found here can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability.

Genetic analysis of seven Italian horse breeds based on mitochondrial DNA D-loop variation

To understand the origin and genetic diversity of Italian horses, mitochondrial DNA D-loop sequences were generated for 163 horses from seven breeds. Sequence analysis of a 480-bp segment revealed a total of 84 haplotypes with 57 polymorphic sites, indicating multiple maternal origins and high genetic diversity. Comparison of the haplotypes with the equine mtDNA haplotype/haplogroup nomenclature showed a haplogroup distribution in the Italian breeds more similar to that found in the Middle East breeds than in the European breeds, probably due to the economic and cultural relationship with the Middle East in the past centuries.

Bovine chromosome 20: milk production QTL and candidate gene analysis in the Italian Holstein-Friesian breed

Abstract Bovine chromosome 20 (BTA20) was studied to identify QTL for milk yield and protein percentage in the Italian Holstein-Friesian breed using a selective milk DNA pooling strategy in a daughter design with sire haplotype analysis. Several QTL were identified. The effect of the known GHR F279Y and PRLR S18N mutations were in for the most part confirmed. However, it was also shown that these markers cannot explain all significant effects observed on BTA20 for the investigated traits.

The BovMAS Consortium: investigation of bovine chromosome 14 for quantitative trait loci affecting milk production and quality traits in the Italian Holstein Friesian breed

Riassunto Studio del cromosoma 14 di bovino per l’identificazione di QTL per la produzione e la qualità del latte nella razza Frisona Italiana. Nel presente studio, utilizzando le metodologie del daughter design e del selective DNA pooling, abbiamo verificato la presenza di un importante QTL per la produzione di latte nella regione prossimale del cromosoma 14 nella razza Frisona Italiana. Inoltre, abbiamo effettuato la ricerca di altri QTL per la percentuale di proteine, la percentuale di grasso e la produzione di latte su questo cromosoma. I risultati mettono in evidenza che il QTL nella regione prossimale è dovuto solo in parte alla mutazione A232K del gene DGAT1 e che probabilmente un altro o altri QTL segregano nella regione centrale-distale del cromosoma. Ulteriori studi sono necessari per confermare e chiarire questi risultati.

Genetic investigation of Italian domestic pigeons increases knowledge about the long-bred history of Columba livia (Aves: Columbidae)

Abstract In this study, we aimed to characterise the genetic diversity of Italian pigeon breeds and describe the relationships among them and other European lineages, conjecturing which processes have led to actual breeds. We analysed the eight most diffused Italian pigeon breeds in addition to 11 foreign lineages that could have shared common ancestors or have been used in the creation of the Italian breeds. We analysed 12 autosomal microsatellite loci in 427 samples collected from 19 breeds belonging to six main groups of domestic pigeons (tumblers and highflyers, structure, owls, wattle, utility and hen). Genetic variability did not differ considerably among breeds, with an average observed heterozygosity (HO) of 0.550 ± 0.072 (max = 0.661 in breed Sottobanca; min = 0.411 in breed Frillback). The 21.34% of total genetic variation found was partitioned among breeds. Italian pigeon breeds were assigned coherently to their respective groups of origin. The analysis supports the origin of homing pigeons from English Carrier and the existence of a close relationship between Old Dutch Capuchine and Italian Owl. Despite the differences in body size, pigeons of the breeds belonging to the hen group are genetically very similar. The sub-populations recognised by breeders inside Italian Owl and Triganino are not genetically supported and their identification as new breeds ought not to be yet proposed, although they are morphologically distinguishable. Consequently, it could also be discussed how the genetic characterisation of domestic lineages could give useful information in breeding and selection processes.

Studies of modern Italian dog populations reveal multiple patterns for domestic breed evolution

Abstract Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves, and an established dataset of 161 globally recognized dog breeds, applying multiple genetic methods to characterize the modes by which breeds are formed within a single geographic region. Our consideration of each of five genetic analyses reveals a series of development events that mirror historical modes of breed formation, but with variations unique to the codevelopment of early dog and human populations. Using 142,840 genome‐wide SNPs and a dataset of 1,609 canines, representing 182 breeds and 16 wild canids, we identified breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.

Investigating the population structure and genetic differentiation of livestock guard dog breeds

Livestock guarding dogs are a valuable adjunct to the pastoral community. Having been traditionally selected for their working ability, they fulfil their function with minimal interaction or command from their human owners. In this study, the population structure and the genetic differentiation of three Italian livestock guardian breeds (Silas Dog, Maremma and Abruzzese Sheepdog and Mannaras Dog) and three functionally and physically similar breeds (Cane Corso, Central Asian Shepherd Dog and Caucasian Shepherd Dog), totalling 179 dogs unrelated at the second generation, were investigated with 18 autosomal microsatellite markers. Values for the number of alleles per locus, observed and expected heterozygosity, Hardy-Weinberg Equilibrium, F stats, Neis and Reynolds genetic distances, clustering and sub-population formation abilities and individual genetic structures were calculated. Our results show clear breed differentiation, whereby all the considered breeds show reasonable genetic variability despite small population sizes and variable selection schemes. These results provide meaningful data to stakeholders in specific breed and environmental conservation programmes.

Search of candidate genes for salting loss of ham by using Fluoro Differential Display (FDD)

Riassunto Ricerca di geni candidati per il calo di salagione del prosciutto mediante Fluoro Differential Display (FDD). Con la presente ricerca abbiamo studiato il livello di espressione di geni nel tessuto muscolare di suino con la tecnica fluoro differential display, per identificare geni espressi in modo variabile in funzione del parametro calo di prima salagione. Sono stati identificati dieci geni, dei quali sei a funzione nota e quattro non ancora caratterizzati, che mostravano un’espressione maggiore negli animali con il calo di prima salagione più alto.