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In the course of evolution, pecorans (i.e., higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as “headgear,” which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae.

Since its domestication, about 5000 years ago, the donkey (Equus asinus) has been extensively used as a work or draft animal in agricultural activities and for the transportation of people and goods. In the last century, technology improvement and growing mechanization strongly affected agriculture and the management and use of this livestock species in the industrialized countries. Nowadays, the use of donkeys for work or transport has almost disappeared, together with the need for mules or hinny breeding. During the last five decades, Italian autochthonous donkey populations suffered from a severe reduction in population size, which led to the extinction of several breeds. At present, eight breeds remain, all classified by FAO as critically endangered or endangered: Asinara, Pantesco, Grigio Siciliano, Romagnolo, Amiatino, Sardo Grigio, Martina Franca, and Ragusano. To evaluate the extant genetic variability of Italian donkeys, we typed 16 microsatellite loci in 258 individuals from these breeds. The results highlighted moderate levels of inbreeding ( F (IS) = 0.127) and a significant partition of genetic variation into breeds, as suggested by fixation index ( F (ST) = 0.109) and analysis of molecular variance (10.86% of total variation assigned to the between-breeds level) analyses. This was confirmed by a Bayesian clustering procedure that also highlighted a further partitioning at lower hierarchical levels corresponding to the farms of origin. This evidence suggests that an effective management strategy for Italian donkey populations should focus on breeds as conservation units. However, this requires a synergic management strategy at the farm level to maintain diversity and avoid inbreeding.

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.

To identify genes with effects on meat quality and production traits we developed an adult porcine skeletal muscle cDNA library. After pre-screening this library with seven genes highly expressed in skeletal muscle, 385 non-hybridizing clones were sequenced from both ends to yield 510 expressed sequence tags (ESTs). Together with those ESTs previously generated from this library, we have produced 701 porcine skeletal muscle ESTs. These ESTs were grouped into 306 different cDNA species and compared with the human skeletal muscle transcriptional profiles obtained from different databases. Furthermore we mapped 107 of these cDNAs using a somatic cell hybrid panel with genes mapping over all the autosomes (except on chromosome 11) and on chromosome X. The mapping of these cDNAs contributed to the construction of a first genomic transcript map of the skeletal muscle tissue in pig.

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. - 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.

Chromosomal assignments are reported for fourteen porcine expressed sequence tags (ESTs)--CALM1, CRYAB, MYH7, MYL1, PDK4, PGAM2, PYGM, REV3L, RFC1, SLN, SPTBN1, SRM160, TPM1 and YWHAG. The ESTs were derived from our porcine skeletal muscle cDNA library. The ESTs sequences selected for mapping included the presence of the 3'-untranslated region. The assignments were performed using two independent somatic cell hybrid panels providing the possibility of confirmation of the results obtained. The observed localizations are compared with the locations predicted from heterologous (human-pig, pig-human) chromosome painting data and knowledge of the map locations of the human homologues. These results add new information to the porcine genome transcript map.

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.

Summary We report on a complete genome scan for quantitative trait loci (QTL) affecting milk protein percentage (PP) in the Italian Holstein-Friesian cattle population, applying a selective DNA pooling strategy in a daughter design. Ten Holstein-Friesian sires were chosen, and for each sire, about 200 daughters, each from the high and low tails of estimated breeding value for PP, were used to construct milk DNA pools. Sires and pools were genotyped for 181 dinucleotide microsatellites covering all cattle autosomes. Sire marker allele frequencies in the pools were obtained by shadow correction of peak height in the electropherograms. After quality control, pool data from eight sires were used for all subsequent analyses. The QTL heterozygosity estimate was lower than that of similar studies in other cattle populations. Multiple marker mapping identified 19 QTL located on 14 chromosomes (BTA1, 2, 3, 4, 5, 6, 8, 9, 12, 14, 17, 20, 23 and 27). The sires were also genotyped for seven polymorphic sites in six candidate genes (ABCG2, SPP1, casein kappa, DGAT1, GHR and PRLR) located within QTL regions of BTA6, 14 and 20 found in this study. The results confirmed or excluded the involvement of some of the analysed markers as the causative polymorphic sites of the identified QTL. The QTL identified, combined with genotype data of these candidate genes, will help to identify other quantitative trait genes and clarify the complex QTL patterns observed for a few chromosomes. Overall, the results are consistent with the Italian Holstein population having been under long-term selection for high PP.

Catria is 1 of the 22 native Italian horse breeds that now survive from a larger number. Thirty individuals, representative of the Catria horse, were analyzed for 11 microsatellites and compared with data of 10 breeds reared in Italy. Three different approaches, genetic distances, correspondence analysis, and clustering methods, were considered to study genetic relationships among Catria and the other horse populations. Genetic differentiation among breeds was highly significant (P < 0.01) for all loci. Average F(ST) values indicate that around 10% of the total genetic variation was explained by the between-breed differences and the 3 approaches utilized gave similar results. Italian native breeds are clearly separated from the other examined breeds. However, by the correspondence analysis, the Catria appears closer to Maremmano and Murgese. The results of Bayesian approaches give further information showing for Catria a common origin with Maremmano and Italian Heavy Draught. Genetic relationships among Catria and the other breeds are consistent with the breed's documented history. The data and information found here can be utilized in the organization of conservation programmes planned to reduce inbreeding and to minimize loss of genetic variability.

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 α 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.

The present paper describes the isolation and linkage mapping of two isoforms of skeletal muscle myosin heavy chain in pig. Two partial cDNAs (pAZMY4 and pAZMY7), coding for the porcine myosin heavy chain-2B and -beta respectively, have been isolated from a pig skeletal muscle cDNA library. Four RFLPs were detected with the putative porcine skeletal myosin heavy chain-2B probe (pAZMY4) and one RFLP was identified with the putative myosin heavy chain-beta probe (pAZMY7). Two myosin heavy chain loci were mapped by linkage analysis performed with the five RFLPs against the PiGMaP linkage consortium ResPig database: the MYH1 locus, which identifies the fast skeletal muscle myosin heavy chain gene cluster, was located at the end of the map of porcine chromosome 12, while the MYH7 locus, which identifies the myosin heavy chain-alpha/-beta gene cluster, was assigned to the long arm of porcine chromosome 7.

Sources/description: Expressed sequence tags, European Molecular Biology Laboratory (EMBL) accession numbers AJ301262, AJ301107, and AJ301170, corresponding respectively to portions of the porcine muscle creatine kinase (CKM), peroxisomal enoyl coenzyme A hydratase 1 (ECH1), and skeletal slow troponin T1 (TNNT1) genes were isolated from an adult porcine skeletal muscle cDNA library. Polymerase chain reaction primers for CKM and ECH1 were designed in the 3¢-untranslated region to amplify fragments of 207 bp and 104 bp, respectively. For TNNT1, primers were designed in the coding sequence, each on a different exon, according to the organization of the human and mouse TNNT1 gene. Partial sequencing confirmed that the obtained amplicon of about 490 bp contained portions of exons 8 and 9 and the intervening intron of the porcine TNNT1 gene (EMBL accession number AJ495809).

Evidence was provided for a new erythrocyte ADA allele (Aw) in the Swedish Landrace breed of pigs. The enzyme activity of Aw variant was considerably less than that of the previously reported erythrocyte ADA variants A and B. The mobility of the Aw variant was identical to that of the A variant, both by electrophoresis and by isoelectric focusing. The in vitro heat stability (at 56 degrees C) of the Aw variant was similar to that of A and B variants. The leucocyte ADA activity was normal in pigs with the erythrocyte ADA Aw variant. The frequencies of the erythrocyte ADA alleles, A, B, Aw, and O (silent allele) in four breeds of pigs in Sweden were: Landrace--0.51, 0.19, 0.11, 0.19; Large White--0.91, 0.03, 0.0, 0.06; Duroc--0.95, 0.05, 0.0, 0.0; Hampshire--0.12, 0.14, 0.0, 0.74.

To investigate the mitochondrial DNA diversity of five Italian donkey breeds (Amiata, Martinafranca, Romagnolo, Asinara, and Ragusano), we sequenced the HVR I region (D-loop, 288 bp) and cytochrome b gene (274 bp) in 121 individuals. In the D-loop we found nineteen mutations corresponding to fourteen different haplotypes, while in cyt b coding gene only six mutations were found, originating five different haplotypes. In particular, three mutations out of six were non-synonymous, causing an aminoacidic substitution. About the D-loop region, the value of nucleotide diversity (π) observed within breeds was relatively low, but not far from values detected in other European breeds. Phylogenetic and network analyses disclosed the presence of two divergent maternal lineages within Italian donkeys. These haplogroups correspond to the well known lineages of ancestors (Equus asinus somaliensis and E. a. africanus), as donkeys were domesticated from distinct wild subspecies living in Eastern Africa regions. ...

Many studies have demonstrated that quantitative trait loci (QTL) can be identified and mapped in commercial dairy cattle populations using genetic markers in daughter and granddaughter designs.The final objective of these studies is to identify genes or markers that can be used in breeding schemes via marker assisted selection (MAS).

The genetic structure of Ventasso Horse (VH) was investigated using 12 microsatellites. The analyses were carried out on 117 VH individuals and the results were compared with those obtained analysing 11 other breeds reared in Italy. All microsatellites were polymorphic in VH and in the other breeds. A total of 124 alleles (from 6 to 19 alleles per microsatellite) were detected. Average heterozygosity was 0.743 in VH and ranged from 0.613 to 0.759 in the other breeds. The mean FST value had an average value of 0.0932. Genetic distances were calculated using Nei’s standard genetic distance (Ds). The smallest Ds values were found between VH and Anglo-Arab, Thoroughbred, Maremmano and Lipizzan horse breeds. Phylogenetic trees constructed using neighbour-joining method showed two clear separate clusters: the first includes Bardigiano, Haflinger and Italian Heavy Draught Horse, the second contains the other 9 breeds.

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.