Benevento, Italy
Benevento, Italy

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Ciani E.,University of Bari | Crepaldi P.,University of Milan | Nicoloso L.,University of Milan | Lasagna E.,University of Perugia | And 16 more authors.
Animal Genetics | Year: 2014

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north-south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long-lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds. © 2013 Stichting International Foundation for Animal Genetics.


Perucatti A.,CNR Institute for Animal Production System In Mediterranean Environment | Genualdo V.,CNR Institute for Animal Production System In Mediterranean Environment | Genualdo V.,University of Bari | Iannuzzi A.,University of Naples Federico II | And 4 more authors.
Cytogenetic and Genome Research | Year: 2011

A new and unusual reciprocal translocation was detected in a heifer of the Agerolese cattle breed during a routine cytogenetic screening carried out on 13 animals (2 males and 11 females) kept at the ConSDABI Conservation Center in Benevento (Southern Italy). The 13 animals investigated had a normal karyotype except for a 1-year-old female, which carried one autosome smaller than the smallest normal bovine autosomes. This small autosome showed very little C-banding in comparison to the other autosomes, while another medium-sized autosome showed 2 distinct and prominent C-bands. RBA-banding and karyotype analysis revealed that these 2 chromosomes were the result of a reciprocal translocation between chromosomes 11 and 25. FISH analysis with BAC142G06 mapping to the proximal (subcentromeric) region of both BTA25 and der11, BAC513H08 (ELN) mapping to BTA25q22dist and der25, and BAC533C11 mapping to the proximal region of BTA11 and der11 confirmed the localization of the breakpoints on band q11 (centromere) of chromosome 11 and q14-21 of chromosome 25. Ag-NOR and sequential RBA/Ag-NOR techniques detected the presence of NORs on both BTA11 and BTA25 and both der11 and der25. To our knowledge, this is the first report of a reciprocal translocation event in cattle with the breakpoint located in the centromeric region. Copyright © 2011 S. Karger AG, Basel.


Iannuzzi A.,National Research Council Italy | Genualdo V.,National Research Council Italy | Perucatti A.,National Research Council Italy | Pauciullo A.,National Research Council Italy | And 5 more authors.
Cytogenetic and Genome Research | Year: 2015

A newborn calf of the Agerolese cattle breed underwent clinical cytogenetic investigation because of hyperflexion of the forelimbs, red eyes and the inability to stand. Anamnesis revealed that the mother, phenotypically normal, carried a chromosomal aberration. The newborn died after 2 weeks, and no remarkable alterations were found by the veterinarian on postmortem examination. The mother was a carrier of a reciprocal balanced translocation rcp(11;25)(q11,q14∼21) detected after a cytogenetic investigation in 2011; however, the analysis of the newborn revealed a different chromosomal aberration with partial trisomy of chromosome 25 and partial monosomy of chromosome 11. In fact, the results showed both chromosomes 25, one chromosome 11 and only one long derivative chromosome (der11). FISH analysis, performed using BAC clones, confirmed the chromosomes and their regions involved. Finally, both the localization of the breakpoints on band q11 (centromere) of chromosome 11 and band q14-21 of chromosome 25, and the complete loss of the der25 identified the aberration as an unbalanced translocation 60,XX,der(11)t(11;25)(q11;q14∼21). A comparison with human chromosomes was also performed to search for similarities and possible genes involved in order to study their effects, thus extending the knowledge of these aberrations by case reports. © 2015 S. Karger AG, Basel.


Fontanesi L.,University of Bologna | Beretti F.,University of Bologna | Beretti F.,University of Palermo | Dall'Olio S.,University of Bologna | And 3 more authors.
Journal of Dairy Research | Year: 2011

Massese is an Italian sheep breed, with black or grey coat colour, mainly reared in the Tuscany and Emilia Romagna regions. Recently, the emerging interests in this breed have resulted in the production of Pecorino cheese obtained with only Massese milk. In order to be profitable, this marketing link between Massese breed and its products should be defended against fraudØsters who could include milk of other sheep breeds or cow milk in Massese labelled productions. To identify the genetic factors affecting coat colour in sheep, we have recently analysed the melanocortin 1 receptor (MC1R) gene and identified several single nucleotide polymorphisms (SNPs). In this work, as a first step to set up a DNA based protocol for authentication of Massese dairy products, we further investigated the presence and distribution of one of these SNPs (c.-31G>A) in 143 Massese sheep and in another 13 sheep breeds (for a total of 351 animals). The Massese breed was fixed for allele c.-31A, whereas in all other breeds allele c.-31 G was the most frequent or with frequency of 0·50. At the same nucleotide position the cattle MC1R gene carries the G nucleotide. Using these data we developed a method to detect adulterating milk (from other sheep breeds or from cow) in Massese dairy products based on the analysis of the c.-31G>A SNP. We first tested the sensitivity of the protocol and then applied it to analyse DNA extracted from ricotta and Pecorino cheese obtained with only Massese milk or obtained with unrestricted sheep and cattle milk. To our knowledge, this system represents the first one that can be used for breed authentication of a sheep production and that, at the same time, can reveal frauds derived from the admixture of milk of an unreported species. © 2010 Proprietors of Journal of Dairy Research.


Bertolini F.,University of Bologna | Galimberti G.,University of Bologna | Calo D.G.,University of Bologna | Schiavo G.,University of Bologna | And 2 more authors.
Journal of Animal Breeding and Genetics | Year: 2015

The genetic identification of the population of origin of individuals, including animals, has several practical applications in forensics, evolution, conservation genetics, breeding and authentication of animal products. Commercial high-density single nucleotide polymorphism (SNP) genotyping tools that have been recently developed in many species provide information from a large number of polymorphic sites that can be used to identify population-/breed-informative markers. In this study, starting from Illumina BovineSNP50 v1 BeadChip array genotyping data available from 3711 cattle of four breeds (2091 Italian Holstein, 738 Italian Brown, 475 Italian Simmental and 407 Marchigiana), principal component analysis (PCA) and random forests (RFs) were combined to identify informative SNP panels useful for cattle breed identification. From a PCA preselected list of 580 SNPs, RFs were computed using ranking methods (Mean Decrease in the Gini Index and Mean Accuracy Decrease) to identify the most informative 48 and 96 SNPs for breed assignment. The out-of-bag (OOB) error rate for both ranking methods and SNP densities ranged from 0.0 to 0.1% in the reference population. Application of this approach in a test population (10% of individuals pre-extracted from the whole data set) achieved 100% of correct assignment with both classifiers. Linkage disequilibrium between selected SNPs was relevant (r2 > 0.6) only in few pairs of markers indicating that most of the selected SNPs captured different fractions of variance. Several informative SNPs were in genes/QTL regions that affect or are associated with phenotypes or production traits that might differentiate the investigated breeds. The combination of PCA and RF to perform SNP selection and breed assignment can be easily implemented and is able to identify subsets of informative SNPs useful for population assignment starting from a large number of markers derived by high-throughput genotyping platforms. © 2015 Blackwell Verlag GmbH.


Barone C.M.A.,University of Naples Federico II | Di Matteo R.,University of Naples Federico II | Rillo L.,ConSDABI | Rossetti C.E.,ConSDABI | And 2 more authors.
Agronomy Research | Year: 2015

In the last decades, the development of livestock has coincided with improvements of the animals performance. The swine has been strongly selected for several traits that determined a significant spread of some genetic types, more productive than the old autochthonous genetic types (AGT). Therefore, the AGT suffered a growing demographic contraction. The AGT are able to reduce the loss of genetic variability, potentially useful for the new generation and they play an important economic role for their productive capacity in harsh environments; furthermore, they can be used to obtain natural and ‘traditional’ products. In the current research the black AGT Casertana (CT) was compared with the crossbreed CT×Duroc in relation to gender (castrated males and entire females) and farming systems: Open Air and Outdoor (plus access to the bush) for some qualitative properties of meat. In addition ‘Fiocco’ ham, a traditional product, from CT, CT×DU and Pen ar Lan pigs was analyzed. The results showed that the CT pigs had a significantly higher percentage of fat, a thicker adipose tissue, and their meat had lower values of hardness, chewiness, shear force, and appeared significantly redder than other genotypes meat. The farming systems and gender did not affect the carcass composition and physical traits of meat. © 2015, Eesti Pollumajandusulikool. All rights reserved.


PubMed | University of Bologna and ConSDABI
Type: Journal Article | Journal: Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie | Year: 2015

The genetic identification of the population of origin of individuals, including animals, has several practical applications in forensics, evolution, conservation genetics, breeding and authentication of animal products. Commercial high-density single nucleotide polymorphism (SNP) genotyping tools that have been recently developed in many species provide information from a large number of polymorphic sites that can be used to identify population-/breed-informative markers. In this study, starting from Illumina BovineSNP50 v1 BeadChip array genotyping data available from 3711 cattle of four breeds (2091 Italian Holstein, 738 Italian Brown, 475 Italian Simmental and 407 Marchigiana), principal component analysis (PCA) and random forests (RFs) were combined to identify informative SNP panels useful for cattle breed identification. From a PCA preselected list of 580 SNPs, RFs were computed using ranking methods (Mean Decrease in the Gini Index and Mean Accuracy Decrease) to identify the most informative 48 and 96 SNPs for breed assignment. The out-of-bag (OOB) error rate for both ranking methods and SNP densities ranged from 0.0 to 0.1% in the reference population. Application of this approach in a test population (10% of individuals pre-extracted from the whole data set) achieved 100% of correct assignment with both classifiers. Linkage disequilibrium between selected SNPs was relevant (r(2) > 0.6) only in few pairs of markers indicating that most of the selected SNPs captured different fractions of variance. Several informative SNPs were in genes/QTL regions that affect or are associated with phenotypes or production traits that might differentiate the investigated breeds. The combination of PCA and RF to perform SNP selection and breed assignment can be easily implemented and is able to identify subsets of informative SNPs useful for population assignment starting from a large number of markers derived by high-throughput genotyping platforms.

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