Search results for "Breed"

Application of SNP reduction approaches and random forest for the identification of population informative markers in cosmopolitan and local cattle b…

2017

In livestock, single nucleotide polymorphism genotyping arrays have been used to differentiate breeds and populations for several downstream applications, including breed allocation of individuals, breeds of origin of crossbred animals, authentication of mono breed products, comparative analyses of selection signatures among several other uses. We already tested a combination of principal component analysis (PCA), used as preselection method, and random forest (RF) used as classification method to assign cosmopolitan Italian breeds with no or very low error rate. In this work, we increased the number of breeds and approaches, to have a more comprehensive view of the strategies available and…

Tracking Zebu Introgression in Mediterranean Cattle Breeds

2017

A recent work investigating genetic origin, admixture and population history of primitive European cattle highlighted, by using genome-wide single nucleotide polymorphisms, zebu gene flow in the Balkan and Italian Podolic cattle populations. Haemoglobin protein polymorphism analysis in Italian breeds highlighted the presence of zebuine markers in both Italian Podolic and Alpine Grey cattle. Based on the above evidences, we here specifically look for genomic regions of zebuine ancestry in a different dataset of 50K genotypes from Mediterranean breeds including 29 Marismena (Spain); 30 Bazadaise and 30 Gasconne (France); 24 Alpine Grey, 97 Piemontese, 51 Chianina, 5 Marchigiana, 121 Romagnola…

Genetic diversity and phylogenetic relationships among four breeds reared in Sicily using β-lactoglobulin promoter region polymorphisms

2011

The aim of this work was to analyze the genetic diversity and the phylogenetic relationships among the Valle del Belice (VDB) breed and the other sheep breeds considered as ancestors, using -lactoglobulin (BLG) promoter region polymorphisms. The BLG promoter region of 50 randomly chosen animals from the four breeds (VDB n=20; Comisana (COM) n=10; Pinzirita (PIN) n=10; Sarda (SAR) n=10) were sequenced and aligned, and results showed the presence of 36 single nucleotide polymorphisms (SNPs) and one deletion. The number of polymorphic sites identified showed high variability within breeds. Nucleotide (π) and haplotype (Hd) diversity were estimated with DnaSP software, whereas PHASE software w…

Analysis of Illumina BovineSNP50 BeadChip data in different Italian cattle breeds to identify useful markers for breed authentication of dairy and be…

2013

The identification of the breed of origin of cattle derived products has recently assumed particular relevance since the increasing interest in marketing mono-breed labelled cheese and beef. These products are usually sold at a higher price creating financial incentives to substituting them with lower value products coming from undifferentiated or common breeds or crossbred animals. Frauds can damage these valuable niche markets that, indirectly, may help to preserve genetic diversity through the economic incentive on raising local breeds, derived by the high value products, that are usually less productive. DNA analysis can help to identify fraudulent behaviour as we already demonstrated f…

The Sicilian cattle breeds in a global context: genome-wide relationship with other worldwide cattle

2015

Genomic technologies, such as high-throughput genotyping based on Single Nucleotide Polymorphism (SNP) arrays, provide background information concerning genome structure in domestic animals. The aims of this study were to cluster animals, to explore the relationships among and within breeds, and to place the Sicilian breeds, Cinisara and Modicana, in a global context. The Illumina Bovine SNP50K v2 BeadChip genotyping data from 144 animals of Sicilian breeds and from other 1,543 animals belonging to 134 domesticated bovid breeds (DRYAD) were used. These breeds arose from 3 domesticated (sub)species: Bos javanicus, B. taurus indicus, and B. t. taurus. Principal Component Analysis (PCA) genera…

High-density single nucleotide polymorphism markers reveal the population structure of 2 local chicken genetic resources

2023

Italy counts a large number of local chicken populations, some without a recognized genetic structure, such as Val Platani (VPL) and Cornuta (COS), which represent noteworthy local genetic resources. In this study, the genotype data of 34 COS and 42 VPL, obtained with the Affymetrix Axiom600KChicken Genotyping Array, were used with the aim to investigate the genetic diversity, the runs of homozygosity (ROH) pattern, as well as the population structure and relationship within the framework of other local Italian and commercial chickens. The genetic diversity indices, estimated using different approaches, displayed moderate levels of genetic diversity in both populations. The identified ROH h…

APPLICATION OF MOLECULAR MARKERS FOR GENETIC TRACEABILITY OF SICILIAN AUTOCHTHONOUS BREEDS AND TYPICAL DAIRY PRODUCTS

In Sicilia, le razze bovine, ovine e caprine e le loro produzioni lattiero-casearie rappresentano una risorsa importante per l’economia del settore zootecnico. Alcuni di questi prodotti di origine animale sono “prodotti monorazza” e rappresentano elementi importanti per la conservazione e lo sviluppo di queste popolazioni, dei territori e delle tradizioni locali. Il processo di valorizzazione, autenticazione e tracciabilità delle produzioni lattiero-casearie richiede una conoscenza approfondita sulla struttura genetica delle razze, sulle caratteristiche morfologiche e attitudinali, sulla distribuzione geografica/ambiente di produzione e sulla diversità genetica entro e tra razze. Uno strume…

Proteomics for milk proteins characterization in Girgentana goat breed

2013

Proteomics has been widely used to characterize milk protein content in livestock species and unravel protein biological functions. The aim of this work was to characterize the Girgentana goat breed whole milk and milk fraction proteins by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry. Bulk milk samples from two farms locate in Palermo and Agrigento (Sicily) areas were collected during the early stage of lactation. Initially, 2D-PAGE and protein detection protocols were set-up. In particular, 2D-PAGE analyses were carried out on whole milk using 18-cm IPG strips ranging from pH 3-10 and 4-7 and 12.5% polyacrylamide gel for first and the second dimension …

Detection of genomic signatures of selection in the North African Brune de l’Atlas cattle

2018

The identification of signatures of selection in indigenous livestock genome is able to elucidate the adaptive mechanisms allowing them to cope with environmental pressures. In the present study, we used genotyping data from 106 Brune de l’Atlas cattle individuals and tests based on the extent of haplotype homozygosity (EHH) to look for footprints of natural selection. We identified 17 genomic regions displaying strong signal of selection (p-value <10-6) overlapping with previously described QTL regions affecting many traits such as meat and milk composition, tuberculosis susceptibility, tick and mastitis resistance. Some of these highly significant candidate regions overlap with four previ…

Selection signatures of fat tail in sheep

2017

The investigation of the genes with a role in lipid metabolism enjoy considerable scientific and commercial interest because of the strong correlations between fat deposition and the risk of cardiovascular disease. The fat tail characteristic of sheep is the adaptive response to harsh environment, and beyond representing a valuable energy reserve for facing future climate changes provides clues for elucidating the physiology of fat deposition. Studies on various sheep populations detected fat-tail signatures on chromosomes 2, 3, 5, 6, 7 and 13. Fat-tailed sheep represent about 25% of the world’s sheep population, and the genes with a role in this phenotype are likely not the same for every …