Search results for "Cattle"
showing 10 items of 608 documents
Using of SNP markers to estimate inbreeding, coancestry and effective population size in Sicilian cattle breeds
2014
Maintaining the highest levels of genetic diversity and limiting the increase in inbreeding is the premise of most conservation programs. The aim of this work was to estimate the inbreeding (F), coancestry (f) and effective population size (Ne) in two Sicilian cattle breeds, Cinisara (CIN) and Modicana (MOD). Rate of molecular inbreeding and coancestry were used to estimate the Ne. A total of 144 animals were genotyped using the Illumina Bovine SNP50K v2 BeadChip. The average molecular F and f coefficients were 0.68±0.024 and 0.67±0.03 in CIN and 0.69±0.020 and 0.70±0.03 in MOD cattle breeds, respectively. The results were not unexpected considering the reduced number of reared animals and …
Survey of milk protein polymorphism in the "Bovina Rossa Siciliana"
2005
The “Rossa Siciliana” is an autochthonous small Sicilian dairy cattle population, accounting for 5-7,000 individuals.This breed is characterized by high ability to live on poor pasture lands, moderate milk production, and traditionally linked to cheese production. Aim of this work was to investigate milk protein polymorphisms in this population. A total of 62 individual milk samples were collected from 19 extensive farms spread in the “Parco dei Nebrodi” area (Messina). All samples were analyzed by isoelectrofocusing (IEF) with pH range 2.5-6. High variability was found at the CSN1S1, CSN2, CSN3, LGB and LALBA loci, while the CSN1S2 locus was monomorphic for the A allele. The allele frequen…
Distribution of functional variants within Runs of Homozygosity in four Italian cattle breeds
2017
Several methods have been used to identify genomic regions subjected to selective sweeps. An alternative method can make use of runs of homozygosity (ROH), defined as stretches of homozygous regions in a genome. The aim of the present study was to detect selective sweeps using ROH in four cattle breeds. Individuals of Cinisara (71), Modicana (72),Reggiana (168) and Italian Holstein (96) were genotyped with the Illumina Bovine50SNP v2 BeadChip. To identify genomic regions that were most commonly associated with ROH within each breed, the percentage of occurrences of a single nucleotide polymorphism (SNP) in ROH was calculated across animals. The genomic regions most commonly associated with …
BOVITA: a first overview on genome-wide genetic diversity of Italian autochthonous cattle breeds
2017
Analysis of genomic data is increasingly becoming part of the livestock industry and is an invaluable resource for effective management of breeding programs in small populations. The recent availability of genome-wide SNP panels allows providing background information concerning genome structure in domestic animals, opening new perspectives to livestock genetics. BOVITA was established to join local efforts and resources for the genomic characterization of Italian local cattle breeds. Despite the growing diffusion of some cosmopolite specialized breeds, several autochthonous breeds are still bred in Italy. The main aim of the BOVITA is to investigate the genomic structure of Italian local c…
Genome-wide characterization of local cattle breeds from central and western Mediterranean
2017
Following-up on previous studies that investigated genetic relationships among several world-wide cattle breeds using genome-wide SNP data, we focus here on the central and western part of the Mediterranean. Notably, 50K genotypes from 30 Marismeña (Spain); 24 Guelmoise (Algeria); 46 Brune de l’Atlas Fauve, 15 Brune de l’Atlas Grise, and 15 Blonde du Cap (Tunisia); 29 Modicana and 30 Cinisara (Sicily); 24 Podolica Italiana (Southern continental Italy); 34 Chianina and 24 Romagnola (Central Italy); 23 Modenese, 24 Reggiana, 23 Alpine Grey and 50 Pezzata Rossa Italiana (Northern Italy); 50 Bruna Italiana and 50 Frisona Italiana were considered. When included in a world-wide dataset, the three…
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…
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…
Survey of milk protein polymorphism in the "Rossa Siciliana" dairy cattle
2005
“Rossa Siciliana” is a dairy cattle population traditionally linked to cheese production protein polymorphisms from 62 individual milk samples from 19 farms were analyzed by isoelectrofocusing. High variability was found at the CNS1S1, CSN2, CSN3, LGB and LALBA loci, while the CNS1S2 locus was monomorphic for the A allele. The casein haplotype frequencies and the occurrence of the linkage disequilibrium, taking into account the association among loci were investigated. The population was not in Hardy-Weinberg equilibrium (Chi-square=19.0, p-value=0.0407), probably due to genetic drift. Frequencies of the three allele detected at CSN1S1 locus were B (0.734), C (0.258) and D (0.008). high fre…