Search results for "Breeds"

APPLICAZIONE DI TECNOLOGIE BIOMOLECOLARI E PROTEOMICHE NELLO STUDIO DELLA BIODIVERSITA’ DI RAZZE ZOOTECNICHE SICILIANE AUTOCTONE

LINKAGE DISEQUILIBRIUM AND GENETIC DIVERSITY IN TWO SICILIAN CATTLE BREEDS ASSESSED BY BOVINE SNP CHIP

2013

The Modicana (MOD) and Cinisara (CIN) are two Sicilian cattle breeds farmed in extensive systems and their economic importance lies on the traditional making of two typical ‘pasta filata’ cheeses. The aim of this study was to explore the genetic structure and the extent of Linkage Disequilibrium (LD) of MOD and CIN cattle breeds. A total of 144 animals were genotyped, using the Bovine SNP50K v2 BeadChip. The squared correlation coefficient between two loci (r2) was used as a measure of LD. Principal components analysis (PCA), molecular inbreeding (F) and Bayesian clustering algorithm (Pritchard et al., 2000) were used to explore the relationship between individuals and populations. The r2 r…

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 …

Linkage disequilibrium and genetic diversity estimation in three Sicilian autochthonous dairy sheep breeds

2014

Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. In the present study, we used the OvineSNP50K BeadChip to characterize LD, identify haplotype blocks and to analyze genetic diversity in the Valle del Belice (VDB), Comisana (COM) and Pinzirita (PIN) dairy sheep breeds. LD between adjacent SNPs and for all pairwise combinations of SNPs on each chromosome was measured using r2. Haplotype blocks were estimated using D’ based method. Genetic diversity and Principal Component Analysis (PCA) were calculated using PLINK. Small differences in average LD value for adjace…

Genetic and protein polymorphism at CSN1S1 locus in two goat breeds.

2006

Genetic polymorphisms of casein have received a considerable research effort for many years because of its potential effect on milk composition. Milk composition, specifically protein content, differs quantitatively and qualitatively among species and also among breeds and individuals. Sicilian goat breeds seem to be an interesting model since they have never been under a selection program, and therefore may carry unique casein polymorphisms. Moreover, the importance of goat milk in infant diets is growing probably because goat milk in some cases is less allergenic than cow milk. It is important to evaluate the genetic polymorphisms at the CSN1S1 locus in the populations of interest, like t…

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…

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…