Search results for "SNP"
showing 10 items of 366 documents
Haplotypes of Single Nucleotide Polymorphisms (SNPs) in casein loci of Girgentana goats explain isoelectrofocusing results.
2006
Goat milk, cheese and yoghurt offer an alternative to cow milk products. In Sicily one of the important goat breeds reared is the Girgentana. Traditionally the milk from Girgentana goats was used for nourishment of infants and elderly. Recently, the Girgentana breed has been in decline. This of concern, as the Girgentana may carry unique milk protein genetic variants. If health benefits of Girgentana goat milk is proven, then increasing production from this population will be of great interest. The most abundant proteins in goat milk, as in other milks, are the caseins, αS1-, β-, αS2- and κ-casein, coded by the loci CSN1S1, CSN2, CSN1S2 and CSN3 respectively. In other goat breeds, the casei…
Italian Goat Consortium: a collaborative project to study the Italian caprine biodiversity.
2017
The Italian Goat Consortium (IGC), joined the effort of many Universities and Research Institutes, in a comprehensive study of the Italian goat population genetic makeup using a medium density (54K) SNPs chip. Currently IGC has genotyped more than 1,000 animals from more than 30 goat breeds and populations from all Italian geographical and agroecological areas of goat rearing. The aim of this work is to obtain a clear picture of the Italian caprine biodiversity, to reconstruct the ancestry, to disentangle the genetic background and to assess the relationships among and within the investigated breeds. To date, the IGC dataset includes about 50 million genotypes. The data were quality checked…
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…
Genome-wide scan for Runs of Homozygosity in Valle del Belice sheep
2017
The current availability of very large numbers of single nucleotide polymorphisms (SNPs) throughout the genome makes these markers particularly suitable for the detection of genomic regions where a reduction in heterozygosity occurred and offers new opportunities to improve the accuracy of inbreeding (F) estimates. Runs of homozygosity (ROH) are contiguous lengths of homozygous segments of the genome where the two haplotypes inherited from the parents are identical. Here, we investigated the occurrence and the distribution of ROH in medium-density SNP genotypes (~ 50 000) in order to characterize autozygosity in 512 individuals of Valle del Belice sheep and identify the regions of the genom…
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 …
Metodo per la tracciabilità/autenticazione di prodotti lattiero-caseari mono-razza
2016
Il brevetto consiste in un metodo per l’autenticazione e la tracciabilità genetica delle produzioni lattiero-casearie mono-razza su base molecolare con approccio statistico-probabilistico. Il metodo si basa sull’impiego di tecniche di analisi ad elevata processività (in particolare SNPs genotyping su Bead Chip Illumina) su pool di DNA e sull’applicazione di metodi computazionali innovativi. Il metodo è già stato validato su produzioni lattiero-casearie ovine quali la Vastedda della Valle del Belice (DOP), sia su prodotti lattiero caseari a DOP ottenuti in laboratorio, che su prodotti a DOP reperibili sul mercato. Il metodo può comunque essere esteso, su richiesta, a qualsiasi altro prodotto…
Relazione tra SNPs ai loci caseinici e tipizzazione lattoproteica nella capra Girgentana
2006
La filogenesi della razza Girgentana ancora oggi rimane più o meno sconosciuta sebbene l’ipotesi più valida sembrerebbe quella che la ricollega alla capra Falconeri o Markor (Himalaya). La consistenza numerica della razza nell’ultimi anni ha subito una notevole contrazione, tanto da potersi annoverare tra le razze in via di estinzione. Il latte della capra Girgentana era utilizzato solo per il consumo diretto. Quando è entrato in vigore il regolamento che vietava la vendita del latte al dettaglio, il valore zoo-economico della razza Girgentana è diminuito notevolmente, contribuendo alla contrazione numerica della razza nell’ultimo ventennio. La rivalutazione della razza sarebbe di fondament…
Analysis of acetyl-CoA carboxylase gene polymorphisms in Valle del Belice dairy breeds
2015
Acetyl-CoA carboxylase is the flux-determining enzyme in the regulation of fatty acid synthesis within animal tissues. The expression of the mammary gland isoform of this enzyme, during lactation, is regulated by the acetyl-CoA carboxylase-α (ACACA) gene. The ovine ACACA gene, with 51 coding exons, is responsible for phenotypic variability observed in milk fat content and milk fatty acids (FAs) composition. However, before attempting association analyses between this enzyme and phenotypic traits of interest, a study on the genetic variability within this locus is required. The aim of this work was to sequence the encoding region of ACACA gene in Valle del Belice dairy ewes in order to ident…
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…