31 research outputs found
Molecular insight into goat diversity
No full textArchaeological and archaeozoological data indicate that goat (Capra hircus) has been the first domesticated livestock species. Molecular data place the most probable domestication site in Eastern Anatolia, although the pre-domestication management of C. aegagrus wild stocks possibly initiated in the Zagros Mountains, in Western Iran. Since then, goats have dispersed around the world accompanying human migrations, conquers and trades. Accordingly, microsatellite and AFLP markers reveal a strong geographic structure of goat nuclear DNA diversity and a decreasing gradient of goat diversity from the domestication site to Central Europe.
The whole genome sequencing of goat genome has fostered the development of a SNP panel and the use of genomic technologies in this species. A focused analysis of Italian breeds with the International goat 50K SNPchip indicates that goat diversity has a strong geographic component also at a smaller geographic scale. In addition the SNP panel permits a finer analysis of the structure of goat genome, revealing admixture, blocks of LD and present and historical Ne
The existing panel can be improved, however, by integrating additional whole genome sequences of goats from different geographic localities representing the areas of the domestication event(s) and potential agroclimatic adaptability. Part of this effort is being achieved by international projects (e.g. EU FP7 NextGen and 3SR projects), but the contribution of a larger number of samples (i.e. as in the 1000 cattle genomes initiative recently launched) is needed to reach a fair representation of the global diversity in goats
Analysis of single nucleotide polymorphisms in Alpine ibex using the GoatSNP50 BeadChip
No full textThe Gran Paradiso National Park is the oldest protected area in the Italian Alps and the Alpine ibex (Capra ibex ibex) is its symbol. This species, threatened with extinction at the end of the 19th century, survived only in the park. From this population, ibex was reintroduced into the European Alps. Single nucleotide polymorphisms (SNPs) are now the markers of choice for exploring genetic diversity in several species. Recently, SNP chips from livestock species have been used to identify SNPs in closely related wild species. In this study the goat 50K SNP chip was used to analyse Alpine ibex from Gran Paradiso National Park. DNA was extracted from blood samples of 8 animals sampled in the Park. Among all goat markers tested 45.966 were monomorphic and 1.329 polymorphic in the Alpine ibex. Minor Allele Frequency (MAF) distribution of polymorphic markers showed that the class that includes the highest number of markers (520) is the 0.4<MAF≤0.5 class, and that overall more than 50% of markers (860) were very informative (MAF≥0.2). Based on their genomic position in domestic goat, polymorphic loci appear distributed on all autosomes and the X chromosome. A preliminary analysis of genetic distances with domestic goat breeds reared in Northern Italy indicates that Reynold’s genetic distances between these breeds and the Alpine ibex ranged from 0.57 to 0.69, with the highest values for Orobica (0.69) and Valdostana (0.64). The high distance observed with Valdostana in our sample disagrees with the supposed introgression of Alpine Ibex in this goat breed, which is reared in the same area of the Gran Paradiso National Park. While waiting for the sequencing of C. ibex genome, this panel of 1329 goat SNPs, is the richest panel of molecular markers nowadays available for the investigation of the genetic diversity of this wild species
Variabilità genetica di otto popolazioni caprine dell’Italia centrale valutata tramite un chip SNP a media densità
No full textItalian Goat Consortium : 50K BeadChip analyses in autochthonous goat breeds
No full textAn Italian Goat Consortium has been established to analyse the genomic diversity of Italian
goat breeds reared in different conditions from the Alps to the main islands. To date, blood
samples have been collected from 12 breeds and a total of 288 unrelated animals. Genomic
DNA has been extracted using commercial kits and genotyped with the 53.347 SNPs Illumina
Infinium iSelectHD Custom Bead Chip. Here we show preliminary results on Orobica, Bionda
dell'Adamello and Valpassiria breeds, reared in Central and Eastern Alps, in Northern Italy, and
on Grigia Ciociara, reared in Central Italy (n = 90). SNP call rate was on average 0.99 ± 0.016
(average ± SD). A total of 98.25% SNPs were polymorphic, 1.1% monomorphic and 0.5% gave
no results. Observed average heterozygosity across breeds was 0.38 ± 0.11, while average
expected heterozigosity 0.41± 0.11. The four breeds analysed had average MAF of 0.32 ± 0.12.
Only 0.9% of SNPs were rare, and 97.6% had a MAF > 1%. Moreover 12.5% of SNPs were out
of HW equilibrium. The analysis of other 8 local breeds from the Alps, and from Sicily and
Sardinian islands is in progress. Large scale genomic information produced by new technologies
has potential application in the genetic improvement of economic traits, in the traceability of
typical goat products linked to local breeds and permits to select SNP subsets informative for
parentage analysis. In addition, a detailed assessment of within and between and breed goat
diversity is useful to reconstruct goat population history and demograpy and in the management
and conservation of genetic resources. Genetic and genomic innovation, coupled to research,
can enhance the sustainable productivity and the competitiveness of goat farms that play a
strategic role in the economy of marginal rural areas. The research was also supported by the
project "INNOVAGEN" (Italian MIPAAF Ministery)
Variabilità genetica di otto popolazioni caprine dell’Italia centrale valutata tramite un chip SNP a media densità
No full textItalian Goat Consortium: a collaborative project to study the Italian caprine biodiversity
No full textThe 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 by excluding markers and individuals on the basis of missing genotypes, minor allele frequency and close individual relatedness. Genetic relationships among and within breeds was investigated by Multi-Dimensional Scaling and Principal Component Analysis. Population structure, ancestry models
and admixture were estimated by ADMIXTURE and fastSTRUCTURE software. Finally, phylogenic trees were reconstructed with PHYLIP software suite starting from shared-allele identity by state, and Reynolds distance matrices, while past migration events were modeled with TreeMix software. The results confirmed high levels of genetic polymorphism and confirmed the North-South geographical pattern of diversity, previously reported on a smaller sample of Italian goat breeds. The analysis also revealed a pivotal role of Central Italy in connecting the genetic resources of the northern and southern areas of the country, and confirms the genetic isolation of insular breeds. Moreover, some breeds show clearly distinctive and homogeneous gene pools, whereas other breeds present complex and, in some cases, dishomogeneous genetic background. Even if “A breed is a group of domestic animals, termed such by common consent of the breeders” (Lush J.L., 1994), genomic tools are useful in understanding the genetic background of populations and in defining their relationships or uniqueness. These tools can complement the traditional ones in providing farmers and their associations a powerful aid for a more conscious management of goat populations and their biodiversity
Italian Goat Consortium: a collaborative project to study the Italian caprine biodiversity
No full textThe 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 by excluding markers and individuals on the basis of missing genotypes, minor allele frequency and close individual relatedness. Genetic relationships among and within breeds was investigated by Multi-Dimensional Scaling and Principal Component Analysis. Population structure, ancestry models and admixture were estimated by ADMIXTURE and fastSTRUCTURE software. Finally, phylogenic trees were reconstructed with PHYLIP software suite starting from shared-allele identity by state, and Reynolds distance matrices, while past migration events were modeled with TreeMix software. The results confirmed high levels of genetic polymorphism and confirmed the North-South geographical pattern of diversity, previously reported on a smaller sample of Italian goat breeds. The analysis also revealed a pivotal role of Central Italy in connecting the genetic resources of the northern and southern areas of the country, and confirms the genetic isolation of insular breeds. Moreover, some breeds show clearly distinctive and homogeneous gene pools, whereas other breeds present complex and, in some cases, dishomogeneous genetic background. Even if “A breed is a group of domestic animals, termed such by common consent of the breeders” (Lush J.L., 1994), genomic tools are useful in understanding the genetic background of populations and in defining their relationships or uniqueness. These tools can complement the traditional ones in providing farmers and their associations a powerful aid for a more conscious management of goat populations and their biodiversity
Italian Goat Consortium: a first overview of genetic variability using a medium density single nucleotide polymorphism array
No full textThe Italian Goat Consortium was established from the Innovagen Project to pool local efforts and resources for the genomic characterisation of Italian goat breeds.
Thirteen Italian goat breeds (Valdostana, Saanen, Orobica, Bionda dell’Adamello, Val Passiria, Grigia Ciociara, Teramana, Nicastrese, Aspromontana, Girgentana, Argentata dell’Etna,
Sarda and Maltese – the latter sampled in Sardinia and Sicily) for a total of 350 animals (15-32 per breed) were analysed using a medium density SNP array. Data editing was based
on the following thresholds: MAF <1%; Missing SNP >5%; Missing animal >5%; HW within breed FDR >20%. After filtering, a total of 51136 SNPs were retained, showing that the adopted
SNP chip is highly informative for the characterization of Italian goat gene pool. Population structure and breed distinctiveness were investigated with the software Admixture,
that revealed the best fitting solution at K=11 partitions. The software also highlighted variable levels of admixture and an early differentiation of Val Passiria, Orobica, Valdostana,
Teramana, Girgentana and Sarda breeds. Within MDS plot, some breeds are clearly appreciable as distinct: Girgentana, Teramana, Orobica and Maltese. PCA analysis revealed a gradient of
diversity North (from alpine breeds) – South (to Sicilian breeds) and East (from Val Passiria breed) - West (to Valdostana breed) in the Alps. The calculation of Fis index indicated
little or no inbreeding, while LD analysis in Chromosome 6 showed levels of disequilibrium much lower than cattle at short physical distance. The research was also supported by the
project "INNOVAGEN" (Italian MIPAAF Ministery)
