La Tomografia sismica in velocità, attenuazione e scattering e l'immagine della struttura dei vulcani.

a) A brief review of the results from travel time tomography at Mt. Vesuvius ed at Campi Flegrei. b) New approaches: (passive) attenuation and scattering tomography. c) Results obtained (passive attenuation and scattering) at Mt. Vesuvio and Campi Flegre

Sharing of either phenotypes or genetic variants can increase the accuracy of genomic prediction of feed efficiency.

BACKGROUND Sharing individual phenotype and genotype data between countries is complex and fraught with potential errors, while sharing summary statistics of genome-wide association studies (GWAS) is relatively straightforward, and thus would be especially useful for traits that are expensive or difficult-to-measure, such as feed efficiency. Here we examined: (1) the sharing of individual cow data from international partners; and (2) the use of sequence variants selected from GWAS of international cow data to evaluate the accuracy of genomic estimated breeding values (GEBV) for residual feed intake (RFI) in Australian cows. RESULTS GEBV for RFI were estimated using genomic best linear unbiased prediction (GBLUP) with 50k or high-density single nucleotide polymorphisms (SNPs), from a training population of 3797 individuals in univariate to trivariate analyses where the three traits were RFI phenotypes calculated using 584 Australian lactating cows (AUSc), 824 growing heifers (AUSh), and 2526 international lactating cows (OVE). Accuracies of GEBV in AUSc were evaluated by either cohort-by-birth-year or fourfold random cross-validations. GEBV of AUSc were also predicted using only the AUS training population with a weighted genomic relationship matrix constructed with SNPs from the 50k array and sequence variants selected from a meta-GWAS that included only international datasets. The genomic heritabilities estimated using the AUSc, OVE and AUSh datasets were moderate, ranging from 0.20 to 0.36. The genetic correlations (rg) of traits between heifers and cows ranged from 0.30 to 0.95 but were associated with large standard errors. The mean accuracies of GEBV in Australian cows were up to 0.32 and almost doubled when either overseas cows, or both overseas cows and AUS heifers were included in the training population. They also increased when selected sequence variants were combined with 50k SNPs, but with a smaller relative increase. CONCLUSIONS The accuracy of RFI GEBV increased when international data were used or when selected sequence variants were combined with 50k SNP array data. This suggests that if direct sharing of data is not feasible, a meta-analysis of summary GWAS statistics could provide selected SNPs for custom panels to use in genomic selection programs. However, since this finding is based on a small cross-validation study, confirmation through a larger study is recommended

Population structure and history of the Welsh sheep breeds determined by whole genome genotyping

BACKGROUND: One of the most economically important areas within the Welsh agricultural sector is sheep farming, contributing around £230 million to the UK economy annually. Phenotypic selection over several centuries has generated a number of native sheep breeds, which are presumably adapted to the diverse and challenging landscape of Wales. Little is known about the history, genetic diversity and relationships of these breeds with other European breeds. We genotyped 353 individuals from 18 native Welsh sheep breeds using the Illumina OvineSNP50 array and characterised the genetic structure of these breeds. Our genotyping data were then combined with, and compared to, those from a set of 74 worldwide breeds, previously collected during the International Sheep Genome Consortium HapMap project. RESULTS: Model based clustering of the Welsh and European breeds indicated shared ancestry. This finding was supported by multidimensional scaling analysis (MDS), which revealed separation of the European, African and Asian breeds. As expected, the commercial Texel and Merino breeds appeared to have extensive co-ancestry with most European breeds. Consistently high levels of haplotype sharing were observed between native Welsh and other European breeds. The Welsh breeds did not, however, form a genetically homogeneous group, with pairwise F(ST) between breeds averaging 0.107 and ranging between 0.020 and 0.201. Four subpopulations were identified within the 18 native breeds, with high homogeneity observed amongst the majority of mountain breeds. Recent effective population sizes estimated from linkage disequilibrium ranged from 88 to 825. CONCLUSIONS: Welsh breeds are highly diverse with low to moderate effective population sizes and form at least four distinct genetic groups. Our data suggest common ancestry between the native Welsh and European breeds. These findings provide the basis for future genome-wide association studies and a first step towards developing genomics assisted breeding strategies in the UK. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-015-0216-x) contains supplementary material, which is available to authorized users

Detection of Chromosome Segments of Zebu and Taurine Origin and Their Effect on Body Weight

Taurine (Bos 'taurus') and zebu (Bos 'indicus') cattle were domesticated independently in the Near East and in India respectively (Beja-Pereira et al., 2006) and are believed to have diverged 117-275,000 years ago (Bradley et al., 2006). Bos 'taurus' cattle were introduced to Australia by European settlers in the end of the 18th century. The main 'B. indicus' breed used for beef production in Australia is the Brahman which was imported in the 20th century. The Brahman breed originated in the United States of America in the early 1900s where it was developed from progeny of four Indian cattle breeds with some infusion of British-bred cattle (http://www.brahman.com.au/history.html). Since then crossbreeding between Brahman and 'B. taurus' breeds has been used to form several composite breeds such as the Santa Gertrudis. Because this crossbreeding has been recent, large chromosome segments of either 'B. taurus' or 'B. indicus' origin should be segregating in these composite breeds. Due to their long separation and different selection pressures, 'B. indicus' and 'B. taurus' cattle may differ substantially in allele frequency at some genes affecting quantitative traits. If we can detect chromosome segments that derive from zebu or taurine origin, we can estimate their effect on quantitative traits and hence detect quantitative trait loci (QTLs) where there is a large difference in allele frequency between the sub-species. In this paper, we present two methods to determine the origin of a chromosome segment based on 50K SNP data and show that, at some positions in the genome, 'B. indicus' and 'B. taurus' chromosome segments differ in their effect on live weight or carcase weight