from the editors animal selection the genomics revolution

The rapid improvements in high-throughput single nucleotide polymorphism (SNP) genotyping technologies, ever-denser SNP arrays accompanied by reduced costs for genotyping and for sequencing, open the possibility of using genomic information in livestock selection. The industry is thus facing the new paradigm of "genomic selection," in which genomic information may reduce costs and accelerate genetic gain by reducing generation intervals. Genetic markers, or SNP, are highly abundant in the genome, and highthroughput molecular technologies allow the inheritance of hundreds of thousands of such markers to be traced through generations for currently less than US $200 per animal. Even if the mutations themselves do not directly affect the phenotype, they can track for the variability of causal mutations in their vicinity. By summing the effects assigned to each SNP, we can create a numeric value (genomic breeding value) that allows the genetic potential of a breeding animal to be assessed. This is an enormously valuable tool for choosing breeding animals as parents of the next generation. In addition, genomic selection may allow the identifi cation of superior individuals for traits not currently considered in animal breeding plans because of technical diffi culties. For example, the fatty acid composition of dairy and beef food products, increased disease resistance (and thus increased animal welfare), and decreased methane emissions in cattle help to address the needs of consumers and society for sustainable and cost-effective food production. The animal breeding industry is currently adapting selection procedures in each species to include this innovative tool. This is causing a worldwide restructuring of the animal breeding industry. As an example in dairy cattle, large international consortia are being formed to develop joint precompetitive research and tools. For similar reasons, in the future, genomic selection might help close the gap between countries with greater and lesser production. The scope of this issue of Animal Frontiers is to provide a worldwide overview and various perspectives on intermediate-term scenarios resulting from the application of genomic tools in different livestock species. Genomic selection has already had a huge impact in genetic selectionrelated industries. Such industries have had the same structure for at least 3 decades. Subsequent to the research conducted by animal geneticists in the 1960s and 1970s, mainly by Charles Henderson and his group, animal selection remained the same for many years. Of course, new traits were included and new species were selected in addition to dairy cattle, but the industry structure generally remained the same. During these years, genetic selection also incorporated new computer technologies and animal reproduction discoveries to improve the identifi cation of superior animals. The genomic revolution created large changes in this structure. New actors appeared on the scene. In this issue of Animal Frontiers, relevant technicians and scientists were invited to focus on the impact of the genomic revolution on the genetics industry and to forecast future developments

Identification of CNV and QTL for productive and functional traits in dairy cattle using dense SNP chips

The thesis identify CNV structural variants as possible markers for genomic selection and identify QTL regions for Fatty Acid Content in the Italian Brown Swiss population. Additionally it maps the QTL for mastitis resistance in the Valdostana Red Pied cattle

Effects of Clustering Herds with Small-Sized Contemporary Groups in Dairy Cattle Genetic Evaluations

Most test-day models used in genetic evaluations of dairy cattle define contemporary groups (CG) as the herd-test-date effect. Fitting this effect as fixed may minimize prediction bias, but requires a minimum number of observations per CG to simultaneously maximize the effective number of observations and minimize the residual error and prediction error variance. Nearly 4 million test-day records from the Portuguese Holstein database of 238,271 cows calving in 1,330 herds from 1994 through 2006 were used to evaluate the effect of clustering CG from small herds based on the similarity of their production environments. Principal component analysis was used to summarize 14 descriptive variables in 5 eigenvectors that explained 88% of the total variation. Based on the distance matrix, 2 different approaches were applied to group the herds. For each approach, 4 data sets were built having at least 3, 5, 10, or 15 observations per CG, respectively. For the data sets of group A, all herds, with or without the required number of observations per CG, were used in the clustering process. For the data sets of group B, only herds without the minimum number of observations were candidates to form clusters. All data sets were analyzed by an autoregressive test-day animal model fitting a fixed herd test date in a multiple-lactation setting, and results were compared with the current clustering procedure used in the Portuguese genetic evaluations. The data set from group B, with a minimum of 3 records per CG, was the one that provided the highest accuracy of prediction and the smaller within-CG variance, revealing a better fit for the data. This procedure also preserved the original herd structure of the database, better maximizing the number of herd groups. Correlations among EBV, rank, prediction error variance, and accuracies of prediction for this data set were high (0.97, 0.97, 0.85, and 0.82, respectively), suggesting that no major reranking is to be expected

Heritabilities and Genetic Correlations of Body Condition Score and Muscularity with Productive Traits and their Trend Functions in Italian Simmental Cattle

With the aim to study the genetics of energy and muscle balance in the Italian Simmental breed, the objectives of this study were: i) the estimation of the genetic parameters for body condition score (BCS) and muscularity (MU) score; ii) the estimation of genetic correlations of BCS and MU with productive traits; iii) the estimation of the expected pattern of BCS and MU over lactation. A total of 47,839 records of first-parity lactating cows, collected from 1999 to 2007 in 2794 herds, were used. Two-trait animal models were analyzed using restricted maximum likelihood (REML) procedures to estimate (co)variance components. The expected patterns of BCS and MU along the lactation of first parity cows were estimated from the solutions of DIM fixed effect obtained from an univariate mixed model for both the traits. The heritability estimated was 0.18 for BCS, 0.38 for MU, and ranged from 0.13 to 0.18 for yield traits. The genetic correlations between BCS, MU and yield traits were negative (-0.17 to -0.63). The genetic correlation between BCS and MU was strongly positive (0.88), indicating that cows that genetically tend to have high BCS are more likely to have high values of MU. The genetic parameters estimated suggested that selection for BCS and MU in dual purpose breeds may be possible, and BCS may indirectly improve MU. The expected patterns for BCS and MU showed the trend of these two traits along the lactation and can help farmers in planning the best management of the lactating cows

Mercury emissions from soils and fumaroles of Nea Kameni volcanic centre, Santorini (Greece)

There have been limited studies to date targeting mercury emissions from volcanic fumarolic systems, and no mercury flux data exist for soil or fumarolic emissions at Santorini volcanic complex, Greece. We present results from the first geochemical survey of Hg and major volatile (CO2, H2S, H2O and H2) concentrations and fluxes in the fumarolic gases released by the volcanic/hydrothermal system of Nea Kameni islet; the active volcanic center of Santorini. These data were obtained using a portable mercury spectrometer (Lumex 915+) for gaseous elemental mercury (GEM) determination, and a Multi-component Gas Analyzer System (Multi-GAS) for major volatiles. Gaseous Elemental Mercury (GEM) concentrations in the fumarole atmospheric plumes were systematically above background levels (~4 ng GEM m-3), ranging from ~4.5 to 121 ng GEM m-3. Variability in the measured mercury concentrations may result from changes in atmospheric conditions and/or unsteady gas release from the fumaroles. We estimate an average GEM/CO2 mass ratio in the fumarolic gases of Nea Kameni of approximately 10-9, which falls in the range of values obtained at other low-T (100°C) volcanic/hydrothermal systems (~10-8); our measured GEM/H2S mass ratio (10-5) also lies within the accepted representative range (10-4 to 10-6) of non-explosive volcanic degassing. Our estimated mercury flux from Nea Kameni's fumarolic field (2.56 × 10-7 t yr-1), while making up a marginal contribution to the global volcanic non-eruptive GEM emissions from closed-conduit degassing volcanoes, represents the first available assessment of mercury emissions at Santorini volcano, and will contribute to the evaluation of future episodes of unrest at this renowned volcanic complex

Genetic parameters and selection for casein content in Italian Holstein and Brown Swiss.

A total of more than 2,000,000 records on casein contents were collected in Lombardia (Italy) during routine milk recording of Italian Holstein and Brown Swiss dairy cows. Variance components for casein were estimated as well as all the genetic correlations of casein with production and type traits considered in selection. According to the heritabilities estimated (12.4% for Brown and 9.36% for Holstein), breeding values were calculated for bulls and compared to the breeding values for total protein. The results of two different selection scenarios were compared for each breed when including protein or casein as selection criterion. Genetic progress expected for all traits selected were compared after 10 years of selection. The genetic variability of casein allows the use of this trait as selection criterion with the estimation of breeding values and its inclusion in selection indexes. Ranking of breeding values for casein and protein are very similar in both breeds. But some differences in genetic values for casein exist for the same level of breeding value for protein. Nevertheless results in genetic gain differ between breeds depending mainly on genetic correlations with the other traits selected. The positive results in selection response estimated for several traits suggest to the Brown Swiss Association the replacement of protein selection with casein. In contrast the smaller effects estimated for the Italian Holstein suggest to wait for more casein data collected before any change in selection program

Leachate analyses of volcanic ashes from Stromboli volcano: A proxy for the volcanic gas plume composition?

Many volcanoes show a change in chemical composition of the gas phase prior to periods of eruptive activity. Fine‐grained tephra erupted from active vents and transported through volcanic plumes can adsorb, and therefore rapidly scavenge, volatile elements such as sulfur, halogens, and metal species in the form of soluble salts adhering to ash surfaces. Analysis of such water‐soluble surface materials is a suitable supplement for remote monitoring of volcanic gases at inaccessible volcanoes. In this work, ash samples of the 2004 to 2009 eruptive activity of Stromboli volcano were sampled, leached, and analyzed for major and trace elements. Data analysis and interpretation was focused on determining the relationship between chemical composition of water‐soluble components adhering to volcanic ash and the volcano’s activity state. First results show significant temporal variations in ash leachate compositions, reflecting changes in the eruptive style of the volcano. In particular, we reveal that ash leachates S/F and Mg/Na ratios showed marked increases prior to a large‐scale explosion on 15 March 2007.PublishedD172041.2. TTC - Sorveglianza geochimica delle aree vulcaniche attiveJCR Journalreserve

investigation of the dgat1 k232a and vntr mutations in dairy and dual purpose cattle breeds

AbstractSeveral studies have reported that the centromeric end of bovine chromosome 14 harbours QTL for milk production and composition traits. The acyl-Coenzyme A:diacylglycerol acyltransferase 1 (DGAT1) gene was indicated to be the quantitative trait gene affecting these traits with a major effect on milk fat content. A two bp mutation in exon 8 causing a nonconservative lysine to alanine amino acid substitution at codon 232 (K232A) showed a confirmed effect across breeds with allele K resulting associated with an increase on fat yield, fat percentage and protein percentage while allele A was associated with higher milk yield. Another mutation in the 5' regulatory region of this gene, a variable number of tandem repeat (VNTR) of 18 bp, was suggested to affect fat percentage. The objective of the present work was to investigate the occurrence of the DGAT1 K232A and VNTR polymorphisms in several Italian dairy and dual purpose cattle breeds as a first step to evaluate their effects on milk production trait..

Genome-wide association studies using copy number variants in Brown Swiss Dairy cattle.

Detecting Copy Number Variation (CNV) in cattle provides the opportunity to study their association with quantitative traits (Winchester et al., 2009; Zhang et al., 2009; Hou et al., 2011; Clop et al., 2012; de Almeida et al., 2016;). The aim of this study was to map CNVs in 1,410 Brown Swiss males and females using Illumina BovineHD Genotyping BeadChip data and to perform a genome-wide association analysis for production functional and health traits. After quality control, CNVs were called with the GoldenHelix SVS 8.3.1 and PennCNV software and were summarized to CNV regions (CNVRs) at a population level, using BEDTools. Additionally, common CNVRs between the two software were set as consensus. CNV-association studies were executed with the CNVRuler software using a linear regression model. Genes within significant associated CNVRs for each trait were annotated with a GO analysis using the DAVID Bioinformatics Resources 6.7.The quality control filtered out 294 samples. The GoldenHelix SVS 8.3.1 software identified 25,030 CNVs summarized to 398 CNVRs while PennCNV identified 62,341 CNVs summarized to 5,578 CNVRs. A total of 127 CNVRs were identified to be significantly associated with one or more of the evaluated traits. The result of this study is a comprehensive genomic analysis of the Brown Swiss breed, which enriches the bovine CNV map in its genome. Finally, the results of the association studies deliver new information for quantitative traits considered in selection programs of the Brown Swiss breed

Genome-wide association study between CNVs and milk production traits in Valle del Belice sheep

Copy number variation (CNV) is a major source of genomic structural variation. The aim of this study was to detect genomic CNV regions (CNVR) in Valle del Belice dairy sheep population and to identify those affecting milk production traits. The GO analysis identified possible candidate genes and pathways related to the selected traits. We identified CNVs in 416 individuals genotyped using the Illumina OvineSNP50 BeadChip array. The CNV association using a correlation-trend test model was examined with the Golden Helix SVS 8.7.0 tool. Significant CNVs were detected when their adjusted p-value was <0.01 after false discovery rate (FDR) correction. We identified 7,208 CNVs, which gave 365 CNVRs after aggregating overlapping CNVs. Thirty-one CNVRs were significantly associated with one or more traits included in the analysis. All CNVRs, except those on OAR19, overlapped with quantitative trait loci (QTL), even if they were not directly related to the traits of interest. A total of 222 genes were annotated within the significantly associated CNVRs, most of which played important roles in biological processes related to milk production and health-related traits. Identification of the genes in the CNVRs associated with the studied traits will provide the basis for further investigation of their role in the metabolic pathways related to milk production and health traits