1,720,959 research outputs found
Dissecting the genetic variability of major genes for pig production traits using whole genomesequencing data.
No full textWhole genome sequencing (WGS) datasets produced from next generation sequencing technologies are making it possible to obtain a comprehensive evaluation of the level of genetic variability within and across breeds and populations in many livestock species and to infer their genetic history and relevant population genetic information useful to manage these animal genetic resources. In this study, we mined WGS datasets from about 500 individual pigs or groups of pigs (obtained from DNApools) belonging to 30 European and 14 Asian breeds, European and Asian wild boars and other species of the Sus genus (Sus barbatus, S. cebifrons, S. celebensis and S. verrucosus) closely related to Sus scrofa. Two thirds of the datasets were retrieved from the European Nucleotide Archive (ENA) or from previous projects and one-third was newly produced for this study and derived from Italian Large White, Italian Landrace and Italian Duroc pigs. Datasets retrieved from ENA were pre-filtered according to a minimum averaged depth of sequencing of 10× whereas the average depth of sequencing of the newly produced WGS datasets was about 23×. A total of 150 genes were selected according to their already established role in affecting relevant production traits (e.g. growth rate, lean meat and fat deposition, reproduction performances, taste preference, meat quality, including boar taint). Short reads from these genomes were first aligned using bowtie to a customized reference sequence generated from the reference pig genome, including sequence of the selected genes. Variant calling was performed with samtools software. The Ensembl Variant Effect Predictor tool was used to inspect the consequences of the identified variants and potentially deleterious mutations were detected with SIFT. About 2.3% of the detected variants were in coding regions and included a total of 340 missense mutations and other variants with predicted functional effects (e.g. stop codon gains/losses, frameshift mutations). Substantial differences in allele frequencies and allele distributions were observed for these putative relevant variants between European and Asian pig breeds and across the other Sus species. This study provided a landscape genome picture of variants that might explain part of the genetic variability of important production traits in pigs.
Acknowledgements
This study was supported by PRIN2017 MUR funds (PigPhenomics project
Signatures of selection detected from whole‐genome sequencing indicate that the small body size in dwarf rabbit breeds is caused by polygenic effects with a few major loci
Get PDFEarly genetic studies have suggested that body size in rabbits can be considered a quantitative trait. Several rabbit breeds can be distinguished based on body size, including a few dwarf breeds differentiated by other morphological characteristics. While a large deletion in the HMGA2 gene is a major locus associated with dwarfism in Netherland Dwarf rabbits, it may not fully explain the reduced body size in this breed or other dwarf breeds. In this study, we compared the genomes of two dwarf rabbit breeds (Dwarf Lop and Netherland Dwarf) with those of non-dwarf rabbits by analysing whole-genome sequencing data obtained using a DNA-pool sequencing approach. We applied the fixation index (FST) and pooled heterozygosity (HP) statistics to identify signatures of selection related to small body size by contrasting dwarf with non-dwarf breeds and comparing dwarf breeds. We identified several genomic regions that contain genes previously linked to body dimensions in various species, including LCORL-NCAPG, COL2A1, GHRHR and CENPE. Functional enrichment analysis of genes within the top differentiated regions revealed biological terms related to skeletal development, further supporting the biological relevance of these loci. Additionally, the use of the latest version of the reference rabbit genome enabled the identification of a genomic region containing FGFR3, a gene linked to achondroplasia. Some genomic regions showed differentiation between the two dwarf breeds, suggesting that their small body size may, in part, arise through different genetic mechanisms. Overall, these findings support a polygenic architecture underlying small size in rabbits, influenced by a few major loci
Description of metabolic differences between castrated males and intact gilts obtained from high-throughput metabolomics of porcine plasma
Get PDFSurgically castrated male pigs, which are commonly produced in pork production systems, have slightly lower production efficiency, compared to intact female pigs (gilts). This is mainly due to an unfavorable feed conversion rate and fatter carcasses. These differences influenced by physiological and genetic factors can be identified through metabolomics, which describes metabolic profiles. In this study, we used untargeted metabolomics to analyze the plasma of 694 Italian Large White pigs (228 castrated males and 466 intact gilts), sampled at slaughter. The metabolomic profiles included 731 metabolites covering 98 sub-pathways. The raw metabolomic data were cleaned and imputed using multivariate imputation by chained equations. The Boruta algorithm was then employed to identify metabolites that have different concentrations between castrated males and intact gilts. To address the random nature of feature selection, multiple Boruta runs were generated, and nested within a 10-fold cross-validation, resulting in 1,250 Boruta datasets. These datasets helped identify 40 informative metabolites, with a reduced core of 15 metabolites consistently confirmed across all runs. Their calculated random forest out-of-bag error was 0.25 and 0.27, respectively. The relevance, ranking, and predictive ability of each selected metabolite were determined based on the mean decrease Gini (MDG) and the area under the curve (AUC) of the receiver operating characteristic curve analysis, with MDG values of 0.024 ± 0.007 and 0.030 ± 0.009 and AUC values of 0.62 ± 0.04 and 0.65 ± 0.03 for the 2 metabolite sets, respectively. Of the 40 selected metabolites, 60% had higher concentrations in castrated males than in intact gilts, while in the 15 metabolites set, this percentage was 80%. Network and biological pathways analyses indicated that the selected metabolites were primarily amino acids and lipids, many of which belonged to their respective sub-pathways, suggesting minimal biological differences between castrated males and intact gilts. These findings support previous results obtained using a targeted metabolomic platform. This study represents the largest investigation to date on the pig sex metabolome, providing essential biological insights that could inform precise husbandry and feeding strategies in pigs, taking into consideration the castration status of the males
Going Beyond Counting First Authors in Author Co-citation Analysis
Get PDFThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Get PDF“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Get PDFWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
Get PDFWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
No full textWe have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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