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Report of the Working Group on the Application of Genetics in Fisheries and Mariculture [Copenhagen, 9- 11 March, 1994]
No full textContributors: Jarle Mork, Geir Dahle, Bjarne Gjerde, Knut Eirik Jørsta
Mapping of quantitative trait loci (QTL) for resistance to pancreas disease in Atlantic salmon (Salmo salar)
No full textPancreas disease (PD) is an emergent disease which causes large economical losses to Atlantic salmon industry and severely affects welfare of fish. Two different subtypes of the PD virus, SAV2 and SAV3, affect Atlantic salmon in Norway. Even subtype SAV2 don’t produce high mortalities, affected individuals reduce their growth and are left with lesions which affect carcass quality. Currently only between-family selection is applied to this trait, which reduces accuracy and selection intensity for resistance to PD. Methods of marker assisted selection (MAS) would improve results of genetic selection of resistance to PD as within family selection would be possible. The aim of this study was to detect linkage of single nucleotide polymorphism (SNPs) with QTLs related to resistance to PD. Fry of Atlantic salmon, from crosses of three unrelated populations, were challenged with SAV2 in fresh water and mortalities were recorded during the test period. In addition, tissue samples were collected from a subset of individuals in the test and genotyped using a custom 57K SNP array. Fry in the test were assigned to possible family groups using estimates of genomic identity by descent (IBD) relationship calculated from SNP data. Heritability of survival to PD, analyzed as a binary trait, was estimated from genotyped individuals using a genomic relationship matrix constructed by two methods. Both methods resulted in similar values, revealing a moderate heritability (h2 ~ 0.2). Genome wide association analysis (GWAS) from genotyped individuals revealed twenty-six putative QTLs. Four of the putative QTLs explained on average 10.9% of the genetic variance (~ 2.5% of the phenotypic variance). Genes related to immune response, metabolism and brain damage (in humans) were found in the area of chromosome twenty-one where the QTL was found. Twenty-two of the significant SNPs were classified as “lonely significant markers” as no SNPs in the neighbor region show association with the trait. In addition, because of the large number of duplicated areas in the Atlantic salmon genome, the exact location in the genome of “lonely significant markers” was put on doubt, leading us to not consider them suitable for MAS. Because of the limited amount of variance explained by the putative QTLs and the uncertainty of the value of the twenty-two “lonely significant markers”, the benefit of MAS may be limited. Genomic selection may be more effective tool to increase accuracy and genetic gain in resistance to PD.M-A
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
Fine mapping to unravel genes for resistance to OsHV-1 virus in Pacific oyster (Crassostrea gigas).
Get PDFSummer mortality and Ostreid herpesvirus-1 (OsHV-1) infection causes detrimental losses in oyster production annually (Whittington et al., 2019; Dégremont et al., 2015b; Burge et al., 2007). Mitigation strategies to protect production populations from infection relies heavily on management strategies due to the limited immune system of the Pacific oyster. However, these are not sufficient which is why selective breeding for increased resistance to OsHV-1 may act as a stable and sustainable prevention strategy.
In this study, whole genome re-sequences of 72 individuals from the F2 generation of populations artificially selected for either susceptibility or resistance were used for genotype imputation using FImpute. A six-fold cross-validation was conducted to determine genotype imputation accuracy. Filtering of SNPs was performed based on SNP specific imputation accuracy at a threshold of 0.6. SNPs with accuracies ≥0.6 were then further used for GWAS analysis.
Variance components were estimated for the survival to OsHV-1, and analysis revealed that the identified SNPs were responsible for 42% of the genetic variation. The estimated heritability of survival was high (0.78±0.03). GWAS detected two important SNPs, one on chromosome four on chromosome four (SNP 4_6854233, p-value: 1.91x10-12) and one on chromosome six (SNP 6_1072809, p-value: 5.89x10-52) that were highly associated with survival, and five genes were identified as having a possible role in the immune response. The combination of SNP genotypes “RR/Rs” from these significant SNPs (4_6854233 and 6_1072809) showed 70% higher survival compared to the homozygous susceptible genotype “ss/ss”. This genotype combination could be used in marker assisted selection.
The estimates of genetic variation resulted in significant heritability estimates providing the possibility to improve survival through selective breeding. Imputation of genotype data certainly assisted to increase the density of genotyping with reasonably good accuracy. The genetic variation captured by the QTLs signal possibilities for MAS.Summer mortality and Ostreid herpesvirus-1 (OsHV-1) infection causes detrimental losses in oyster production annually (Whittington et al., 2019; Dégremont et al., 2015b; Burge et al., 2007). Mitigation strategies to protect production populations from infection relies heavily on management strategies due to the limited immune system of the Pacific oyster. However, these are not sufficient which is why selective breeding for increased resistance to OsHV-1 may act as a stable and sustainable prevention strategy.
In this study, whole genome re-sequences of 72 individuals from the F2 generation of populations artificially selected for either susceptibility or resistance were used for genotype imputation using FImpute. A six-fold cross-validation was conducted to determine genotype imputation accuracy. Filtering of SNPs was performed based on SNP specific imputation accuracy at a threshold of 0.6. SNPs with accuracies ≥0.6 were then further used for GWAS analysis.
Variance components were estimated for the survival to OsHV-1, and analysis revealed that the identified SNPs were responsible for 42% of the genetic variation. The estimated heritability of survival was high (0.78±0.03). GWAS detected two important SNPs, one on chromosome four on chromosome four (SNP 4_6854233, p-value: 1.91x10-12) and one on chromosome six (SNP 6_1072809, p-value: 5.89x10-52) that were highly associated with survival, and five genes were identified as having a possible role in the immune response. The combination of SNP genotypes “RR/Rs” from these significant SNPs (4_6854233 and 6_1072809) showed 70% higher survival compared to the homozygous susceptible genotype “ss/ss”. This genotype combination could be used in marker assisted selection.
The estimates of genetic variation resulted in significant heritability estimates providing the possibility to improve survival through selective breeding. Imputation of genotype data certainly assisted to increase the density of genotyping with reasonably good accuracy. The genetic variation captured by the QTLs signal possibilities for MAS
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
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