1,721,095 research outputs found
Genome-wide association study for morphological and hunting-behavior traits in Braque Français Type Pyr ́en ́ees dogs: A preliminary study
No full textHigh-throughput genotyping offers great potential to increase our understanding of the genomic basis of canid
variation. Braque Français Type Pyrénées (BRA) are smart, agile, and friendly dogs originally developed for
tracking, hunting, and retrieving feathered game. On a population of 44 unrelated BRA dogs, single nucleotide
polymorphism (SNP) genotype data from the CanineHD Whole-Genome Genotyping BeadChip and evaluation
scores for 12 traits related to morphology and hunting performance were available. After quality filtering, 95,859
SNPs on the 38 dog autosomes (CFA) were retained. Phenotypic scores were expressed on a scale from 1 (worst)
to 6 (best) and were mostly poorly to moderately correlated except for some morphological traits (e.g. r = 0.81
between the conformation of the head and that of the eye). From GWAS, a total of 378 SNP-phenotype associations
with posterior odds of association > 1 have been detected. The strongest associations were found for the
eye conformation, for the skull/muzzle ratio, and for connection to the hunter. These included both new and
previously identified markers and genes potentially involved with type and behavior traits in BRA. Six of the
significant markers mapped within SETDB2, a gene known to be related to pointing behavior in dogs. These
results advance our understanding of the genetic basis for morphology and hunting behavior in dogs and identify
new variants which are potential targets for further research
Genome-wide diversity and runs of homozygosity in the “Braque Français, type Pyrénées” dog breed
Full text linkAbstract
Objective
Braque Français, type Pyrénées is a French hunting-dog breed whose origin is traced back to old pointing gun-dogs used to assist hunters in finding and retrieving game. This breed is popular in France, but seldom seen elsewhere. Despite the ancient background, the literature on its genetic characterization is surprisingly scarce. A recent study looked into the demography and inbreeding using pedigree records, but there is yet no report on the use of molecular markers in this breed. The aim of this work was to genotype a population of Braque Français, type Pyrénées dogs with the high-density SNP array to study the genomic diversity of the breed.
Results
The average observed () and expected () heterozygosity were 0.371 () and 0.359 (). Effective population size () was 27.5635 runs of homozygosity (ROH) were identified with average length of 2.16 MB. A ROH shared by of the dogs was detected at the beginning of chromosome 22. Inbreeding coefficients from marker genotypes were in the range . Inbreeding estimated from ROH () had mean ), with range [0.0526, 0.225]. These results show that the Braque Français, type Pyrénées breed is a relatively inbred population, but with still sufficient genetic variability for conservation and genetic improvement
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe 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
Genetic analysis of production, immunity and behaviour in laying hens
No full textThe new regulations about the husbandry of laying hens and the so-called genomic revolution offer both opportunities and challenges for the breeding of layers. Hens are currently housed mainly in battery cages of 4 individuals each. Following recent developments of the communitarian legislation, many countries will soon adopt furnished cages or non-cage systems, which will lead to larger groups of hens. Also, beak-trimming will be prohibited in EU countries in the near future. Advancements in sequencing technology are making an always greater number of genetic markers available at increasingly cheaper prices, making genome-wide studies possible and helping geneticists to start unraveling the mystery of the genetic make-up of animals, which until a few years ago was considered a black-box. This thesis touches upon the impact of such innovations on the breeding of laying hens. Use of pooled data in the genetic evaluation of laying hens Hens are usually housed in cages and therefore pooled instead of individual egg records are often available: a pooled egg record is the total production of a cage, when the egg production of the individual hens is unknown. Current selection schemes are carried out in nucleus herds where hens are housed individually, so that egg production of individual birds can be recorded and used for genetic evaluations. Based on this information sires and dams are selected. Such a selection scheme based on individually housed hens introduces a discrepancy between the environment where hens are selected and the environment in which hens are kept for commercial egg production (group housing). Selecting animals in one environment and using them in a different environment might lead to genotype x environment interaction (Besbes and Ducroq, 2003), thereby reducing the realized response to selection. Future husbandry conditions, with larger groups of hens or hens housed in furnished cages might make this problem even worse. A method to use pooled data in the genetic evaluation of laying hens would therefore be of interest. In Chapters 2 and 3 of this thesis it is described how to use pooled records for the estimation of heritability and breeding values. In chapter 2 the use of individual and pooled observations is compared. Individual body weights of hens at different ages were available: these were then pooled by cage in order to create pooled records. Heritabilities estimated from pooled and individual data correlated well: the standard error of estimates based on pooled records was however about twice that of estimates based on individual records. The accuracy of EBVs from pooled data is lower than the accuracy of EBVs from individual data; in the case of sires with at least 10 offspring the reduction in accuracy was about 23%. This loss of precision in estimating genetic parameters and breeding values is understandable considering that pooled records are a less detailed of information. However, this lower accuracy should be interpreted in the context of direct vs indirect selection. The breeding goal is the trait under commercial conditions (group housing), and if testing is under individual housing, the genetic correlation between group and individual housing is relevant. The ratio of the selection response for direct and indirect selection is a function of the accuracies for both situations, the standard deviations of the traits and the genetic correlation between the traits (Falconer, 1989). Similarly, the ratio between accuracies based on pooled and individual data provides a threshold for the genetic correlation between individual and group housing below which pooled data would result in a greater selection response. In practical breeding also the costs of individual housing relative to the costs of group housing are relevant. Since group housing is cheaper than individual housing, more selection candidates could be tested for the same level of costs. This would in turn result in higher selection intensity and larger response to selection. In chapter 3 the method of analyzing pooled data developed in chapter 2 was compared with an approximation consisting in assigning cage means to each hen in a cage, then treating them as individual observations. Cross-validation was used to compare the two methods: the method developed in Chapter 2 performed consistently better than the approximate method in terms of predicting ability. In the general discussion, finally, it was described how to estimate genetic and phenotypic correlations from pooled data. Across-line association studies for immune response and feather pecking behaviour The great number of genetic markers available at increasingly lower prices has been fostering developments in genomic research. Association studies between genetic markers and phenotypes are typically conducted within populations (breeds, or lines): the amount of LD conserved in a population is exploited using high marker density, such as SNP chips, and markers relatively close to QTLs are expected to show significant effects in association studies. In this thesis we propose to take it one step further and perform association studies across lines. This requires higher marker density but increases the resolution. The amount of LD conserved across lines is expected to be lower than within lines and the phase of the marker-phenotype association might be different in the different lines. On the other hand markers that happen to show significant effects in an across-line association study are likely to be close to the QTL. These issues in conducting marker-phenotype association studies across populations were addressed in Chapters 4 and 5 of this thesis, where it was shown how to deal with multiple populations when analyzing hens from 9 different genetic lines of White Leghorn and Rhode Island Red origin genotyped for a panel of 1536 SNP (Single Nucleotide Polymorphism) markers. The traits analysed were immunological parameters and plumage damage due to feather pecking behaviour, two classes of traits for which, given that they have relatively low heritability and are difficult and expensive to measure, genomic information may be particularly valuable. Immunological parameters might be used in selection programmes aimed at improving disease resistance of laying hens, while information on the genetic background of feather pecking behaviour can be useful in reducing problems due to this behavioural disorder of layers. Under future husbandry conditions susceptibility to infectious diseases and feather pecking are expected to become more serious problems: both aspects of layer production are in fact related to the number of individuals that interact with each other, which will increase as a result of the application of the EU directive 1999/74/EC. In addition, the ban of beak-trimming will make it more difficult to control the consequences of feather pecking (plumage damage, cannibalism, mortality). Genetic selection might represent an appealing addition to the current control measures. The association studies identified several regions of interest. The gene for interleukin 17 (IL17), on chromosome 3, was found to be associated with natural and acquired antibody titres, and with the classical and alternative pathways of complement activation. The major histocompatibility complex (MHC) genes on chromosome 16 showed significant association with natural and acquired antibody titres and classical complement activity. The interleukin 12B gene (IL12B) on chromosome 13 was associated with natural antibody titres. As for feather pecking behaviour, a role of the gene for the serotonin receptor 2C (HTR2C) on chromosome 4 was found. This supports existing evidence of a prominent involvement of the serotonergic system in the modulation of this behavioural disorder in laying hens. The genes for IL9, IL4, CCL4 and NFKB were found to be associated to plumage condition, revealing relationships between the immune system and behaviour. <br/
Variations on the Author
Full text link“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
Full text linkWe 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
Full text linkWe 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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