MAPfastR : quantitative trait loci mapping in outbred line crosses

MAPfastR is a software package developed to analyze QTL data from inbred and outbred line-crosses. The package includes a number of modules for fast and accurate QTL analyses. It has been developed in the R language for fast and comprehensive analyses of large datasets. MAPfastR is freely available at: http://www.computationalgenetics.se/?page_id=7.

Recensionernas retorik : Om könsroller i kulturjournalistiken

At the centre of this study lies the question if normative gender thinking affects the way poetry gets reviewed and how the reviews are written, this in relation to both the gender of the reviewer and the poet. The study crosses three academic fields; gender studies, poetry and journalism, and is based on the cultural studies theory of media affecting and even creating the world around it. The study is based on two types of analysis. One quantitative analysis based on the thematic criticism theory about detail studies that shows bigger patterns, this analysis focuses on how the poet and his/hers work are being treated in the reviews in areas such as how much space they´re given in the newspapers, how they are named by the reviewer and the tendency to quote the reviewed work.  And one qualitative analysis based on the new criticism method of close reading, that focuses on the reviewers way of writing and how that may be connected with theories of gender differences, this both connected to the gender of the reviewers and the poets. The material chosen for this study are all the reviews that were published in the same newspapers and that reviewed two specific poetry works by two specific poets chosen with great sensibility to age and career so that their difference in gender would be the most significant difference between them. The works were chosen based on year of publishing, they were supposed to be published as newly as possible and as close to each other in time as possible. The works I ended up with were Dimman av allt (2001) and Svart som silver (2008) by Bruno K. Öijer and Silverskåp (2000) and Nu försvinner vi eller ingår (2007) by Birgitta Lillpers. The results of this study show several differences in how poetry is being judged and how poetry reviews are being written are connected with the gender of the poets and the reviewer. Lillpers got 35% less space in the newspapers and Öijers poetry got quoted a lot more which confirms that female poetry often is considered as less important than the male poetry, and that men in general tends to be judged as more professional than woman. The male reviewers tended to express themselves with greater certainty than the female reviewers who held a more professional tone in their reviews and focused more on the technical aspects of the poetry. This confirms the theory of the male words are being looked upon as the truth but contradicts the theory of women writing more based on personal experience and of women being less skilled in language techniques. In conclusion, there are differences in how poetry gets reviewed and how the reviews are written that are connected to the genders of the poet and the reviewer but these differences are complex and does not show a clear normative way of thinking about gender

Fine mapping and replication of QTL in outbred chicken advanced intercross lines

Background: Linkage mapping is used to identify genomic regions affecting the expression of complex traits. However, when experimental crosses such as F2 populations or backcrosses are used to map regions containing a Quantitative Trait Locus (QTL), the size of the regions identified remains quite large, i.e. 10 or more Mb. Thus, other experimental strategies are needed to refine the QTL locations. Advanced Intercross Lines (AIL) are produced by repeated intercrossing of F2 animals and successive generations, which decrease linkage disequilibrium in a controlled manner. Although this approach is seen as promising, both to replicate QTL analyses and fine-map QTL, only a few AIL datasets, all originating from inbred founders, have been reported in the literature. Methods: We have produced a nine-generation AIL pedigree (n = 1529) from two outbred chicken lines divergently selected for body weight at eight weeks of age. All animals were weighed at eight weeks of age and genotyped for SNP located in nine genomic regions where significant or suggestive QTL had previously been detected in the F2 population. In parallel, we have developed a novel strategy to analyse the data that uses both genotype and pedigree information of all AIL individuals to replicate the detection of and fine-map QTL affecting juvenile body weight. Results: Five of the nine QTL detected with the original F2 population were confirmed and fine-mapped with the AIL, while for the remaining four, only suggestive evidence of their existence was obtained. All original QTL were confirmed as a single locus, except for one, which split into two linked QTL. Conclusions: Our results indicate that many of the QTL, which are genome-wide significant or suggestive in the analyses of large intercross populations, are true effects that can be replicated and fine-mapped using AIL. Key factors for success are the use of large populations and powerful statistical tools. Moreover, we believe that the statistical methods we have developed to efficiently study outbred AIL populations will increase the number of organisms for which in-depth complex traits can be analyzed.

Modelling dominance in a flexible intercross analysis

The aim of this paper is to develop a flexible model for analysis of quantitative trait loci (QTL) in outbred line crosses, which includes both additive and dominance effects. Our flexible intercross analysis (FIA) model accounts for QTL that are not fixed within founder lines and is based on the variance component framework. Genome scans with FIA are performed using a score statistic, which does not require variance component estimation. RESULTS: Simulations of a pedigree with 800 F2 individuals showed that the power of FIA including both additive and dominance effects was almost 50% for a QTL with equal allele frequencies in both lines with complete dominance and a moderate effect, whereas the power of a traditional regression model was equal to the chosen significance value of 5%. The power of FIA without dominance effects included in the model was close to those obtained for FIA with dominance for all simulated cases except for QTL with overdominant effects. A genome-wide linkage analysis of experimental data from an F2 intercross between Red Jungle Fowl and White Leghorn was performed with both additive and dominance effects included in FIA. The score values for chicken body weight at 200 days of age were similar to those obtained in FIA analysis without dominance. CONCLUSION: We have extended FIA to include QTL dominance effects. The power of FIA was superior, or similar, to standard regression methods for QTL effects with dominance. The difference in power for FIA with or without dominance is expected to be small as long as the QTL effects are not overdominant. We suggest that FIA with only additive effects should be the standard model to be used, especially since it is more computationally efficient.