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Tache 1

Tache 1. Construction d’un simulateur. Objectifs.

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Tache 1

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  1. Tache 1 Construction d’un simulateur

  2. Objectifs Disposer d’un simulateur d’une population présentant un déséquilibre de liaison historique, afin d’évaluer les propriétés distributionnelles de statistiques de test préexistantes ou développées dans le cadre de R&T, ainsi que l’efficacité de protocoles expérimentaux.

  3. L’engagement • Programme: Starting from existing elements - LDSO, a simulator developed by F Ytournel during her thesis (Ytournel et al (2008)) ; routines developed by F Guillaume during his thesis on the dairy cattle MAS programme – a more versatile simulation program will be developed. The software aims at generating a population of individuals similar (in terms of pedigree, and, when needed of genotypes at markers) to an existing one. The founders of this population show Linkage Disequilibrium generated by a history of mutations, selection, crosses and drift (this history being parameterized by the user). All potential causes of LD are thus represented. The population history is simulated in two steps: from the origins (generation 0) to the first individuals belonging to the known pedigree (generation N), and from founders in generation N up to the last generation N+n (from which are chosen phenotyped individuals which are the support of the QTL detection design)

  4. Les moyens • Partners’ contribution: ST and DR will be in charge of the practical work (which will be a part of their thesis); JME and AR will supervise from their expertise in genetics and computing sciences; FG (and F Ytournel, now post doc in Germany, who kindly accepted to contribute) will provide their software resources and know how. • Methods:The programming language will be FORTRAN 90, still largely used in our field, and corresponding to the elements already existing • Risks and solutions: The only risk for this type of work is a delay as compared to the planed calendar. Extra force (from JME, AR and FG) will be put on the task if this risk occurs..

  5. En gros c’est fini • Travail Florence, Simon et Dana • Publication (et droit de référence à R&T ?) • Mais on devrait pouvoir faire mieux ? • Quels besoins ? • Epistasie • Historique avec plus de deux lignées • Autres ? • Quelles démarches ? • Approche par coalescence (Bertrand) • Approche intra génotype

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