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PhD offer | Local Adaptation and Climate change : genetic end epigenetic factors in small ruminants

par Webmaster - 17 février 2016 ( dernière mise à jour : 8 mars 2016 )

To apply, contact before March 20th 2016

Since the time of their domestication, 10,000 years ago in the Middle East, sheep (Ovis aries) and goats (Capra hircus), have spread all over the world, evolving in a large variety of locally adapted populations in response to human and environmental forcing. Local populations have gradually accumulated several traits making them well adapted to extremely contrasted environmental conditions (climate, topography, biotic interactions involving pathogens or symbionts, etc.). These two species constitute textbook models for depicting the mechanisms underlying the adaptation to local conditions, and their congruence in closely related species. The recent developments of Next Generation Sequencing methods allowed the production of Whole Genome Data and lead to the discovery of more and more candidate genes involved in the adaptation of a variety of species. However, many questions should still be addressed for a global understanding of adaptive mechanisms.
Our group is producing hundreds of whole genome data for identifying genomic regions involved in the domestication process of sheep and goat, from the initial steps of domestication (by comparing domestic animals to their closely related wild relatives) to the most recent apparition of adaptive mechanisms (by comparing animals living in diversified environments). These adaptations result from the selection of genome variants (SNPs, structural variations) involving genic but also intergenic regions, what questions the relative importance of the selection of genes vs. regulatory sequences in the set up of adaptive responses. Moreover, it is now admitted that epigenetic marks, such as DNA methylation, contribute to the variation of ecological traits under selection, for instance by controlling gene expression. Then epigenetic regulation might interfere with the selection of genetically inherited variations in shaping adaptive traits. To address this question, we are also characterizing the variation of genomic patterns of DNA-methylation in relation to different climatic condition.

The objective of this project is to characterize the mechanisms of adaptation to environmental factors that vary in the context of global changes. The PhD student will have to :
- characterize the mechanisms of local adaptation by identifying genomic regions harbouring signatures of selection related to environmental factors (e.g. variation of abiotic and possibly biotic conditions)
- test the congruence of adaptive mechanisms among species (ie. sheep/goat comparisons) and/or within species (i.e., breed comparisons)
- evaluate the spatial distribution of adaptive and its predicted shift in relation to scenarios of climate change.
- Evaluate the possible impact of epigenetic variations by characterizing Differentially Methylated Regions of genomes coming from contrasted environments.

In the frame of EU projects (NextGen and ClimGen) and French projects (France Génomique, AGIR), we have been producing several hundreds of whole genome data in dozens of sheep and goat breeds for which metadata are available (e.g., climate, topography, …). Moreover, we are producing MeDipSeq data for characterizing methylation patterns at the whole genome scale. Thus, a core set of data is already available.

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