DS0502 - Enjeux agroalimentaires

A NGS APPROACH TO STUDY PLANT SEX CHROMOSOMES – NGSex

Submission summary

Despite the importance of plants with separate sexes (= dioecious) for studying the evolution of sex chromosomes and sex determination, and the existence of many dioecious crops for which knowledge on sex chromosomes and sex determination is of crucial economical importance, little is known about plant sex chromosomes. Sequencing of a Y chromosome from a plant (or any other organism) indeed remains one of the greatest challenges of current genomics due to the abundance of repeats in the Y chromosomes.
Several unconventional strategies have been recently developed, including one relying on RNAseq data from different male and female individuals, which is cheap and particularly useful for organisms without a reference genome or any other genomic resources at disposal. We have contributed to the development of this strategy and applied it on the dioecious plant Silene latifolia, which allowed the identification of hundreds of novel genes on the X/Y chromosomes (= sex-linked genes) in this species. This methodological effort was however very empirical and specific to our S. latifolia dataset. Despite its high potential this strategy is currently limited by the absence of a tool to identify the sex-linked genes in the RNAseq data in any organism.
Here we propose to complete the development of such a tool (SEX-DETector) that we have started. SEX-DETector, contrary to previous tools, relies on a probabilistic model accounting for genotyping errors and estimates the probabilities of a gene being sex-linked or autosomal. A first version of SEX-DETector has been implemented and tried on real and simulated data, which indicate our tool is performing well. We want to make SEX-DETector accept any kind of RNAseq data (from parents+F1s and also from individuals from an inbred or a natural population) and we want to imbed it in a Galaxy workflow to make its use easy by anyone. We then propose to apply SEX-DETector to other dioecious Silene species to conduct a comparative study of sex chromosome evolution in this genus, in particular taking advantage of the existence of three independent dioecious systems of different ages in Silene. Finally, we want to apply SEX-DETector to three other dioecious systems: (i) Coccinia grandis -a close relative of melon and cucumber- where we have a chance to identify the first sex-determining genes in a dioecious plant, (ii) palm trees, which have unusually old sex chromosomes for plants and where identifying sexual markers is of agronomical importance, and (iii) Amborella, the most basal angiosperms, for which studying dioecy will have important implications for inferring the breeding system of all-extant-angiosperm ancestor.
All these data will provide an unprecedented comparative framework. Novel findings and a broad view on plant sex chromosomes and sex determination are to be expected. Our tool is also expected to be useful for the improvement/management of dioecious crops. For this project, we require RNAseq data in all these systems, postdocs for the bioinformatics/evolutionary analysis and also technical personnel and resources for some follow-up experimental studies. The consortium includes several leading French labs working on plant sex chromosomes and sex determination: G. Marais (Lyon), P. Touzet (Lille), A. Bendahmane (Evry), C. Scutt (Lyon) and F. Aberlenc/J. Tregear (Montpellier). A total budget of ~500,000 € is requested.

Project coordinator

Monsieur Gabriel Marais (Laboratoire Biométrie et Biologie Evolutive)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.

Partner

LBBE - CNRS Laboratoire Biométrie et Biologie Evolutive
GEPV Laboratoire de Genetique et Evolution des populations Vegetales
INRA Unité de recherche en génomique végétale (URGV) Evry
RDP Laboratoire de Reproduction et Développement des Plantes
IRD - UMR DIADE INSTITUT DE RECHERCHE POUR LE DEVELOPPEMENT

Help of the ANR 499,999 euros
Beginning and duration of the scientific project: September 2014 - 42 Months

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