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Genomics of Brassica species

Genomics of Brassica species

Research

Context and Issues

Brassica species have undergone four to five successive rounds of whole genome duplications (polyploidy) since the origin of angiosperms. Two recent ploidy events occurred in the genus Brassica since its divergence with the Arabidopsis lineage (~13-17 MYA). Within Brassica, the hybridization between the two diploid species, B. rapa (AA, 2n=20) and B. oleracea (CC, 2n=18), and its genome doubling gave rise (1000 to 8000 years ago) to the natural oilseed rape (B. napus, AACC, 2n=38), which has a polyphyletic origin. For several years, we have developed dense genetic maps of oilseed rape. The recent availability of the allotetraploid B. napus (Chalhoub et al. 2014) and its diploid progenitor genomes (B. rapa: Wang et al. 2011; B. oleracea: Liu et al. 2014) as well as the constant progress in Next Generation Sequencing technologies now offer the opportunity to elucidate very precisely the evolution of their genome organization and their gene expression.

Objectives 

Elucidate the structural and functional evolution of the allotetraploid B. napus genome by comparison with its diploid progenitors, with a particular emphasis on the evolution of duplicated regions of interest (e.g. involved in the resistance to various pathogens).

Methodology

Genetic and epigenetic analyses of the polyploid B. napus and of its two progenitors. These data will be completed by sequencing and functional analyses of diploid varieties, of corresponding synthetics B. napus and of several pure lines of B. napus.

Main Results

  • Development of an international reference map (Wang et al. 2011)
  • Contribution to B. rapa (Wang et al. 2011) and B. napus (Chalhoub et al. 2014) sequencing projects 

Partners

UMR URGV, Evry
UMR GDEC, Clermont Ferrand
International consortium for Brassica genome sequence

Funding and Support

ANR Seq Polynap (2009-2012) (P.I.: B. Chalhoub)
Sofiprotéol (2009-2012)
ERA CAPS Evo-Genapus (2014-2016)
France Génomique PolySuccess (2014- )

Publications

Chalhoub B., …, Just J., Falentin C., …, Lassalle G., Schnel N., ..., Deniot G., …, Delourme R., Renard M. et al.. (2014). Early allopolyploid evolution in the post-neolithic Brassica napus genome. Science 345 : 950-953.

Wang J, Lydiate DJ, Parkin, Falentin C, Delourme R, Carion PWC,  King GJ. (2011) Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa. BMC Genomics 12:101.

Wang, X., …Chalhoub, B., …G., Lassalle, …H., Belcram, …Just, J., et al. (2011) The genome of the mesopolyploid crop species Brassica rapa. Nat Genet 43, 1035-1039.

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