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An International consortium of more than 30 research institutes, coordinated by scientists at INRA and CEA-Genoscope and associating CNRS and University of Evry, just succeeded in deciphering the complex genome of the recent oilseed rape1 (Brassica napus L, also known as rapeseed, rape or canola), the most important oilseed crop in Europe, Canada, and Australia. This scientific breakthrough paves the way to a fundamental understanding of the origins of crop species through polyploidy (consisting in inter-species hybridization and association of several genomes) and provides a foundational resource for accelerating on-going breeding efforts in the crop. This work is published in Science on 22 August 2014.
A breakthrough achievement
In the framework of the Seq-Poly-Nap project, primarily financed by the French National Research Agency (ANR), scientists from INRA, CEA (Genoscope), CNRS, and University of Evry, in collaboration with International teams, achieved the sequencing of the reference genome of oilseed rape, along with genomes of a collection of varieties representing the diversity of the species. A reference genome is the assembled and ordered sequences of all genes, which will be invaluable for future research on the genetics of the species."The main difficulty for oilseed rape has been to differentiate its different sub-genomes. This has been achieved by the development of an original sequencing strategy, bioinformatics tools and the analysis of duplicated gene expression and their regulation", says Boulos Chalhoub who coordinated the research and federated research efforts within the International consortium.
It is the first time that a recent polyploid genome has been completely sequenced and compared to those of its relative parental species, the Mediterranean cabbage and Asian turnip (for which INRA contributed to the recent deciphering of their genomes).
Oilseed rape: a champion of recurring genome duplication
Researchers have shown that apart from the post-Neolithic hybridization that led to its formation, oilseed rape holds one of the most highly duplicated genome of all flowering plants (Angiosperms), because of numerous older polyploidizations that occurred during its evolution. This recurring phenomenon led to the accumulation of a great number of genes, 101,000 in total, the highest gene densities of any previously sequenced organism, more than four times more than the 20,000-25,000 genes of humans.
Subtle cohabitation and "cross-talk" between constituent sub-genomes
Because all flowering plants originated from polyploidization events, but in most cases millions of years ago, the post-Neolithic rapeseed genome provides unique insight into the early evolutionary processes of plant speciation. Interestingly, in its first few thousand years,
B. napushas retained almost all of the genes of its two parental species. Scientists report that most of the genes in rapeseed are duplicated; in other words genes exist in two copies, with similar to almost identical sequences. Almost all these duplicated genes jointly participate in gene function."We suggest that duplicated genes are an important reservoir for diversification, emergence of new functions, adaptation and improvement of the species", says Boulos Chalhoub."
This "cross-talk" also occurs through exchanges of genes or DNA between the two rapeseed sub-genomes. Chalhoub explains"Thus, for a duplicated gene, normally present on both sub-genomes, one copy can be replaced by the sequence of its counterpart from the other sub-genome". The mechanisms at work and the selective advantages still need to be determined, though it has already been shown that this phenomenon leads to diversification.
A unique resource for rapeseed improvement
Rapeseed is a fairly recent species with high potential for genetic improvement."The sequencing of the genome is a unique resource in the world and offers great opportunities to identify genes of agronomic interest and rapidly use them in breeding programs", predicts Chalhoub. It would therefore be possible to improve the content and composition of oil, resistance to pathogens, tolerance to cold, yield, or even nitrogen use efficiency.
Numerous projects referring to this resource for a sustainable agriculture are underway, notably at INRA.
 Oilseed rape is considered a recent species since its formation dates from the post-Neolithic era, around 5,500 B.C.
Boulos Chalhoub, France Denoeud, Shengyi Liu, Isobel A. P. Parkin, Haibao Tang, Xiyin Wang, Julien Chiquet, Harry Belcram, Chaobo Tong, Birgit Samans, Margot Corréa, Corinne Da Silva, Jérémy Just, Cyril Falentin, Chu Shin Koh, Isabelle Le Clainche, Maria Bernard, Pascal Bento, Benjamin Noel, Karine Labadie, Adriana Alberti, Mathieu Charles, Dominique Arnaud, Hui Guo, Christian Daviaud, Salman Alamery, Kamel Jabbari, Meixia Zhao, Patrick P. Edger, Houda Chelaifa, David Tack, Gilles Lassalle, Imen Mestiri, Nicolas Schnel, Marie-Christine Le Paslier, Guangyi Fan, Victor Renault, Philippe E. Bayer, Agnieszka A. Golicz, Sahana Manoli, Tae-Ho Lee, Vinh Ha Dinh Thi, Smahane Chalabi, Qiong Hu, Chuchuan Fan, Reece Tollenaere, Yunhai Lu, Christophe Battail, Jinxiong Shen, Christine H. D. Sidebottom, Xinfa Wang, Aurélie Canaguier, Aurélie Chauveau, Aurélie Bérard, Gwenaëlle Deniot, Mei Guan, Zhongsong Liu, Fengming Sun, Yong Pyo Lim, Eric Lyons, Christopher D. Town, Ian Bancroft, Xiaowu Wang, Jinling Meng, Jianxin Ma, J. Chris Pires, Graham J. King, Dominique Brunel, Régine Delourme, Michel Renard, Jean-Marc Aury, Keith L. Adams, Jacqueline Batley, Rod J. Snowdon, Jorg Tost, David Edwards, Yongming Zhou, Wei Hua, Andrew G. Sharpe, Andrew H. Paterson, Chunyun Guan, Patrick Wincker "Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome". Science 22 August 2014 Vol. 345 no. 6199 pp. 950-953 DOI: 10.1126/science.1253435
CEA is a French government-funded technological research organisation in four main areas: low-carbon energies, defense and security, information technologies and health technologies. A prominent player in the European Research Area, it is involved in setting up collaborative projects with many partners around the world.