Rosebush: Production of a high-quality genome reference sequence, an essential tool for plant breeding

The rosebush is the most important ornamental plant worldwide for its economic, cultural, hedonic and symbolic value. The roses are cultivated all over the world and sold as garden, cutting or potted roses.

In order to better understand important ornamental traits and to accelerate breeding of new rose varieties, it is necessary to have access to a high-quality genome sequence. This new sequence will allow genetic and epigenetic studies to identified key genes controlling ornamental traits such as recurrent blooming, number of petals, thorns, self-incompatibility or resistance to diseases.

Thanks to high-density genetic maps, the genome has been assembled into 7 pseudomolecules, representing the 7 rose chromosomes. The sequence genome has a total size of 512Mbp, representing 551 contigs. The rose genome contains around 44000 genes.

Characterization of the gene controlling the number of petals in rose.
Using this new genome sequence, the scientists were able to identify the gene, which is responsible of the number of petals (difference between simple and double flowers). With the development of a genetic marker that allows to predict the number of petal, the consortium is making freely available to the international community these tools that can be used in assisted marker selection.

Towards more resistant varieties
This new genome is a key resource for the community working on rose breeding. The genome will accelerate the breeding of more resistant rose varieties in order to reduce the use of pesticides. On this thematic, in Angers, scientists study the diversity of rosebush and their differences to identify which genes are involved in foliar disease resistance. A PhD project is also using the new obtained rose sequence to understand how the wild roses are classified, this might allow us to identify new sources of resistance against disease, and in a long term, to better control crosses.

Partnership

The rose genome sequencing was obtained thanks to the financial support of ‘Région des Pays de la Loire’, ANR (National Research Agency), the RFI Objectif Végétal and INRA.

Fabrice Foucher, Research director at INRA, group leader of the GDO team at the unit IRHS, has coordinated the rose international genome sequencing consortium.

Partnership

• INRA, Institut de Recherche en Horticulture et Semences, Angers, France;
• ILVO, Flanders Research Institute for Agriculture, Melle, Belgium;
• University of Angers, Institut de Recherche en Horticulture et Semences, Angers, France;
• Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia;
• Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands;
• ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Belgium;
• Leibniz Universitat, Hannover, Germany;
• Wageningen University & Research, business unit Bioscience, Wageningen, The Netherlands;
• INRA, US 1279 EPGV, Universite Paris-Saclay, F-91000 Evry, France;
• URGI, INRA, Universite Paris-Saclay, 78026, Versailles, France;
• Osaka Institute of Technology, Osaka, Japan;
• Agrocampus-Ouest, Institut de Recherche en Horticulture et Semences, Angers, France

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits
L. Hibrand Saint-Oyant, T. Ruttink, L. Hamama, I. Kirov, D. Lakhwani, N. N. Zhou, P. M. Bourke, N. Daccord, L. Leus, D. Schulz, H. Van de Geest, T. Hesselink, K. Van Laere, K. Debray, S. Balzergue, T. Thouroude, A. Chastellier, J. Jeauffre, L. Voisine, S. Gaillard, T. J. A. Borm, P. Arens, R. E. Voorrips, C. Maliepaard, E. Neu, M. Linde, M. C. Le Paslier, A. Bérard, R. Bounon, J. Clotault, N. Choisne, H. Quesneville, K. Kawamura, S. Aubourg, S. Sakr, M. J. M. Smulders, E. Schijlen, E. Bucher, T. Debener, J. De Riek and F. Foucher
doi: https://doi.org/10.1038/s41477-018-0166-1

Angers, 1st European center for rose research

The “Région Pays de la Loire” is the first area for garden rose production. So, the region has funded on part of the rose genome sequencing project.

In Angers, 60 persons from the research unit IRHS (Institute of Research in Horticulture and Seeds), which gathers persons from INRA, Agrocampus-Ouest and the University of Angers, concentrate their scientific works on rosebush, as a model plant to:

• Characterize the genetic diversity within the genus Rosa and its evolution in response to human practices and natural selection.
• Understand the genetic and environmental determinism of important ornamental traits such as blooming seasonality, plant architecture, number of thorns and resistant to foliar diseases.

The IRHS unit has also established:

• Genetic resources with a progeny with more than 1000 individuals (part of the biological Resource Center ‘Pip Fruits and rose’)
• Knowledge on genetics, genomics, cellular biology, that are internationally recognized.

Moreover in Angers, interdisciplinary approaches in long-time collaboration with historians, economists, mathematicians, sociologists and geographers have been developed and strengthened the expertise in rose.