Rose bush: reaching a very high-quality genome

An international consortium led by a team from Angers from the Research Institute for Horticulture and Seeds (IRHS) have reached a genome of the rose bush of a very high quality. This opens up new perspectives in terms of the creation of varieties, thanks in particular to the identification of genes involved in the number of petals or the density of thorns. The results of this research, involving members of the UA, were published in the prestigious magazine Nature Plants on 11 June 2018.

One year after delivering an apple genome, the IRHS is once again attracting the attention of the scientific community. Bringing together 40 researchers from France, Belgium, Germany, the Netherlands, Russia and Japan, a consortium coordinated by Fabrice Foucher, head of the Genetics and Diversity of Ornamental Plants team at the IRHS, has just shared a very high quality rose genome, with a full 44,481 genes. Coming as the result of long term research.

Latifa Hamama, Laurence Hibrand-Saint-Oyant, Fabrice Foucher, Jérémy Clotault and other researchers focused on one variety, Rosa chinensis "Old Blush"The idea was discussed at an international meeting in 2007. « But we were stuck on technical obstacles », recalls Fabrice Foucher. Progress in bioinformatics and breakthroughs in the field of DNA sequencing have made it possible for the project to take off in 2012.

To achieve its goals, the IRHS relied on the experimental rose garden at the Campus du Végétal (The Vegetal Campus), which is unique worldwide for the type of crossbreeding it hosts. Researchers focused on one variety, Rosa chinensis 'Old Blush'. Of Chinese origin, it was introduced to Europe three centuries ago and is the source of many modern varieties. Another interest: it includes "only" a double set of chromosomes, two lots, one of paternal origin, the other maternal of 7 chromosomes each (14, compared to 70 for some roses)..

A giant jigsaw puzzle

Instead of reconstructing the two genomes of paternal and maternal origin, the researchers focused on a single genome, a mosaic resulting from the paternal and maternal lots. « We obtained 512 million letters A, C, G, and T which had to be put back in the right order », sums up Fabrice Foucher, A, C, G and T representing adenine, cytosine, guanine and thymine.

The reconstruction of the « jigsaw puzzle », the sequencing, made it possible to form 551 fragments, using almost 95% of the letters. By using a genetic map with a high density of molecular markers, it was possible to group these fragments into 7 pseudo-molecules, representing the 7 chromosomes of the rose bush.

Concrete applications

Knowledge of the rose's genetic material « will enable us to make much more rapid progress in research, and will in particular accelerate our understanding of the characteristics expressed by the rosebush », Fabrice Foucher explains.

Already in the course of their work, scientists have identified the gene responsible for duplicating (which determines the number of petals or whether a rose will produce single or double flowers) and the gene controlling the density of thorns. With the consortium, « we have developed tools that enable breeders to know very quickly, based on DNA extraction, whether the rose plant they have just created will produce single or double flowers », explains Laurence Hibrand-Saint-Oyant, research engineer and joint-author of the publication in Nature Plants magazine.

Towards more disease-resistant varieties

Researchers in Angers are now focusing on identifying the genes involved in disease resistance, in particular the black spots of the rose bush. The aim is to enable the creation of more resistant varieties and thus reduce the use of pesticides.

Another study is in progress, in connection with obtaining this high-quality genome. Led by Jérémy Clotault, senior lecturer at the University of Angers, who also co-signed the paper, it aims to understand how wild Rosebushes are classified (around 150 species worldwide) and, beyond that, to understand the genetic evolution of roses as a plant. Here too, research could help identify new sources of disease resistance.

« In perfect connection with the local area »

The consortium's work is « in perfect connection with the local area which is strongly involved in horticultural production », recalls Jean-Pierre Renou, Head of the IRHS.

The Pays de la Loire region is the leading producer of garden roses. The project has received strong financial support from Regional Council but also fromThe National Research Agency (ANR), the RFI program Objectif Végétal and the Inra.

Angers Télé devoted a report to this research. Watch again here (from 4'30''):