The rose genome deciphered: from the origin of modern roses to the characteristics of their blooms

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Rosa chinensis

Rosa chinensis

The rose: an ornamental plant emblematic of the cultural and economic history of mankind. An international consortium involving INRA, ENS de Lyon, CEA, CNRS and Université Claude Bernard Lyon 1, has deciphered the genome of the rose. This work has enabled them to trace the respective contributions of European and Chinese roses to the genome of modern plants, and identify all the genes involved in the pathways for the biosynthesis of perfume and colour. Published on 30 April 2018, these findings are essential to the breeding of new varieties that will notably optimise flower qualities in a context of global change.

Celebrated since Antiquity by numerous artists, appreciated for the perfume and beauty of its blooms, the rose is now the most widely purchased cut flower in France, while roses are essential ornamental plants in our gardens and on our balconies, the result of innumerable crosses and hybridisations. Thanks to an international consortium1 involving INRA, ENS de Lyon, CEA, CNRS and Université Claude Bernard Lyon 1, the genome of the rose has now been deciphered; an essential step towards understanding its biology and the origins of its diversity.

A high quality reference genome that informs evolution of the Rosaceae family

Eight years of effort, combined with the most innovative strategies and tools, enabled them to sequence and decipher the genetic information carried by the seven pairs of chromosomes in Rosa chinensis ’Old Blush’ and to annotate all its 36,377 genes, thus constituting a reference genome for the Rosa genus.
Comparison of this genome of the Rosa genus with those of other plants in the Rosaceae family (strawberry, raspberry, apple, pear peach, plum, etc.) showed that the rose, strawberry and raspberry are evolutionarily very close, and enabled a reconstitution of the history of the rose within the Rosaceae family.

The origins of modern roses explained

The scientists studied the origin of the chromosomes in the hybrid ’La France’ rose obtained in the Lyon region in 1867. This hybrid combines the vigorous growth of European species with the recurrent blooming of those from China. To achieve this, they projected onto the reference genome the genomic data concerning the main varieties of roses originating from Europe, the Middle East and China, which all contributed to domestication of the rose. They thus identified the origin of the genes implicated in defining the traits most appreciated in modern roses, such as recurrent blooming, which is mainly of Chinese origin.

Blooming, perfume and colour: genes identified and biosynthetic pathways reconstructed

The team identified the principal genes involved in blooming, flower development, reproduction, fragrance and the synthesis of pigments giving rise to red tints (anthocyanin family). They reconstituted the biosynthetic pathways in which these genes intervene. In particular, they demonstrated a group of genes implicated in regulating both the colour and perfume of flowers.

This work provides solid foundations to untangle the molecular and genetic mechanisms which govern the traits of roses and their diversity. In the longer term, they will contribute to accelerating the breeding and improved quality of this queen of flowers. This knowledge will also be of considerable value when studying other species in the Rosaceae family and other ornamental plants.

Central to the technique

The scientists chose to study Rosa chinensis ’Old Blush’, originating from China and an important ancestor of the modern rose varieties that bloom several times each year.
In the rose, differences between the chromosomal sequences inherited from the two parents complicate the sequencing of genomic fragments identified by sequencing robots. The scientists therefore combined two approaches :
o A cell culture strategy to obtain a rose with a genome in which each gene came from a single parent;
o A high-throughput sequencing strategy using one of the most recent robots (PacBio type) which generates sequences that are much longer than those produced by previous technologies, thus facilitating their assembly and the reconstitution of chromosomes.

1 involved in the research: UMR Reproduction et développement des plantes (INRA, CNRS, ENS de Lyon, Univ. Claude Bernard Lyon 1); Laboratoire des Interactions plantes-microorganismes (INRA, CNRS); UMR Biométrie et biologie évolutive (Univ. Claude Bernard Lyon 1, CNRS); UMR Ecologie des hydrosystèmes naturels et anthropisés (Univ. Claude Bernard Lyon 1, ENTPE, CNRS, INRA); Institut des Sciences des plantes de Paris-Saclay (CNRS, Univ. Paris-Sud, INRA, Univ. Evry, Univ. Paris-Diderot); le Genoscope, CEA; le Laboratoire de Biotechnologies végétales appliquées aux plantes aromatiques et médicinales (Univ. Jean Monnet, CNRS); l’UR Genomique-Info, INRA; UMR Génétique, diversité et écophysiologie des céréales (INRA, Univ. Clermont-Auvergne); Institut méditerranéen de la biodiversité et d’écologie marine et continentale (Univ. Aix Marseille, CNRS, IRD, Univ. Avignon et Pays du Vaucluse); Institut de Biologie moléculaire des plantes, CNRS; Key Laboratory of Horticultural Plant Biology (Huazhong Agricultural University, China); Institute of Vegetables and Flowers (CAAS, China); The Center for Plant Molecular Biology (Univ. Tübingen, Germany).

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