Next Generation Sequencing reveals reference genome sequence for the rose

Published on
June 28, 2018

Researchers have produced a high-quality reference rose genome sequence that will represent an essential resource for the rose community and also for rose breeders. Using this new reference sequence, important structural features of the genome were analysed. Plant researchers from Wageningen contributed to this research with work using Next Generation Sequencing techniques on Shared Research Facilities’ Illumina HiSeq en PacBio Sequel.

The HiSeq works on the concept of sequencing by synthesis produces sequence reads up to 250 base pairs long derived from billions of surface-amplified DNA fragments simultaneously. The PacBio Sequel system rapidly and cost-effectively generates high-quality whole genome de novo assemblies and also full length whole transcriptome analysis for alternative splice variant detection projects.

The rose study: a new reference

The rose is the world’s most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels.

The objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. Rosa 'Old Blush' is a China rose, and generally accepted as the first East Asian rose cultivar to reach Europe.

The researchers showed that this new reference sequence can be used to analyse loci controlling ornamental traits, such as continuous flowering, double flower, self-incompatibility and prickle density. This study will accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.