Abstract
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. Our 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. We produced a doubled haploid rose line (‘HapOB’) from Rosa chinensis ‘Old Blush’ and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1–96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also 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.
Highlights
Rose is the world’s most important ornamental plant, with economic, cultural and symbolic value
Using a combination of genomic and genetic approaches (F1 progenies and genome-wide association study (GWAS) diversity panel), we have demonstrated 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 (Fig. 4)
We propose that a rose APETALA2/TOE homologue controls the switch from simple to double flower and, unexpectedly, the number of petals within double flowers
Summary
Rose is the world’s most important ornamental plant, with economic, cultural and symbolic value. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It 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. Roses are used for scent production and for culinary purposes[3] Despite their genetic complexity and lack of biotechnological resources, rose represents a model for ornamental plant species, allowing the investigation of traits such as bloom seasonality or flower morphology. Completeness measures suggest that the assembly is fairly complete in terms of the gene space covered, it is highly fragmented (83,189 scaffolds, N50 of 90 kb)
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