A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

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.

Fig. 1. Development of the HapOB haploid line from R. chinensis ‘Old Blush’.

a, The R. chinensis variety ‘Old Blush’ painted by Redouté in 1817. Paul Fearn/Alamy Stock Photo. b, A flower from the R. chinensis variety ‘Old Blush’. c, A cross-section of the floral stage used for the anther culture. d, DAPI staining on mid-to-late uninucleate microspores. Similar results were observed on more than 15 microspores in one experiment. e, The HapOB callus was obtained after the anther culture at the appropriate stage and used for genome sequencing.

Fig. 2. Identification of centromeric regions in the HapOB reference genome.

a, The cluster CL226 identified by RepeatExplorer. b, Agarose gel electrophoresis of tandem repeat fragments amplified from the genomic DNA of HapOB using OBC226 PCR primers (right lane) along with the lambda-PstI size ladder (left lane). Similar results were obtained in two independent experiments. c, FISH with carboxy tetramethylrhodamine (TAMRA)-labelled OBC226 oligo probes on R. chinensis metaphase chromosomes. Chromosome numbers are labelled from 1 to 7. Similar results were observed in at least 10 metaphase cells in two independent experiments. d, Circos representation of the distribution of OBC226 (purple), the pericentromeric region (blue), Ty3/Gypsy (orange) and Ty1/Copia repeat elements (green) along the seven pseudo-chromosomes and Chr0 (scale in Mb).

Fig. 3. Resequencing of eight Rosa species.

a, The phylogenetic relationships of the eight sequenced Rosa species and the reference genome HapOB, using a genome-wide set of homozygous SNPs. b, Analysis of genetic diversity in eight species of the Rosa genus along the seven pseudo-chromosomes of the HapOB reference sequence. Circles from outside to inside show: gene density (red), transposable element density (green), SNP density for R. xantina (purple), R. chinensis var. spontanea (yellow), R. gallica (blue), R. laevigata (light green), R. moschata (light orange), R. rugosa (light purple), R. persica (light red) and R. minutifolia alba (light blue). Scales are in Mb.

Fig. 4. A region at the end of Chr3 controls important ornamental traits.

a, Major genes and QTLs that control continuous flowering, double flower, self-incompatibility and prickle density are shown together with candidate genes for each trait. Detailed analyses per locus are described in Supplementary Figs. 5, 7, 9 and 10, respectively. For prickle density in OW progeny (OW2017 and OW2016), the boxes represent the 1-LOD (log of the odds ratio) interval and the lines the 2-LOD interval. b,c, GWAS analysis showing the P values of the association between SNPs positioned along Chr3 and the number of petals, indicating regions that control the number of petals. The petal number is considered as a qualitative trait (simple versus double flowers; GLM) (b) or as a quantitative trait (MLM) (c). The horizontal red line shows Bonferroni-corrected significance levels (1.78 × 10^–6). Other significant associations detected by GWAS are shown in Supplementary Fig. 12. n = 96 cultivars with 3 flowers scored by cultivar. d,e, QTL analysis for prickle density in two F1 progenies using the OW mapping population based on scoring from 2016 and 2017, n = 151 individuals (d), and the YW mapping population, n = 174 individuals (e). Lod, log likelihood ratio.