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Rose, as many other important ornamental, vegetable and field crops, is polyploid. This poses constraints in genetic analyses due to the occurrence of multiple alleles at marker and trait loci and the existence of multiple allele dosages. Developments in marker discovery (next generation sequencing), detection (SNP arrays) and analysis (software for dosage scoring) now make it feasible to develop high-density molecular marker maps for the homologous chromosomes in tetraploids separately, and thus perform QTL analysis in tetraploids. We developed a SNP array for rose to develop genetic maps in tetraploid garden roses and cut roses, which are to be used for inheritance studies and genetic mapping. Here we have indicated the general strategy followed for developing a SNP array and for scoring and using the SNP data generated, and elaborated on the activities undertaken to use the WagRhSNP Axiom array in rose. The array design is not proprietary but can be used by all researchers working in rose

Rose is one of the most economically important ornamental crops worldwide. Rosa sp. can become a model for woody ornamentals. Its genome size is relatively small (560 Mb), its genetic history with ploïdy events is well documented, and rose has a short life for a woody plant. Furthermore, different tools are available, including transcriptomic tools, genetic maps and genetic transformation protocols. Rose represents an original model for studying some ornamental traits that cannot be addressed in other model plant species such as Arabidopsis. Some of these traits, such recurrent blooming, flower morphogenesis or scent production and emission, are of economic interest. Different groups involved in rose genetics and genomics gathered to form the ‘Rose Genome Sequence Initiative’. Our objective is to obtain a high quality rose genome sequence of the diploid R. chinensis ‘Old Blush’. One important issue is the high level of heterozygosity of roses. To tackle this issue, different strategies are proposed: production of a haploid and development a high density genetic map to anchor the genome. This genetic map will be developed from a cross between ‘Old Blush’ and R. wichurana. The genotype R. chinensis ‘Old Blush’ will be sequenced using NGS technologies. The data will be assembled and arranged using the high-density map. In order to increase ESTs and to facilitate genome annotation, we have recently produced ESTs from various tissues of ‘Old Blush’ under different conditions. Digital expression (RNA Seq) was obtained from the different tissues and data are available on the following web site (https:// iant.toulouse.inra.fr/plants/rosa/FATAL/). The rose genome sequence will be a great step to help identifying the molecular basis of ornamental traits and also to study genetic diversity and genome evolution in the genus Rosa and in the Rosaceae family

In order to develop a versatile and large SNP array for rose, we set out to mine ESTs from diverse sets of rose germplasm. For this RNA-Seq libraries containing about 700 million reads were generated from tetraploid cut and garden roses using Illumina paired-end sequencing, and from diploid Rosa multiflora using 454 sequencing. Separate de novo assemblies were performed in order to identify single nucleotide polymorphisms (SNPs) within and between rose varieties. SNPs among tetraploid roses were selected for constructing a genotyping array that can be employed for genetic mapping and marker-trait association discovery in breeding programs based on tetraploid germplasm, both from cut roses and from garden roses. In total 68,893 SNPs were included on the WagRhSNP Axiom array. Next, an orthology-guided assembly was performed for the construction of a non-redundant rose transcriptome database. A total of 21,740 transcripts had significant hits with orthologous genes in the strawberry (Fragaria vesca L.) genome. Of these 13,390 appeared to contain the full-length coding regions. This newly established transcriptome resource adds considerably to the currently available sequence resources for the Rosaceae family in general and the genus Rosa in particular.