Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 538539
Title A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits
Author(s) Hibrand Saint-Oyant, L.; Ruttink, T.; Hamama, L.; Kirov, I.; Lakhwani, D.; Zhou, N.N.; Bourke, P.M.; Daccord, N.; Leus, L.; Schulz, D.; Geest, H. van de; Hesselink, T.; Laere, K. Van; Debray, K.; Balzergue, S.; Thouroude, T.; Chastellier, A.; Jeauffre, J.; Voisine, L.; Gaillard, S.; Borm, T.J.A.; Arens, P.; Voorrips, R.E.; Maliepaard, C.; Neu, E.; Linde, M.; Paslier, M.C. Le; Bérard, A.; Bounon, R.; Clotault, J.; Choisne, N.; Quesneville, H.; Kawamura, K.; Aubourg, S.; Sakr, S.; Smulders, M.J.M.; Schijlen, E.; Bucher, E.; Debener, T.; Riek, J. De; Foucher, F.
Source Nature Plants 4 (2018). - ISSN 2055-026X - p. 473 - 484.
DOI https://doi.org/10.1038/s41477-018-0166-1
Department(s) Laboratory of Plant Breeding
PRI BIOS Applied Bioinformatics
PRI BIOS Applied Metabolic Systems
WUR Plant Breeding
EPS
WUR PB Siergewassen, Tissue Culture
PE&RC
WUR PB Kwantitatieve Aspecten
PBR Kwantitatieve Aspecten
WUR PB Biodiversiteit en Genetische Variatie
Publication type Refereed Article in a scientific journal
Publication year 2018
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.

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