1. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits
- Author
-
Hibrand Saint-Oyant, L., Ruttink, T., Hamama, L., Kirov, I., Lakhwani, D., Zhou, N. N., Bourke, P. M., Daccord, N., Leus, L., Schulz, D., Van de Geest, H., Hesselink, T., Van Laere, K., 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., Le Paslier, M. C., 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., De Riek, J., Foucher, F., Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institute for Agricultural and Fisheries Research (ILVO), Institute for Agricultural and Fisheries Research, Russian State Agrarian University - Moscow Agricultural Academy named after K.A. Timiryazev, Wageningen University and Research Centre [Wageningen] (WUR), Leibniz Universität Hannover [Hannover] (LUH), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Unité de Recherche Génomique Info (URGI), Osaka Institute of Technology (OIT), ANR-13-BSV7-0014,DODO,Identification et caractérisation des mutations DOMINANT DOUBLE (DODO) and DOUBLE FLOWER (DF) chez le pétunia et la rose(2013), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Research Institute for Agricultural, Fisheries and Food (ILVO), Wageningen University and Research [Wageningen] (WUR), Osaka Institute of Technology = Osaka Kogyo Daigaku (OIT), CEA-IG/CNG, ‘Région Pays de la Loire’ (Rose Genome Project, Genorose project in the framework of RFI ‘Objectif Végétal’, EPICENTER ConnecTalent grant of the Pays de la Loire), ANR [ANR-13-BSV7-0014], JSPS [JSPS KAKENHI no.17H04616], German Ministry of Economic Affairs (Aif programme ZI), Deutsche Forschungsgemeinschaft [DFG program GRK1798], TTI Green Genetics, TKI Polyploids projects [BO-26.03-002-001, BO-50-002-022], AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Leibniz Universität Hannover=Leibniz University Hannover, Cliquet, Catherine, and Blanc 2013 - Identification et caractérisation des mutations DOMINANT DOUBLE (DODO) and DOUBLE FLOWER (DF) chez le pétunia et la rose - - DODO2013 - ANR-13-BSV7-0014 - Blanc 2013 - VALID
- Subjects
Male ,GENUS ROSA ,Arabidopsis ,Haploidy ,TETRAPLOID ROSE ,Laboratorium voor Plantenveredeling ,Genome structure ,PBR Siergewassen, Tissue Culture ,[SDV.BV] Life Sciences [q-bio]/Vegetal Biology ,[SDV.SA.HORT]Life Sciences [q-bio]/Agricultural sciences/Horticulture ,In Situ Hybridization, Fluorescence ,Phylogeny ,PBR Kwantitatieve aspecten ,food and beverages ,PBR Ornamentals, tissue culture and gene transfer ,Agriculture ,Genomics ,PE&RC ,READ ALIGNMENT ,ddc:580 ,BIOS Applied Metabolic Systems ,PBR Biodiversity and genetic variation ,Genome, Plant ,Agricultural genetics ,GENES ,SELF-INCOMPATIBILITY ,Centromere ,Quantitative Trait Loci ,Flowers ,Rosa ,Fragaria ,Synteny ,Article ,Chromosomes, Plant ,PBR Quantitative aspects of Plant Breeding ,BIOS Applied Bioinformatics ,PBR Biodiversiteit en Genetische Variatie ,[SDV.SA.HORT] Life Sciences [q-bio]/Agricultural sciences/Horticulture ,Quantitative Trait, Heritable ,Genetics ,Humans ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,Life Science ,FLOWER DEVELOPMENT ,Konferenzschrift ,Genetic association study ,Indoleacetic Acids ,Arabidopsis Proteins ,fungi ,Genetic Variation ,Sequence Analysis, DNA ,MOLECULAR EVOLUTION ,DNA-SEQUENCES ,Plant Breeding ,Fertility ,ARABIDOPSIS-THALIANA ,TFL1 HOMOLOG ,Rosa chinensis ,EPS - 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., A high-quality reference genome of rose is generated by sequencing a doubled haploid line. The researchers analysed the genome structure and uncovered candidate genes associated with major ornamental traits through integrated genetic and genomic analyses.
- Published
- 2018
- Full Text
- View/download PDF