Details
| Originalsprache | Englisch |
|---|---|
| Seiten (von - bis) | 473-484 |
| Seitenumfang | 12 |
| Fachzeitschrift | Nature plants |
| Jahrgang | 4 |
| Frühes Online-Datum | 11 Juni 2018 |
| Publikationsstatus | Veröffentlicht - Juli 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.
ASJC Scopus Sachgebiete
- Agrar- und Biowissenschaften (insg.)
- Pflanzenkunde
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in: Nature plants, Jahrgang 4, 07.2018, S. 473-484.
Publikation: Beitrag in Fachzeitschrift › Artikel › Forschung › Peer-Review
}
TY - JOUR
T1 - A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits
AU - Saint-Oyant, L. Hibrand
AU - Ruttink, T.
AU - Hamama, L.
AU - Kirov, I.
AU - Lakhwani, D.
AU - Zhou, N. N.
AU - Bourke, P. M.
AU - Daccord, N.
AU - Leus, L.
AU - Schulz, D.
AU - Van De Geest, H.
AU - Hesselink, T.
AU - Van Laere, K.
AU - Debray, K.
AU - Balzergue, S.
AU - Thouroude, T.
AU - Chastellier, A.
AU - Jeauffre, J.
AU - Voisine, L.
AU - Gaillard, S.
AU - Borm, T. J.A.
AU - Arens, P.
AU - Voorrips, R. E.
AU - Maliepaard, C.
AU - Neu, E.
AU - Linde, M.
AU - Le Paslier, M. C.
AU - Bérard, A.
AU - Bounon, R.
AU - Clotault, J.
AU - Choisne, N.
AU - Quesneville, H.
AU - Kawamura, K.
AU - Aubourg, S.
AU - Sakr, S.
AU - Smulders, M. J.M.
AU - Schijlen, E.
AU - Bucher, E.
AU - Debener, T.
AU - De Riek, J.
AU - Foucher, F.
N1 - Funding information: We thank the ImHorPhen team of IRHS and the experimental unit (UE Horti) for their technical assistance in plant management. We thank the PTM ANAN (M. Bahut) of the SFR Quasav and the Gentyane platforms (especially C. Poncet) for the SSR and SNP analyses, respectively. We acknowledge A. Chauveau and I. Le Clainche for libraries preparation and E. Marquand and A. Canaguier for data processing. This work was supported by CEA-IG/CNG, by conducting the DNA quality control and by providing access to the INRA-EPGV group for their Illumina Sequencing Platform. We acknowledge J.-L. Gaignard (from the communication service of the INRA) for his help to fund the project. We thank the GDR team, and particularly P. Zheng, S. Jung and D. Main, for management of the genome sequence at the GDR database. We thank ‘Région Pays de la Loire’ for funding the sequencing of HapOB (Rose Genome Project), the resequencing of eight wild species (Genorose project in the framework of RFI ‘Objectif Végétal’) and for the EPICENTER ConnecTalent grant of the Pays de la Loire (N.D. and E.B.). F.F. and L.H.S.-O. thank the ANR for funding the genetic determinism of flower development (ANR-13-BSV7-0014). K.K. thanks the JSPS for funding the analysis of the S-locus (JSPS KAKENHI no.17H04616). T.D. thanks the German Ministry of Economic Affairs for funding the GWAS analysis (Aif programme ZI) and the Deutsche Forschungsgemeinschaft for the RNA-seq data generation (DFG program GRK1798). The development of the high-density SNP maps was partly funded by TTI Green Genetics and by the TKI Polyploids projects (BO-26.03-002-001 and BO-50-002-022). We thank the ImHorPhen team of IRHS and the experimental unit (UE Horti) for their technical assistance in plant management. We thank the PTM ANAN (M. Bahut) of the SFR Quasav and the Gentyane platforms (especially C. Poncet) for the SSR and SNP analyses, respectively. We acknowledge A. Chauveau and I. Le Clainche for libraries preparation and E. Marquand and A. Canaguier for data processing. This work was supported by CEA-IG/CNG, by conducting the DNA quality control and by providing access to the INRA-EPGV group for their Illumina Sequencing Platform. We acknowledge J.-L. Gaignard (from the communication service of the INRA) for his help to fund the project. We thank the GDR team, and particularly P. Zheng, S. Jung and D. Main, for management of the genome sequence at the GDR database. We thank 'Région Pays de la Loire' for funding the sequencing of HapOB (Rose Genome Project), the resequencing of eight wild species (Genorose project in the framework of RFI 'Objectif Végétal') and for the EPICENTER ConnecTalent grant of the Pays de la Loire (N.D. and E.B.). F.F. and L.H.S.-O. thank the ANR for funding the genetic determinism of flower development (ANR-13-BSV7-0014). K.K. thanks the JSPS for funding the analysis of the S-locus (JSPS KAKENHI no.17H04616). T.D. thanks the German Ministry of Economic Affairs for funding the GWAS analysis (Aif programme ZI) and the Deutsche Forschungsgemeinschaft for the RNA-seq data generation (DFG program GRK1798). The development of the high-density SNP maps was partly funded by TTI Green Genetics and by the TKI Polyploids projects (BO-26.03-002-001 and BO-50-002-022).
PY - 2018/7
Y1 - 2018/7
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85048322737&partnerID=8YFLogxK
U2 - 10.1038/s41477-018-0166-1
DO - 10.1038/s41477-018-0166-1
M3 - Article
C2 - 29892093
AN - SCOPUS:85048322737
VL - 4
SP - 473
EP - 484
JO - Nature plants
JF - Nature plants
SN - 2055-0278
ER -