1
|
Noh YM, Ait Hida A, Raymond O, Comte G, Bendahmane M. The scent of roses, a bouquet of fragrance diversity. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1252-1264. [PMID: 38015983 DOI: 10.1093/jxb/erad470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 11/27/2023] [Indexed: 11/30/2023]
Abstract
Roses have been domesticated since antiquity for their therapeutic, cosmetic, and ornamental properties. Their floral fragrance has great economic value, which has influenced the production of rose varieties. The production of rose water and essential oil is one of the most lucrative activities, supplying bioactive molecules to the cosmetic, pharmaceutical, and therapeutic industries. In recent years, major advances in molecular genetics, genomic, and biochemical tools have paved the way for the identification of molecules that make up the specific fragrance of various rose cultivars. The aim of this review is to highlight current knowledge on metabolite profiles, and more specifically on fragrance compounds, as well as the specificities and differences between rose species and cultivars belonging to different rose sections and how they contribute to modern roses fragrance.
Collapse
Affiliation(s)
- Yuo-Myoung Noh
- Laboratoire Reproduction et Développement des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, Lyon, France
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Lyon, France
| | - Amal Ait Hida
- Institut Agronomique et Vétérinaire, Complexe Horticole, Agadir, Morocco
| | - Olivier Raymond
- Laboratoire Reproduction et Développement des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, Lyon, France
| | - Gilles Comte
- UMR Ecologie Microbienne, CNRS, INRA, VetAgro Sup, UCBL, Université de Lyon, Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, INRA-CNRS-Lyon1-ENS, Ecole Normale Supérieure de Lyon, Lyon, France
| |
Collapse
|
2
|
Asagoshi Y, Hitomi E, Nakamura N, Takeda S. Gene-flow investigation between garden and wild roses planted in close distance. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:283-288. [PMID: 38434113 PMCID: PMC10905366 DOI: 10.5511/plantbiotechnology.23.0708a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/08/2023] [Indexed: 03/05/2024]
Abstract
Rose is a major ornamental plant, and a lot of cultivars with attractive morphology, color and scent have been generated by classical breeding. Recent progress of genetic modification produces a novel cultivar with attractive features. In both cases, a major problem is the gene-flow from cultivated or genetically modified (GM) plants to wild species, causing reduction of natural population. To investigate whether gene-flow occurs in wild species, molecular analysis with DNA markers with higher efficient technique is useful. Here we investigated the gene-flow from cultivated roses (Rosa×hybrida) to wild rose species planted in close distance in the field. The overlapping flowering periods and visiting insects suggest that pollens were transported by insects between wild and cultivated roses. We examined the germination ratio of seeds from wild species, and extracted DNA and checked with KSN and APETALA2 (AP2) DNA markers to detect transposon insertions. Using two markers, we successfully detected the outcross between wild and cultivated roses. For higher efficiency, we established a bulking method, where DNA, leaves or embryos were pooled, enabling us to that check the outcross of many plants. Our results suggest that wild species and garden cultivars can cross in close distance, so that they should be planted in distance, and checked the outcross with multiple DNA markers.
Collapse
Affiliation(s)
- Yuna Asagoshi
- Department of Agricultural and Life Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo Hangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
| | - Eri Hitomi
- Department of Agricultural and Life Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo Hangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
| | - Noriko Nakamura
- Research Institute, Suntory Global Innovation Center Ltd., Seikadai 8-1-1, Seika-cho, Kyoto 619-0284, Japan
| | - Seiji Takeda
- Department of Agricultural and Life Science, Graduate School of Life and Environmental Sciences, Kyoto Prefectural University, Shimogamo Hangi-cho, Sakyo-ku, Kyoto 606-8522, Japan
- Biotechnology Research Department, Kyoto Prefectural Agriculture, Forestry and Fisheries Technology Center, Kitaina Yazuma Oji 74, Seika-cho, Kyoto 619-0244, Japan
| |
Collapse
|
3
|
Chong Y, Tu X, Lu Y, Gao Z, He X, Hong J, Wu J, Wu D, Xi D, Deng W. Two High-Quality Cygnus Genome Assemblies Reveal Genomic Variations Associated with Plumage Color. Int J Mol Sci 2023; 24:16953. [PMID: 38069278 PMCID: PMC10707585 DOI: 10.3390/ijms242316953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 11/26/2023] [Accepted: 11/28/2023] [Indexed: 12/18/2023] Open
Abstract
As an exemplary model for examining molecular mechanisms responsible for extreme phenotypic variations, plumage color has garnered significant interest. The Cygnus genus features two species, Cygnus olor and Cygnus atratus, that exhibit striking disparities in plumage color. However, the molecular foundation for this differentiation has remained elusive. Herein, we present two high-quality genomes for C. olor and C. atratus, procured using the Illumina and Nanopore technologies. The assembled genome of C. olor was 1.12 Gb in size with a contig N50 of 26.82 Mb, while its counterpart was 1.13 Gb in size with a contig N50 of 21.91 Mb. A comparative analysis unveiled three genes (TYR, SLC45A2, and SLC7A11) with structural variants in the melanogenic pathway. Notably, we also identified a novel gene, PWWP domain containing 2A (PWWP2A), that is related to plumage color, for the first time. Using targeted gene modification analysis, we demonstrated the potential genetic effect of the PWWP2A variant on pigment gene expression and melanin production. Finally, our findings offer insight into the intricate pattern of pigmentation and the role of polygenes in birds. Furthermore, these two high-quality genome references provide a comprehensive resource and perspective for comparative functional and genetic studies of evolution within the Cygnus genus.
Collapse
Affiliation(s)
- Yuqing Chong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Xiaolong Tu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Ying Lu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Zhendong Gao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Xiaoming He
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Jieyun Hong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Jiao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Dongdong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China;
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Y.C.); (Y.L.); (Z.G.); (X.H.); (J.H.); (J.W.); (D.X.)
| |
Collapse
|
4
|
Xu X, Wang N, Feng L, Wang J. Simple Sequence Repeat Fingerprint Identification of Essential-Oil-Bearing Rosa rugosa via High-Resolution Melting (HRM) Analysis. Biomolecules 2023; 13:1468. [PMID: 37892150 PMCID: PMC10605111 DOI: 10.3390/biom13101468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/23/2023] [Accepted: 09/26/2023] [Indexed: 10/29/2023] Open
Abstract
Oil-bearing Rosa rugosa are popular in the essential oil and perfume markets. The similar botanical characteristics between high-oil-yield or low-oil-yield cultivars are confusing and it is hard for farmers or breeders to identify the high-oil-yield cultivar by phenotype difference. High-resolution melting (HRM) analysis of simple sequence repeats (SSRs) can construct accurate DNA fingerprints quickly, which was shown to be effective for identification of closely related cultivars of R. rugosa. Optimization of HRM-SSR indicated that the 10 µL HRM reaction mixture containing 20 ng of genomic DNA of R. rugosa and 0.75 µL of 10 µmol/L of each primer with an annealing temperature of 64 °C was a robust SSR genotyping protocol. Using this protocol, 9 polymorphic SSR markers with 3-9 genotypes among the 19 R. rugosa cultivars were identified. The top three polymorphic makers SSR9, SSR12 and SSR19 constructed a fingerprint of all cultivars, and the rare insertion in the flanking sequences of the repeat motif of SSR19 generated three characteristic genotypes of three high-oil-yield cultivars. These results may be economical and practical for the identification of high-oil-yield R. rugosa and be helpful for the selection and breeding of oil-bearing roses.
Collapse
Affiliation(s)
| | | | - Liguo Feng
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (X.X.); (N.W.)
| | - Jianwen Wang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China; (X.X.); (N.W.)
| |
Collapse
|
5
|
Da L, Li J, Zhao F, Liu H, Shi P, Shi S, Zhang X, Yang J, Zhang H. RoseAP: an analytical platform for gene function of Rosa rugosa. FRONTIERS IN PLANT SCIENCE 2023; 14:1197119. [PMID: 37457357 PMCID: PMC10348015 DOI: 10.3389/fpls.2023.1197119] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/23/2023] [Indexed: 07/18/2023]
Abstract
Rosa rugosa, a perennial shrub belonging to family Rosaceae, is a well-known ornamental plant. Its petals contain an abundance of essential oils and anthocyanins with enormous economic and health benefits when used as edible or cosmetic ingredients. The whole genome of R. rugosa was sequenced in 2021, which provided opportunities and challenges for gene regulation. However, many gene functions remain unknown. Therefore, an analytical platform named RoseAP (http://www.gzybioinformatics.cn/RoseAP/index.php) for the functional analysis of R. rugosa genes was constructed. It improved the gene annotation rate by integrating and analyzing genomic and transcriptomic datasets. First, 38,815 genes, covering 97.76% of the coding genes, were annotated functionally and structurally using a variety of algorithms and rules. Second, a total of 33 transcriptome samples were integrated, including 23 samples from our lab and 10 samples from the SRA database. A co-expression network containing approximately 29,657 positive or negative gene pairs, covering 74.7% of the coding genes, was constructed based on PCC and MR algorithms. Network analysis revealed that the DFR function was closely related to anthocyanin metabolism. It demonstrated the reliability of the network. Several SAUR genes of R. rugosa shared similar expression patterns. RoseAP was used to determine the sequence, structure, functional annotation, expression profile, regulatory network, and functional modules at the transcriptional and protein levels by inputting gene IDs. In addition, auxiliary analytical tools, including BLAST, gene set enrichment, orthologue conversion, gene sequence extraction, gene expression value extraction, and JBrowse, were utilized. Regular updates to RoseAP are expected to facilitate mining of gene function and promote genetic improvement in R. rugosa.
Collapse
Affiliation(s)
- Lingling Da
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Jiande Li
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Fan Zhao
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Huilin Liu
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Pengxia Shi
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Shaoming Shi
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Xinxin Zhang
- College of Life Science, Northwest Normal University, Lanzhou, China
| | - Jiaotong Yang
- Resource Institute for Chinese and Ethnic Materia Medica, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Hui Zhang
- College of Life Science, Northwest Normal University, Lanzhou, China
| |
Collapse
|
6
|
BOX38, a DNA Marker for Selection of Essential Oil Yield of Rosa × rugosa. Biomolecules 2023; 13:biom13030439. [PMID: 36979374 PMCID: PMC10046031 DOI: 10.3390/biom13030439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 02/13/2023] [Accepted: 02/22/2023] [Indexed: 03/03/2023] Open
Abstract
Rosa rugosa L. was a famous aromatic plant whose cultivars (Rosa × rugosa) have been widely used in the perfume industry in Asia. The perfume market looks for rose cultivars bearing higher essential oil, while the oil yields of most R. × rugosa have not been evaluated due to limiting conditions, such as insufficient cultivation areas. Here, we tested the yield and the aroma components of essential oil of 19 R. × rugosa. The results indicated that the yields of nerol, citronellol, and geraniol could represent an alternative index of the total yield of essential oil. Sequence syntenic analysis indicated that the Rosa genus specific cis-element Box38 was highly polymorphic. The Box38 region isolation of Rosa × rugosa by flanked primers proved that Box38 repeat number was significantly positively correlated with the essential oil yield of the corresponding cultivar. In the breeding of Rosa × rugosa, six-Box38-repeat could be a robust threshold for selection of high-essential-oil roses. Together, we found that Box38 was a DNA marker for essential oil yield and that it would be helpful in the early selection and breeding of essential oil roses.
Collapse
|
7
|
Wang J, Cheng Y, Shi X, Feng L. GT Transcription Factors of Rosa rugosa Thunb. Involved in Salt Stress Response. BIOLOGY 2023; 12:biology12020176. [PMID: 36829455 PMCID: PMC9952457 DOI: 10.3390/biology12020176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 01/24/2023]
Abstract
Rosa rugosa was a famous aromatic plant while poor salt tolerance of commercial cultivars has hindered its culture in saline-alkali soil. In many plants, the roles of GT (or trihelix) genes in salt stresses responses have been emerging. In the wild R. rugosa, a total of 37 GTs (RrGTs) were grouped into GT-1, GT-2, GTγ, SH4, and SIP1 lineages. SIP1 lineage expanded by transposition. The motifs involved in the binding of GT cis-elements were conserved. Four RrGTs (RrGT11/14/16/18) significantly differentially expressed in roots or leaves under salt stress. The responsive patterns within 8 h NaCl treatment indicated that RrGTγ-4 (RrGT18) and RrGT-1 (RrGT16) were significantly induced by salt in roots of R. rugosa. Subcellular localizations of RrSIP1 (RrGT11) and RrGTγ-4 were on chloroplasts while RrGT-1 and RrSIP2 (RrGT14) located on cell nucleus. Regulation of ion transport could be the most important role of RrSIPs and RrGTγ-4. And RrGT-1 could be a halophytic gene with higher transcription abundance than glycophytic GT-1. These results provide key clue for further investigations of roles of RrGTs in salt stress response and would be helpful in the understanding the salt tolerance regulation mechanism of R. rugosa.
Collapse
Affiliation(s)
| | | | | | - Liguo Feng
- Correspondence: ; Tel.: +86-514-8797-1026
| |
Collapse
|
8
|
Comprehensive Genome-Wide Analysis of Histone Acetylation Genes in Roses and Expression Analyses in Response to Heat Stress. Genes (Basel) 2022; 13:genes13060980. [PMID: 35741743 PMCID: PMC9222719 DOI: 10.3390/genes13060980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2022] [Revised: 05/25/2022] [Accepted: 05/25/2022] [Indexed: 11/17/2022] Open
Abstract
Roses have high economic values as garden plants and for cut-flower and cosmetics industries. The growth and development of rose plants is affected by exposure to high temperature. Histone acetylation plays an important role in plant development and responses to various stresses. It is a dynamic and reversible process mediated by histone deacetylases (HDAC) and histone acetyltransferases (HAT). However, information on HDAC and HAT genes of roses is scarce. Here, 23 HDAC genes and 10 HAT genes were identified in the Rosa chinensis ‘Old Blush’ genome. Their gene structures, conserved motifs, physicochemical properties, phylogeny, and synteny were assessed. Analyses of the expression of HDAC and HAT genes using available RNAseq data showed that these genes exhibit different expression patterns in different organs of the three analyzed rose cultivars. After heat stress, while the expression of most HDAC genes tend to be down-regulated, that of HAT genes was up-regulated when rose plants were grown at high-temperature conditions. These data suggest that rose likely respond to high-temperature exposure via modification in histone acetylation, and, thus, paves the way to more studies in order to elucidate in roses the molecular mechanisms underlying rose plants development and flowering.
Collapse
|
9
|
Kawamura K, Ueda Y, Matsumoto S, Horibe T, Otagaki S, Wang L, Wang G, Hibrand-Saint Oyant L, Foucher F, Linde M, Debener T. The identification of the Rosa S-locus provides new insights into the breeding and wild origins of continuous-flowering roses. HORTICULTURE RESEARCH 2022; 9:uhac155. [PMID: 36196069 PMCID: PMC9527601 DOI: 10.1093/hr/uhac155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 10/01/2022] [Accepted: 07/03/2022] [Indexed: 06/16/2023]
Abstract
This study aims to: (i) identify the Rosa S-locus controlling self-incompatibility (SI); (ii) test the genetic linkage of the S-locus with other loci controlling important ornamental traits, such as the continuous-flowering (CF) characteristic; (iii) identify the S-alleles (SC ) of old Chinese CF cultivars (e.g, Old Blush, Slater's Crimson China) and examine the changes in the frequency of cultivars with Sc through the history of breeding; (iv) identify wild species carrying the Sc-alleles to infer wild origins of CF cultivars. We identified a new S-RNase (SC2 ) of Rosa chinensis in a contig from a genome database that has not been integrated into one of the seven chromosomes yet. Genetic mapping indicated that SC2 is allelic to the previously-identified S-RNase (SC1 ) in chromosome 3. Pollination experiments with half-compatible pairs of roses confirmed that they are the pistil-determinant of SI. The segregation analysis of an F1 -population indicated genetic linkage between the S-locus and the floral repressor gene KSN. The non-functional allele ksn is responsible for the CF characteristic. A total of five S-alleles (SC1-5 ) were identified from old CF cultivars. The frequency of cultivars with SC dramatically increased after the introgression of ksn from Chinese to European cultivars and remains high (80%) in modern cultivars, suggesting that S-genotyping is helpful for effective breeding. Wild individuals carrying SC were found in Rosa multiflora (SC1 ), Rosa chinensis var. spontanea (SC3 ), and Rosa gigantea (SC2 , SC4 ), supporting the hypothesis of hybrid origins of CF cultivars and providing a new evidence for the involvement of Rosa multiflora.
Collapse
Affiliation(s)
| | - Yoshihiro Ueda
- Gifu International Academy of Horticulture, Japan
- Gifu World Rose Garden, Japan
| | - Shogo Matsumoto
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan
| | - Takanori Horibe
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan
- College of Bioscience and Biotechnology, Chubu University, Japan
| | - Shungo Otagaki
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan
| | - Li Wang
- College of Life Sciences, Sichuan University, China
| | - Guoliang Wang
- Jiangsu Provincial Department of Agriculture and Rural Affairs, China
- Agricultural University of Nanjing, China
| | | | - Fabrice Foucher
- Univ Angers, INRAE, Institut Agro, IRHS, SFR QUASAV, F-49000 Angers, France
| | | | | |
Collapse
|