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Jariani P, Shahnejat-Bushehri AA, Naderi R, Zargar M, Naghavi MR. Molecular and Phytochemical Characteristics of Flower Color and Scent Compounds in Dog Rose ( Rosa canina L.). Molecules 2024; 29:3145. [PMID: 38999097 PMCID: PMC11242971 DOI: 10.3390/molecules29133145] [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: 02/18/2024] [Revised: 03/12/2024] [Accepted: 03/16/2024] [Indexed: 07/14/2024] Open
Abstract
This study delves into the chemical and genetic determinants of petal color and fragrance in Rosa canina L., a wild rose species prized for its pharmacological and cosmetic uses. Comparative analysis of white and dark pink R. canina flowers revealed that the former harbors significantly higher levels of total phenolics (TPC) and flavonoids (TFC), while the latter is distinguished by elevated total anthocyanins (TAC). Essential oils in the petals were predominantly composed of aliphatic hydrocarbons, with phenolic content chiefly constituted by flavonols and anthocyanins. Notably, gene expression analysis showed an upregulation in most genes associated with petal color and scent biosynthesis in white buds compared to dark pink open flowers. However, anthocyanin synthase (ANS) and its regulatory gene RhMYB1 exhibited comparable expression levels across both flower hues. LC-MS profiling identified Rutin, kaempferol, quercetin, and their derivatives as key flavonoid constituents, alongside cyanidin and delphinidin as the primary anthocyanin compounds. The findings suggest a potential feedback inhibition of anthocyanin biosynthesis in white flowers. These insights pave the way for the targeted enhancement of R. canina floral traits through metabolic and genetic engineering strategies.
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Affiliation(s)
- Parisa Jariani
- Division of Biotechnology, Department of Agronomy and Plant Breeding, College of Agricultural and Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - Ali-Akbar Shahnejat-Bushehri
- Division of Biotechnology, Department of Agronomy and Plant Breeding, College of Agricultural and Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - Roohangiz Naderi
- Department of Horticulture Science, College of Agriculture and Natural Resources, University of Tehran, Karaj 31587-77871, Iran
| | - Meisam Zargar
- Department of Agrobiotechnology, Institute of Agriculture, RUDN University, 117198 Moscow, Russia
| | - Mohammad Reza Naghavi
- Division of Biotechnology, Department of Agronomy and Plant Breeding, College of Agricultural and Natural Resources, University of Tehran, Karaj 31587-77871, Iran
- Department of Agrobiotechnology, Institute of Agriculture, RUDN University, 117198 Moscow, Russia
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Yudanova SS, Dorogina OV, Vasilyeva OY. Morphological and molecular analysis of rose cultivars from the Grandiflora and Kordesii garden groups. Vavilovskii Zhurnal Genet Selektsii 2024; 28:55-62. [PMID: 38465252 PMCID: PMC10917683 DOI: 10.18699/vjgb-24-07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/11/2023] [Accepted: 12/11/2023] [Indexed: 03/12/2024] Open
Abstract
The breeding of remontant rose cultivars that are resistant to diseases and adverse conditions, with high decorative value and continuous flowering is the most important task during work with the gene pool of garden roses. Currently, intercultivar hybridization within a single garden group has largely outlived its usefulness. It is necessary to breed for highly decorative forms or cultivars that have outstanding resistance, morphological characters and patterns of seasonal rhythms, and use these plants as parental forms in further breeding. This study represents a comparative analysis of rose cultivars from two garden groups, Grandiflora (Gurzuf, Lezginka, Korallovy Syurpriz, Queen Elizabeth, Komsomolsky Ogonyok, Love) and Rosa Kordesii (Letniye Zvyozdy, Dortmund, Gutsulochka). These cultivars proved themselves during many years of testing in harsh climatic conditions. The objectives of the study were to determine the genetic relationship within the groups and to assign phenotypically different cultivars to one or another garden group. The analysis was carried out by morphological, phenological and ISSR markers. According to the phenological observations on the Grandiflora cultivars, Komsomolsky Ogonyok had later budding and flowering stages. Polymorphic data generated from the ISSR markers showed that this cultivar was the most distant from the others and formed a separate cluster on the dendrogram. A comparison of the morphological characters (flower diameter, number of petals, peduncle length, bush height) showed a significant difference ( p < 0.05) between Komsomolsky Ogonyok and the other Grandiflora cultivars. A dendrogram based on a molecular analysis showed a lack of close relationships between Komsomolsky Ogonyok and the Kordesii group, which formed a separate cluster. A pairwise comparison of the morphological characters in Komsomolsky Ogonyok with the Kordesii group revealed a significant ( p <0.05) difference in three of the four characters studied. The exceptions were flower diameter when comparing with Dortmund and Letniye Zvyozdy and peduncle length when comparing with Gutsulochka. Although Komsomolsky Ogonyok has a pattern of seasonal development similar to Dortmund in the Kordesii group, the molecular analysis did not assign the former to this group of roses. The cultivars that have valuable characters that no average rose does and that are phenotypically different from such roses represent the most valuable breeding material.
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Affiliation(s)
- S S Yudanova
- Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O V Dorogina
- Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - O Yu Vasilyeva
- Central Siberian Botanical Garden of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Xie L, Bai X, Zhang H, Qiu X, Jian H, Wang Q, Wang H, Feng D, Tang K, Yan H. Loss of Rose Fragrance under Chilling Stress Is Associated with Changes in DNA Methylation and Volatile Biosynthesis. Genes (Basel) 2023; 14:genes14030692. [PMID: 36980964 PMCID: PMC10048243 DOI: 10.3390/genes14030692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/08/2023] [Accepted: 03/08/2023] [Indexed: 03/14/2023] Open
Abstract
Rose plants are widely cultivated as cut flowers worldwide and have economic value as sources of natural fragrance and flavoring. Rosa ‘Crimson Glory’, whose petals have a pleasant fragrance, is one of the most important cultivars of edible rose plants. Flower storage at low-temperature is widely applied in production to maintain quality; however, chilling results in a decrease in aromatic volatiles. To determine the molecular basis underlying the changes in aromatic volatile emissions, we investigated the changes in volatile compounds, DNA methylation patterns, and patterns of the transcriptome in response to chilling temperature. The results demonstrated that chilling roses substantially reduced aromatic volatile emissions. We found that these reductions were correlated with the changes in the methylation status of the promoters and genic regions of the genes involved in volatile biosynthesis. These changes mainly occurred for CHH (H = A, T, or C) which accounted for 51% of the total methylation. Furthermore, transcript levels of scent-related gene Germacrene D synthase (RhGDS), Nudix hydrolase 1 (RhNUDX1), and Phenylacetaldehyde reductase (RhPAR) of roses were strikingly depressed after 24 h at low-temperature and remained low-level after 24 h of recovery at 20 °C. Overall, our findings indicated that epigenetic regulation plays an important role in the chilling tolerance of roses and lays a foundation for practical significance in the production of edible roses.
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Affiliation(s)
- Limei Xie
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
- Institute of Resource Plants, Yunnan University, Kunming 650000, China
| | - Xue Bai
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
- Institute of Resource Plants, Yunnan University, Kunming 650000, China
| | - Hao Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Xianqin Qiu
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Hongying Jian
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Qigang Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Huichun Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Dedang Feng
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Kaixue Tang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
- Correspondence: (K.T.); (H.Y.)
| | - Huijun Yan
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, Kunming 650205, China
- National Engineering Research Center for Ornamental Horticulture, Kunming 650000, China
- Correspondence: (K.T.); (H.Y.)
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Genetic and Biochemical Aspects of Floral Scents in Roses. Int J Mol Sci 2022; 23:ijms23148014. [PMID: 35887360 PMCID: PMC9321236 DOI: 10.3390/ijms23148014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 07/15/2022] [Accepted: 07/18/2022] [Indexed: 12/12/2022] Open
Abstract
Floral scents possess high ornamental and economic values to rose production in the floricultural industry. In the past two decades, molecular bases of floral scent production have been studied in the rose as well as their genetic inheritance. Some significant achievements have been acquired, such as the comprehensive rose genome and the finding of a novel geraniol synthase in plants. In this review, we summarize the composition of floral scents in modern roses, focusing on the recent advances in the molecular mechanisms of floral scent production and emission, as well as the latest developments in molecular breeding and metabolic engineering of rose scents. It could provide useful information for both studying and improving the floral scent production in the rose.
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Giovannini A, Laura M, Nesi B, Savona M, Cardi T. Genes and genome editing tools for breeding desirable phenotypes in ornamentals. PLANT CELL REPORTS 2021; 40:461-478. [PMID: 33388891 PMCID: PMC7778708 DOI: 10.1007/s00299-020-02632-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 10/27/2020] [Indexed: 05/05/2023]
Abstract
We review the main genes underlying commercial traits in cut flower species and critically discuss the possibility to apply genome editing approaches to produce novel variation and phenotypes. Promoting flowering and flower longevity as well as creating novelty in flower structure, colour range and fragrances are major objectives of ornamental plant breeding. The novel genome editing techniques add new possibilities to study gene function and breed new varieties. The implementation of such techniques, however, relies on detailed information about structure and function of genomes and genes. Moreover, improved protocols for efficient delivery of editing reagents are required. Recent results of the application of genome editing techniques to elite ornamental crops are discussed in this review. Enabling technologies and genomic resources are reviewed in relation to the implementation of such approaches. Availability of the main gene sequences, underlying commercial traits and in vitro transformation protocols are provided for the world's best-selling cut flowers, namely rose, lily, chrysanthemum, lisianthus, tulip, gerbera, freesia, alstroemeria, carnation and hydrangea. Results obtained so far are described and their implications for the improvement of flowering, flower architecture, colour, scent and shelf-life are discussed.
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Affiliation(s)
- A. Giovannini
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - M. Laura
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - B. Nesi
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Via dei Fiori 8, 51017 Pescia, Italy
| | - M. Savona
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Corso degli Inglesi 508, 18038 Sanremo, Italy
| | - T. Cardi
- CREA Research Centre for Vegetable and Ornamental Crops (CREA OF), Via Cavalleggeri 25, 84098 Pontecagnano Faiano, Italy
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Just J, Bendahmane M. Rosa spp. Trends Genet 2019; 36:146-147. [PMID: 31836193 DOI: 10.1016/j.tig.2019.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 11/08/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Jeremy Just
- Laboratoire Reproduction et Développement des Plantes, INRA, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, F-69364 Lyon, France
| | - Mohammed Bendahmane
- Laboratoire Reproduction et Développement des Plantes, INRA, Univ Lyon, ENS de Lyon, UCB Lyon 1, CNRS, F-69364 Lyon, France.
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Ding Y, Xue L, Guo RX, Luo GJ, Song YT, Lei JJ. De Novo Assembled Transcriptome Analysis and Identification of Genic SSR Markers in Red-Flowered Strawberry. Biochem Genet 2019; 57:607-622. [PMID: 30825077 DOI: 10.1007/s10528-019-09912-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Accepted: 02/19/2019] [Indexed: 10/27/2022]
Abstract
Red-flowered strawberry is a new ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla). To date, few molecular markers have been reported for this plant. RNA sequencing provides a relatively fast and low-cost approach for large-scale detection of simple sequence repeats (SSRs). In the present study, we profiled the transcriptome of red-flowered strawberry by Illumina HiSeq 2500 to identify SSRs related to petal color. Based on 2 million clean reads of red and white flowers from red-flowered strawberry hybrids, we assembled 91,835 unigenes with an average length of 717 bp. After functional annotation and prediction, there were 47,058 unigenes; of these, 26,861 had a gene ontology annotation, with 14,264 SSR loci. Mononucleotide SSRs were the predominant repeat type (47.20%, n = 6724), followed by di- (32.50%, n = 4641), tri- (19.10%, n = 2729), tetra- (0.90%, n = 132), hexa- (0.2%, n = 21), and penta- (0.10%, n = 16) nucleotide repeats. The most frequent di-, tri-, and tetra-nucleotide repeats were AG/CT, AAG/CTT, and AAAG/CTTT, respectively. PCR amplification with 105 SSR primer pairs yielded four bands specific to red flowers, namely UgRFsr57622, UgRFsr94149, UgRFsr40142, and UgRFsr54608; corresponding 4 trait-specific markers were found to co-segregate with white and red flower color in hybrid population, demonstrating that the genic SSR marker is useful to discriminate between white and red flowers in strawberry. Markers to discriminate flower color in red-flowered strawberry will be useful for early selection of progeny and for breeding management.
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Affiliation(s)
- Yan Ding
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Li Xue
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Rui-Xue Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Gang-Jun Luo
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yu-Tong Song
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Jia-Jun Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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Li S, Zhong M, Dong X, Jiang X, Xu Y, Sun Y, Cheng F, Li DZ, Tang K, Wang S, Dai S, Hu JY. Comparative transcriptomics identifies patterns of selection in roses. BMC PLANT BIOLOGY 2018; 18:371. [PMID: 30579326 PMCID: PMC6303930 DOI: 10.1186/s12870-018-1585-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 11/30/2018] [Indexed: 05/09/2023]
Abstract
BACKGROUND Roses are important plants for human beings with pivotal economical and biological traits like continuous flowering, flower architecture, color and scent. Due to frequent hybridization and high genome heterozygosity, classification of roses and their relatives remains a big challenge. RESULTS Here, to identify potential markers for phylogenetic reconstruction and to reveal the patterns of natural selection in roses, we generated sets of high quality and comprehensive reference transcriptomes for Rosa chinensis 'Old Blush' (OB) and R. wichuriana 'Basye's Thornless' (BT), two species exhibiting contrasted traits of high economical importance. The assembled reference transcriptomes showed transcripts N50 above 2000 bp. Two roses shared about 10,073 transcripts (N50 = 2282 bp), in which a set of 5959 transcripts was conserved within genera of Rosa. Further comparison with species in Rosaceae identified 4447 transcripts being common (Rosaceae-common) in Rosa, Malus, Prunus, Rubus, and Fragaria, while a pool of 164 transcripts being specific for roses (Rosa-specific). Among the Rosaceae-common transcripts, 409 transcripts showed a signature of positive selection and a clustered expression in different tissues. Interestingly, nine of these rapidly evolving genes were related to DNA damage repair and responses to environmental stimulus, a potential associated with genome confliction post hybridization. Coincident with this fast evolution pattern in rose genes, 24 F-box and four TMV resistant proteins were significantly enriched in the Rosa-specific genes. CONCLUSIONS We expect that these Rosaceae-common and Rosa-specific transcripts should facilitate the phylogenetic analysis of Rosaceae plants as well as investigations of Rosa-specific biology. The data reported here could provide fundamental genomic tools and knowledge critical for understanding the biology and domestication of roses and for roses breeding.
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Affiliation(s)
- Shubin Li
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
- Flower Research Institute, Yunnan Agricultural Academy of Sciences, Kunming, 650231 China
| | - Micai Zhong
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Xue Dong
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Xiaodong Jiang
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yuxing Xu
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Yibo Sun
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Fang Cheng
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - De-zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
| | - Kaixue Tang
- Flower Research Institute, Yunnan Agricultural Academy of Sciences, Kunming, 650231 China
| | - Siqing Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, 35 East Qinghua Road, Beijing, 100083 China
| | - Jin-Yong Hu
- Group of Plant Molecular Genetics and Adaptation, CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 China
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Wang Y, Jin X, Rui H, Liu T, Hou J. Cold Temperature Regulation of Zoospore Release in Phytophthora sojae: The Genes That Differentially Expressed by Cold Temperature. RUSS J GENET+ 2018. [DOI: 10.1134/s1022795418060133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Yan H, Shi S, Ma N, Cao X, Zhang H, Qiu X, Wang Q, Jian H, Zhou N, Zhang Z, Tang K. Graft-accelerated virus-induced gene silencing facilitates functional genomics in rose flowers. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:34-44. [PMID: 28895654 DOI: 10.1111/jipb.12599] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 09/10/2017] [Indexed: 05/02/2023]
Abstract
Rose has emerged as a model ornamental plant for studies of flower development, senescence, and morphology, as well as the metabolism of floral fragrances and colors. Virus-induced gene silencing (VIGS) has long been used in functional genomics studies of rose by vacuum infiltration of cuttings or seedlings with an Agrobacterium suspension carrying TRV-derived vectors. However, VIGS in rose flowers remains a challenge because of its low efficiency and long time to establish silencing. Here we present a novel and rapid VIGS method that can be used to analyze gene function in rose, called 'graft-accelerated VIGS', where axillary sprouts are cut from the rose plant and vacuum infiltrated with Agrobacterium. The inoculated scions are then grafted back onto the plants to flower and silencing phenotypes can be observed within 5 weeks, post-infiltration. Using this new method, we successfully silenced expression of the RhDFR1, RhAG, and RhNUDX1 in rose flowers, and affected their color, petal number, as well as fragrance, respectively. This grafting method will facilitate high-throughput functional analysis of genes in rose flowers. Importantly, it may also be applied to other woody species that are not currently amenable to VIGS by conventional leaf or plantlet/seedling infiltration methods.
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Affiliation(s)
- Huijun Yan
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Shaochuan Shi
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, 100193 Beijing, China
| | - Nan Ma
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, 100193 Beijing, China
| | - Xiaoqian Cao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, 100193 Beijing, China
| | - Hao Zhang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Xianqin Qiu
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Qigang Wang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Hongying Jian
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Ningning Zhou
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, 100193 Beijing, China
| | - Kaixue Tang
- Flower Research Institute of Yunnan Academy of Agricultural Sciences, 650205 Kunming, China
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Han Y, Wan H, Cheng T, Wang J, Yang W, Pan H, Zhang Q. Comparative RNA-seq analysis of transcriptome dynamics during petal development in Rosa chinensis. Sci Rep 2017; 7:43382. [PMID: 28225056 PMCID: PMC5320579 DOI: 10.1038/srep43382] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/23/2017] [Indexed: 12/21/2022] Open
Abstract
The developmental process that produces the ornate petals of the China rose (Rosa chinensis) is complex and is thought to depend on the balanced expression of a functionally diverse array of genes; however, the molecular basis of rose petal development is largely unknown. Here, petal growth of the R. chinensis cultivar 'Old Blush' was divided into four developmental stages, and RNA-seq technology was used to analyse the dynamic changes in transcription that occur as development progresses. In total, 598 million clean reads and 61,456 successfully annotated unigenes were obtained. Differentially expressed gene (DEG) analysis comparing the transcriptomes of the developmental stages resulted in the identification of several potential candidate genes involved in petal development. DEGs involved in anthocyanin biosynthesis, petal expansion, and phytohormone pathways were considered in depth, in addition to several candidate transcription factors. These results lay a foundation for future studies on the regulatory mechanisms underlying rose petal development and may be used in molecular breeding programs aimed at generating ornamental rose lines with desirable traits.
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Affiliation(s)
- Yu Han
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation &Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Huihua Wan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation &Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Tangren Cheng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation &Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation &Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Weiru Yang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation &Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Huitang Pan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation &Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation &Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
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12
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Zhang C, Zhang H, Zhan Z, Liu B, Chen Z, Liang Y. Transcriptome Analysis of Sucrose Metabolism during Bulb Swelling and Development in Onion ( Allium cepa L.). FRONTIERS IN PLANT SCIENCE 2016; 7:1425. [PMID: 27713754 PMCID: PMC5031786 DOI: 10.3389/fpls.2016.01425] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Accepted: 09/07/2016] [Indexed: 05/25/2023]
Abstract
Allium cepa L. is a widely cultivated and economically significant vegetable crop worldwide, with beneficial dietary and health-related properties, but its sucrose metabolism is still poorly understood. To analyze sucrose metabolism during bulb swelling, and the development of sweet taste in onion, a global transcriptome profile of onion bulbs was undertaken at three different developmental stages, using RNA-seq. A total of 79,376 unigenes, with a mean length of 678 bp, was obtained. In total, 7% of annotated Clusters of Orthologous Groups (COG) were involved in carbohydrate transport and metabolism. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, "starch and sucrose metabolism" (147, 2.40%) constituted the primary metabolism pathway in the integrated library. The expression of sucrose transporter genes was greatest during the early-swelling stage, suggesting that sucrose transporters (SUTs) participated in sucrose metabolism mainly at an early stage of bulb development. A gene-expression analysis of the key enzymes of sucrose metabolism suggested that sucrose synthase, cell wall invertase, and invertase were all likely to participate in the hydrolysis of sucrose, generating glucose, and fructose. In addition, trehalose was hydrolyzed to two molecules of glucose by trehalase. From 15 to 40 days after swelling (DAS), both the glucose and fructose contents of bulbs increased, whereas the sucrose content decreased. The growth rate between 15 and 30 DAS was slower than that between 30 and 40 DAS, suggesting that the latter was a period of rapid expansion. The dataset generated by our transcriptome profiling will provide valuable information for further research.
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Affiliation(s)
- Chunsha Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Beijing, China
| | - Hongwei Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Beijing, China
| | - Zongxiang Zhan
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Bingjiang Liu
- Key Laboratory for Biology of Greenhouse Vegetable of Shandong Province, Institute of Vegetables and Flowers, Shandong Academy of Agricultural SciencesJinan, China
| | - Zhentai Chen
- Vegetable Research Laboratory, Institute of Agricultural Sciences of Xuhuai Region in JiangsuLianyungang, China
| | - Yi Liang
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Beijing, China
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Yan H, Zhang H, Wang Q, Jian H, Qiu X, Baudino S, Just J, Raymond O, Gu L, Wang J, Bendahmane M, Tang K. The Rosa chinensis cv. Viridiflora Phyllody Phenotype Is Associated with Misexpression of Flower Organ Identity Genes. FRONTIERS IN PLANT SCIENCE 2016; 7:996. [PMID: 27462328 PMCID: PMC4941542 DOI: 10.3389/fpls.2016.00996] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2015] [Accepted: 06/24/2016] [Indexed: 05/21/2023]
Abstract
Phyllody is a flower abnormality in which leaf-like structures replace flower organs in all whorls. Here, we investigated the origin and the molecular mechanism of phyllody phenotype in Rosa chinensis cv. Viridiflora, an ancient naturally occurring Chinese mutant cultivar. Reciprocal grafting experiments and microscopy analyses, demonstrated that the phyllody phenotype in Viridiflora is not associated with phytoplasmas infection. Transcriptome comparisons by the mean of RNA-Seq identified 672 up-regulated and 666 down-regulated genes in Viridiflora compared to its closely related genotype R. chinensis cv. Old Blush. A fraction of these genes are putative homologs of genes known to be involved in flower initiation and development. We show that in flower whorl 2 of Viridiflora, a down-regulation of the floral organ identity genes RcPISTILLATA (RcPI), RcAPETALA3 (RcAP3) and RcSEPALLATA3 (RcSEP3), together with an up-regulation of the putative homolog of the gene SUPPRESSOR of OVEREXPRESSION of CONSTANS1 (RcSOC1) are likely at the origin of the loss of petal identity and leaf-like structures formation. In whorl 3 of Viridiflora, ectopic expression of RcAPETALA2 (RcAP2) along with the down regulation of RcPI, RcAP3, and RcSEP3 is associated with loss of stamens identity and leaf-like structures formation. In whorl 4, the ectopic expression of RcAP2 associated with a down-regulation of RcSEP3 and of the C-class gene RcAGAMOUS correlate with loss of pistil identity. The latter also suggested the antagonist effect between the A and C class genes in the rose. Together, these data suggest that modified expression of the ABCE flower organ identity genes is associated with the phyllody phenotype in the rose Viridiflora and that these genes are important for normal flower organs development.
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Affiliation(s)
- Huijun Yan
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Hao Zhang
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Qigang Wang
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Hongying Jian
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Xianqin Qiu
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Sylvie Baudino
- Université de Lyon, UJM-Saint-Etienne, CNRS, BVpam FRE 3727Saint-Etienne, France
| | - Jeremy Just
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRALyon, France
| | - Olivier Raymond
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRALyon, France
| | - Lianfeng Gu
- Haixia Institute of Science and Technology, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Jihua Wang
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
| | - Mohammed Bendahmane
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon 1, CNRS, INRALyon, France
| | - Kaixue Tang
- Flower Research Institute of Yunnan Academy of Agricultural SciencesKunming, China
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Sahebi M, Hanafi MM, Azizi P, Hakim A, Ashkani S, Abiri R. Suppression Subtractive Hybridization Versus Next-Generation Sequencing in Plant Genetic Engineering: Challenges and Perspectives. Mol Biotechnol 2016; 57:880-903. [PMID: 26271955 DOI: 10.1007/s12033-015-9884-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Suppression subtractive hybridization (SSH) is an effective method to identify different genes with different expression levels involved in a variety of biological processes. This method has often been used to study molecular mechanisms of plants in complex relationships with different pathogens and a variety of biotic stresses. Compared to other techniques used in gene expression profiling, SSH needs relatively smaller amounts of the initial materials, with lower costs, and fewer false positives present within the results. Extraction of total RNA from plant species rich in phenolic compounds, carbohydrates, and polysaccharides that easily bind to nucleic acids through cellular mechanisms is difficult and needs to be considered. Remarkable advancement has been achieved in the next-generation sequencing (NGS) field. As a result of progress within fields related to molecular chemistry and biology as well as specialized engineering, parallelization in the sequencing reaction has exceptionally enhanced the overall read number of generated sequences per run. Currently available sequencing platforms support an earlier unparalleled view directly into complex mixes associated with RNA in addition to DNA samples. NGS technology has demonstrated the ability to sequence DNA with remarkable swiftness, therefore allowing previously unthinkable scientific accomplishments along with novel biological purposes. However, the massive amounts of data generated by NGS impose a substantial challenge with regard to data safe-keeping and analysis. This review examines some simple but vital points involved in preparing the initial material for SSH and introduces this method as well as its associated applications to detect different novel genes from different plant species. This review evaluates general concepts, basic applications, plus the probable results of NGS technology in genomics, with unique mention of feasible potential tools as well as bioinformatics.
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Affiliation(s)
- Mahbod Sahebi
- Laboratory of Plantation Crops, Institute of Tropical Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia,
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Li YH, Zhang W, Li Y. Transcriptomic Analysis of Flower Blooming in Jasminum sambac through De Novo RNA Sequencing. Molecules 2015; 20:10734-47. [PMID: 26065837 PMCID: PMC6272439 DOI: 10.3390/molecules200610734] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Revised: 06/01/2015] [Accepted: 06/08/2015] [Indexed: 12/21/2022] Open
Abstract
Flower blooming is a critical and complicated plant developmental process in flowering plants. However, insufficient information is available about the complex network that regulates flower blooming in Jasminum sambac. In this study, we used the RNA-Seq platform to analyze the molecular regulation of flower blooming in J. sambac by comparing the transcript profiles at two flower developmental stages: budding and blooming. A total of 4577 differentially-expressed genes (DEGs) were identified between the two floral stages. The Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses revealed that the DEGs in the “oxidation-reduction process”, “extracellular region”, “steroid biosynthesis”, “glycosphingolipid biosynthesis”, “plant hormone signal transduction” and “pentose and glucuronate interconversions” might be associated with flower development. A total of 103 and 92 unigenes exhibited sequence similarities to the known flower development and floral scent genes from other plants. Among these unigenes, five flower development and 19 floral scent unigenes exhibited at least four-fold differences in expression between the two stages. Our results provide abundant genetic resources for studying the flower blooming mechanisms and molecular breeding of J. sambac.
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Affiliation(s)
- Yong-Hua Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
| | - Wei Zhang
- College of Life Sciences, Xinyang Normal University, Xinyang 464000, China.
| | - Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China.
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Koning-Boucoiran CFS, Esselink GD, Vukosavljev M, van 't Westende WPC, Gitonga VW, Krens FA, Voorrips RE, van de Weg WE, Schulz D, Debener T, Maliepaard C, Arens P, Smulders MJM. Using RNA-Seq to assemble a rose transcriptome with more than 13,000 full-length expressed genes and to develop the WagRhSNP 68k Axiom SNP array for rose (Rosa L.). FRONTIERS IN PLANT SCIENCE 2015; 6:249. [PMID: 25954285 PMCID: PMC4404716 DOI: 10.3389/fpls.2015.00249] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/27/2015] [Indexed: 05/18/2023]
Abstract
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.
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Affiliation(s)
| | - G. Danny Esselink
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Mirjana Vukosavljev
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | | | - Virginia W. Gitonga
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Frans A. Krens
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Roeland E. Voorrips
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - W. Eric van de Weg
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Dietmar Schulz
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Thomas Debener
- Abteilung Molekulare Pflanzenzüchtung, Institute for Plant Genetics, Leibnitz University HannoverHannover, Germany
| | - Chris Maliepaard
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Paul Arens
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
| | - Marinus J. M. Smulders
- Wageningen UR Plant Breeding, Wageningen University and Research CentreWageningen, Netherlands
- *Correspondence: Marinus J. M. Smulders, Wageningen UR Plant Breeding, Wageningen University and Research Centre, PO Box 386, NL-6708 PB Wageningen, Netherlands
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17
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Early responses of silkworm midgut to microsporidium infection – A Digital Gene Expression analysis. J Invertebr Pathol 2015; 124:6-14. [DOI: 10.1016/j.jip.2014.10.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2014] [Revised: 10/04/2014] [Accepted: 10/07/2014] [Indexed: 02/03/2023]
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18
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Li X, Wang C, Cheng J, Zhang J, da Silva JAT, Liu X, Duan X, Li T, Sun H. Transcriptome analysis of carbohydrate metabolism during bulblet formation and development in Lilium davidii var. unicolor. BMC PLANT BIOLOGY 2014; 14:358. [PMID: 25524032 PMCID: PMC4302423 DOI: 10.1186/s12870-014-0358-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/27/2014] [Indexed: 05/09/2023]
Abstract
BACKGROUND The formation and development of bulblets are crucial to the Lilium genus since these processes are closely related to carbohydrate metabolism, especially to starch and sucrose metabolism. However, little is known about the transcriptional regulation of both processes. To gain insight into carbohydrate-related genes involved in bulblet formation and development, we conducted comparative transcriptome profiling of Lilium davidii var. unicolor bulblets at 0 d, 15 d (bulblets emerged) and 35 d (bulblets formed a basic shape with three or four scales) after scale propagation. RESULTS Analysis of the transcriptome revealed that a total of 52,901 unigenes with an average sequence size of 630 bp were generated. Based on Clusters of Orthologous Groups (COG) analysis, 8% of the sequences were attributed to carbohydrate transport and metabolism. The results of KEGG pathway enrichment analysis showed that starch and sucrose metabolism constituted the predominant pathway among the three library pairs. The starch content in mother scales and bulblets decreased and increased, respectively, with almost the same trend as sucrose content. Gene expression analysis of the key enzymes in starch and sucrose metabolism suggested that sucrose synthase (SuSy) and invertase (INV), mainly hydrolyzing sucrose, presented higher gene expression in mother scales and bulblets at stages of bulblet appearance and enlargement, while sucrose phosphate synthase (SPS) showed higher expression in bulblets at morphogenesis. The enzymes involved in the starch synthetic direction such as ADPG pyrophosphorylase (AGPase), soluble starch synthase (SSS), starch branching enzyme (SBE) and granule-bound starch synthase (GBSS) showed a decreasing trend in mother scales and higher gene expression in bulblets at bulblet appearance and enlargement stages while the enzyme in the cleavage direction, starch de-branching enzyme (SDBE), showed higher gene expression in mother scales than in bulblets. CONCLUSIONS An extensive transcriptome analysis of three bulblet development stages contributes considerable novel information to our understanding of carbohydrate metabolism-related genes in Lilium at the transcriptional level, and demonstrates the fundamentality of carbohydrate metabolism in bulblet emergence and development at the molecular level. This could facilitate further investigation into the molecular mechanisms underlying these processes in lily and other related species.
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Affiliation(s)
- XueYan Li
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - ChunXia Wang
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - JinYun Cheng
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - Jing Zhang
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | | | - XiaoYu Liu
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - Xin Duan
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - TianLai Li
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
| | - HongMei Sun
- />College of Horticulture, Shenyang Agricultural University, Shenyang, Liaoning 110866 P R China
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19
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Broderick SR, Wijeratne S, Wijeratn AJ, Chapin LJ, Meulia T, Jones ML. RNA-sequencing reveals early, dynamic transcriptome changes in the corollas of pollinated petunias. BMC PLANT BIOLOGY 2014; 14:307. [PMID: 25403317 PMCID: PMC4245787 DOI: 10.1186/s12870-014-0307-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/27/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Pollination reduces flower longevity in many angiosperms by accelerating corolla senescence. This response requires hormone signaling between the floral organs and results in the degradation of macromolecules and organelles within the petals to allow for nutrient remobilization to developing seeds. To investigate early pollination-induced changes in petal gene expression, we utilized high-throughput sequencing to identify transcripts that were differentially expressed between corollas of pollinated Petunia × hybrida flowers and their unpollinated controls at 12, 18, and 24 hours after opening. RESULTS In total, close to 0.5 billion Illumina 101 bp reads were generated, de novo assembled, and annotated, resulting in an EST library of approximately 33 K genes. Over 4,700 unique, differentially expressed genes were identified using comparisons between the pollinated and unpollinated libraries followed by pairwise comparisons of pollinated libraries to unpollinated libraries from the same time point (i.e. 12-P/U, 18-P/U, and 24-P/U) in the Bioconductor R package DESeq2. Over 500 gene ontology terms were enriched. The response to auxin stimulus and response to 1-aminocyclopropane-1-carboxylic acid terms were enriched by 12 hours after pollination (hap). Using weighted gene correlation network analysis (WGCNA), three pollination-specific modules were identified. Module I had increased expression across pollinated corollas at 12, 18, and 24 h, and modules II and III had a peak of expression in pollinated corollas at 18 h. A total of 15 enriched KEGG pathways were identified. Many of the genes from these pathways were involved in metabolic processes or signaling. More than 300 differentially expressed transcription factors were identified. CONCLUSIONS Gene expression changes in corollas were detected within 12 hap, well before fertilization and corolla wilting or ethylene evolution. Significant changes in gene expression occurred at 18 hap, including the up-regulation of autophagy and down-regulation of ribosomal genes and genes involved in carbon fixation. This transcriptomic database will greatly expand the genetic resources available in petunia. Additionally, it will guide future research aimed at identifying the best targets for increasing flower longevity by delaying corolla senescence.
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Affiliation(s)
- Shaun R Broderick
- />Department of Horticulture and Crop Science, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691 USA
| | - Saranga Wijeratne
- />Molecular and Cellular Imaging Center, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691 USA
| | - Asela J Wijeratn
- />Molecular and Cellular Imaging Center, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691 USA
| | - Laura J Chapin
- />Department of Horticulture and Crop Science, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691 USA
| | - Tea Meulia
- />Molecular and Cellular Imaging Center, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691 USA
| | - Michelle L Jones
- />Department of Horticulture and Crop Science, The Ohio Agricultural Research and Development Center, The Ohio State University, 1680 Madison Ave, Wooster, OH 44691 USA
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Qiang-long Z, Shi L, Peng G, Fei-shi L. High-throughput Sequencing Technology and Its Application. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/s1006-8104(14)60073-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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21
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Yu C, Luo L, Pan H, Guo X, Wan H, Zhang Q. Filling gaps with construction of a genetic linkage map in tetraploid roses. FRONTIERS IN PLANT SCIENCE 2014; 5:796. [PMID: 25628638 PMCID: PMC4292389 DOI: 10.3389/fpls.2014.00796] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 12/21/2014] [Indexed: 05/21/2023]
Abstract
Rose (Rosa sp.) is one of the most economically important ornamental crops worldwide. The present work contains a genetic linkage map for tetraploid roses that was constructed from an F1 segregation population using AFLPs and SSRs on 189 individuals. The preliminary 'Yunzheng Xiawei' and 'Sun City' maps consisted of 298 and 255 markers arranged into 26 and 32 linkage groups, respectively. The recombined parental maps covered 737 and 752 cM of the genome, respectively. The integrated linkage map was composed of 295 polymorphic markers that spanned 874 cM, and it had a mean intermarker distance of 2.9 cM. In addition, a set of newly developed EST-SSRs that are distributed evenly throughout the mapping population were released. The work identified 67 anchoring points that came from 43 common SSRs. The results that were produced from a large number of individuals (189) and polymorphic SSRs (242) will enhance the ability to construct higher density consensus maps with the available diploid level rose maps, and they will definitely serve as a tool for accurate QTL detection and marker assisted selection.
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Affiliation(s)
| | | | | | | | | | - Qixiang Zhang
- *Correspondence: Qixiang Zhang, Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and rural ecological environment and College of Landscape Architecture, Beijing Forestry University, 35# Qinghua East Road, Beijing, 100083, China e-mail:
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