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Talhinhas P, Carvalho R, Tavares S, Ribeiro T, Azinheira H, Ramos AP, Silva MDC, Monteiro M, Loureiro J, Morais-Cecílio L. Diploid Nuclei Occur throughout the Life Cycles of Pucciniales Fungi. Microbiol Spectr 2023; 11:e0153223. [PMID: 37289058 PMCID: PMC10433954 DOI: 10.1128/spectrum.01532-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 05/14/2023] [Indexed: 06/09/2023] Open
Abstract
Within Eukaryotes, fungi are the typical representatives of haplontic life cycles. Basidiomycota fungi are dikaryotic in extensive parts of their life cycle, but diploid nuclei are known to form only in basidia. Among Basidiomycota, the Pucciniales are notorious for presenting the most complex life cycles, with high host specialization, and for their expanded genomes. Using cytogenomic (flow cytometry and cell sorting on propidium iodide-stained nuclei) and cytogenetic (FISH with rDNA probe) approaches, we report the widespread occurrence of replicating haploid and diploid nuclei (i.e., 1C, 2C and a small proportion of 4C nuclei) in diverse life cycle stages (pycnial, aecial, uredinial, and telial) of all 35 Pucciniales species analyzed, but not in sister taxa. These results suggest that the Pucciniales life cycle is distinct from any cycle known, i.e., neither haplontic, diplontic nor haplodiplontic, corroborating patchy and disregarded previous evidence. However, the biological basis and significance of this phenomenon remain undisclosed. IMPORTANCE Within Eukaryotes, fungi are the typical representatives of haplontic life cycles, contrasting with plants and animals. As such, fungi thus contain haploid nuclei throughout their life cycles, with sexual reproduction generating a single diploid cell upon karyogamy that immediately undergoes meiosis, thus resuming the haploid cycle. In this work, using cytogenetic and cytogenomic tools, we demonstrate that a vast group of fungi presents diploid nuclei throughout their life cycles, along with haploid nuclei, and that both types of nuclei replicate. Moreover, haploid nuclei are absent from urediniospores. The phenomenon appears to be transversal to the organisms in the order Pucciniales (rust fungi) and it does not occur in neighboring taxa, but a biological explanation or function for it remains elusive.
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Affiliation(s)
- Pedro Talhinhas
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Rita Carvalho
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Sílvia Tavares
- Section for Plant and Soil Science, Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Frederiksberg, Copenhagen, Denmark
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Teresa Ribeiro
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Helena Azinheira
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | - Ana Paula Ramos
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- LPVVA, Laboratório de Patologia Vegetal “Veríssimo de Almeida”, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
| | - Maria do Céu Silva
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
- Centro de Investigação das Ferrugens do Cafeeiro, Instituto Superior de Agronomia, Universidade de Lisboa, Oeiras, Portugal
| | | | - João Loureiro
- CFE-Centre for Functional Ecology and Terra Associated Laboratory, Departamento de Ciências da Vida, Universidade de Coimbra, Coimbra, Portugal
| | - Leonor Morais-Cecílio
- LEAF-Linking Landscape, Environment, Agriculture and Food Research Centre and Terra Associated Laboratory, Instituto Superior de Agronomia, Universidade de Lisboa, Lisbon, Portugal
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Jiang H, Zhang X, Leng L, Gong D, Zhang X, Liu J, Peng D, Wu Z, Yang Y. A chromosome-scale and haplotype-resolved genome assembly of carnation ( Dianthus caryophyllus) based on high-fidelity sequencing. FRONTIERS IN PLANT SCIENCE 2023; 14:1230836. [PMID: 37600187 PMCID: PMC10437072 DOI: 10.3389/fpls.2023.1230836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/19/2023] [Indexed: 08/22/2023]
Abstract
Dianthus caryophyllus is an economic species often considered excellent cut flowers and is suitable for bouquets and gardens. Here, we assembled the haplotype-resolved genome of D. caryophyllus 'Aili' at the chromosome level for the first time. The total lengths of the two assembled haplotypes of carnation were 584.88 Mb for haplotype genome 1 (hap1) and 578.78 Mb for haplotype genome 2 (hap2), respectively. We predicted a total of 44,098 and 42,425 protein-coding genes, respectively. The remarkable structure variation was identified between two haplotypes. Moreover, we identified 403.80 Mb of transposable elements (TEs) in hap1, which accounted for 69.34% of the genome. In contrast, hap2 had 402.70 Mb of TEs, representing 69.61% of the genome. Long terminal repeats were the predominant transposable elements. Phylogenetic analysis showed that the species differentiation time between carnation and gypsophila was estimated to be ~54.43 MYA. The unique gene families of carnation genomes were identified in 'Aili' and previously published 'Francesco' and 'Scarlet Queen'. The assembled and annotated haplotype-resolved D. caryophyllus genome not only promises to facilitate molecular biology studies but also contributes to genome-level evolutionary studies.
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Affiliation(s)
- Heling Jiang
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaoni Zhang
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Luhong Leng
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Desheng Gong
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Xiaohui Zhang
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Junyang Liu
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Dan Peng
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
| | - Zhiqiang Wu
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Yingxue Yang
- Center for Chinese Medicinal Omics and Floriculture, Kunpeng Institute of Modern Agriculture at Foshan, Foshan, China
- The Plant Genomics Research Center, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
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Wos G, Macková L, Kubíková K, Kolář F. Ploidy and local environment drive intraspecific variation in endoreduplication in Arabidopsis arenosa. AMERICAN JOURNAL OF BOTANY 2022; 109:259-271. [PMID: 35137947 DOI: 10.1002/ajb2.1818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 09/28/2021] [Accepted: 09/28/2021] [Indexed: 06/14/2023]
Abstract
PREMISE Endoreduplication, nonheritable duplication of a nuclear genome, is widespread in plants and plays a role in developmental processes related to cell differentiation. However, neither ecological nor cytological factors influencing intraspecific variation in endoreduplication are fully understood. METHODS We cultivated plants covering the range-wide natural diversity of diploid and tetraploid populations of Arabidopsis arenosa in common conditions to investigate the effect of original ploidy level on endoreduplication. We also raised plants from several foothill and alpine populations from different lineages and of both ploidies to test for the effect of elevation. We determined the endoreduplication level in leaves of young plants by flow cytometry. Using RNA-seq data available for our populations, we analyzed gene expression analysis in individuals that differed in endoreduplication level. RESULTS We found intraspecific variation in endoreduplication that was mainly driven by the original ploidy level of populations, with significantly higher endoreduplication in diploids. An effect of elevation was also found within each ploidy, yet its direction exhibited rather regional-specific patterns. Transcriptomic analysis comparing individuals with high vs. low endopolyploidy revealed a majority of differentially expressed genes related to the stress and hormone response and to modifications especially in the cell wall and in chloroplasts. CONCLUSIONS Our results support the general assumption of higher potential of low-ploidy organisms to undergo endoreduplication and suggest that endoreduplication is further integrated within the stress response pathways for a fine-tune adjustment of the endoreduplication process to their local environment.
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Affiliation(s)
- Guillaume Wos
- Department of Botany, Charles University, Benátská 2, 12801 Prague, Czech Republic
| | - Lenka Macková
- Department of Botany, Charles University, Benátská 2, 12801 Prague, Czech Republic
| | - Kateřina Kubíková
- Department of Zoology, Charles University, Viničná 7, 12845 Prague, Czech Republic
| | - Filip Kolář
- Department of Botany, Charles University, Benátská 2, 12801 Prague, Czech Republic
- Institute of Botany of the Czech Academy of Sciences, Zámek 1, CZ-252 43 Průhonice, Czech Republic
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Evaluation of endopolyploidy patterns in selected Capsicum and Nicotiana species (Solanaceae). Biologia (Bratisl) 2021. [DOI: 10.1007/s11756-021-00704-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Hardion L, Perrier A, Martinez M, Navrot N, Gaquerel E, Tournay F, Nguefack J, Combroux I. Integrative revision of Dianthus superbus subspecies reveals different degrees of differentiation, from plasticity to species distinction. SYST BIODIVERS 2020. [DOI: 10.1080/14772000.2020.1737979] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Laurent Hardion
- Laboratoire Image Ville Environnement (LIVE), University of Strasbourg, CNRS, Strasbourg, France
| | - Antoine Perrier
- Laboratoire Image Ville Environnement (LIVE), University of Strasbourg, CNRS, Strasbourg, France
- Department of Environmental Sciences, University of Basel, Basel, 4056, Switzerland
| | - Marion Martinez
- Faculty of Life Sciences, Herbarium of the University of Strasbourg (STR), Strasbourg, France
| | - Nicolas Navrot
- Institut de Biologie Moléculaire des Plantes (IBMP), University of Strasbourg, CNRS, Strasbourg, France
| | - Emmanuel Gaquerel
- Institut de Biologie Moléculaire des Plantes (IBMP), University of Strasbourg, CNRS, Strasbourg, France
| | - Frédéric Tournay
- Faculty of Life Sciences, Botanical Garden of the University of Strasbourg, Strasbourg, France
| | | | - Isabelle Combroux
- Laboratoire Image Ville Environnement (LIVE), University of Strasbourg, CNRS, Strasbourg, France
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Bateman RM, Guy JJ, Rudall PJ, Leitch IJ, Pellicer J, Leitch AR. Evolutionary and functional potential of ploidy increase within individual plants: somatic ploidy mapping of the complex labellum of sexually deceptive bee orchids. ANNALS OF BOTANY 2018; 122:133-150. [PMID: 29672665 PMCID: PMC6025197 DOI: 10.1093/aob/mcy048] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Accepted: 03/15/2018] [Indexed: 05/07/2023]
Abstract
Background and Aims Recent tissue-level observations made indirectly via flow cytometry suggest that endoreplication (duplication of the nuclear genome within the nuclear envelope in the absence of subsequent cell division) is widespread within the plant kingdom. Here, we also directly observe ploidy variation among cells within individual petals, relating size of nucleus to cell micromorphology and (more speculatively) to function. Methods We compared the labella (specialized pollinator-attracting petals) of two European orchid genera: Dactylorhiza has a known predisposition to organismal polyploidy, whereas Ophrys exhibits exceptionally complex epidermal patterning that aids pseudocopulatory pollination. Confocal microscopy using multiple staining techniques allowed us to observe directly both the sizes and the internal structures of individual nuclei across each labellum, while flow cytometry was used to test for progressively partial endoreplication. Key Results In Dactylorhiza, endoreplication was comparatively infrequent, reached only low levels, and appeared randomly located across the labellum, whereas in Ophrys endoreplication was commonplace, being most frequent in large peripheral trichomes. Endoreplicated nuclei reflected both endomitosis and endocycling, the latter reaching the third round of genome doubling (16C) to generate polytene nuclei. All Ophrys individuals studied exhibited progressively partial endoreplication. Conclusions Comparison of the two genera failed to demonstrate the hypothesized pattern of frequent polyploid speciation in genera showing extensive endoreplication. Endoreplication in Ophrys appears more strongly positively correlated with cell size/complexity than with cell location or secretory role. Epigenetic control of gene overexpression by localized induction of endoreplication within individual plant organs may represent a significant component of a plant's developmental programme, contributing substantially to organ plasticity.
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Affiliation(s)
| | - Jessica J Guy
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- School of Biological Sciences, University of Reading, Reading, UK
| | - Paula J Rudall
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Ilia J Leitch
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Jaume Pellicer
- Jodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, UK
| | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
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Cano A, Sánchez-García AB, Albacete A, González-Bayón R, Justamante MS, Ibáñez S, Acosta M, Pérez-Pérez JM. Enhanced Conjugation of Auxin by GH3 Enzymes Leads to Poor Adventitious Rooting in Carnation Stem Cuttings. FRONTIERS IN PLANT SCIENCE 2018; 9:566. [PMID: 29755501 PMCID: PMC5932754 DOI: 10.3389/fpls.2018.00566] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/10/2018] [Indexed: 05/05/2023]
Abstract
Commercial carnation (Dianthus caryophyllus) cultivars are vegetatively propagated from axillary stem cuttings through adventitious rooting; a process which is affected by complex interactions between nutrient and hormone levels and is strongly genotype-dependent. To deepen our understanding of the regulatory events controlling this process, we performed a comparative study of adventitious root (AR) formation in two carnation cultivars with contrasting rooting performance, "2101-02 MFR" and "2003 R 8", as well as in the reference cultivar "Master". We provided molecular evidence that localized auxin response in the stem cutting base was required for efficient adventitious rooting in this species, which was dynamically established by polar auxin transport from the leaves. In turn, the bad-rooting behavior of the "2003 R 8" cultivar was correlated with enhanced synthesis of indole-3-acetic acid conjugated to aspartic acid by GH3 proteins in the stem cutting base. Treatment of stem cuttings with a competitive inhibitor of GH3 enzyme activity significantly improved rooting of "2003 R 8". Our results allowed us to propose a working model where endogenous auxin homeostasis regulated by GH3 proteins accounts for the cultivar dependency of AR formation in carnation stem cuttings.
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Affiliation(s)
- Antonio Cano
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain
| | | | - Alfonso Albacete
- Departamento de Nutrición Vegetal, Centro de Edafología y Biología Aplicada del Segura-Consejo Superior de Investigaciones Científicas, Murcia, Spain
| | | | | | - Sergio Ibáñez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Manuel Acosta
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain
| | - José Manuel Pérez-Pérez
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
- *Correspondence: José Manuel Pérez-Pérez, arolab.edu.umh.es;
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Kocová V, Straková N, Kolarčik V, Rákai A, Mártonfi P. Endoreduplication as a part of flower ontogeny in Trifolium pratense cultivars. BOTANICAL STUDIES 2016; 57:34. [PMID: 28597444 PMCID: PMC5430558 DOI: 10.1186/s40529-016-0150-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 10/22/2016] [Indexed: 05/13/2023]
Abstract
BACKGROUND Endoreduplication appears in numerous plant species and plays a vital role during ontogeny. The presence of polyploid cells in an otherwise diploid organism is tied specifically to the taxonomy, ecology and physiology of the studied specimen. Little is known about the changes in endopolyploidy levels of floral organs during their development. In order to uncover the workings of endoreduplication in polysomatic species, our study examines flowers of T. pratense in three ontogenetic stages by means of flow cytometry. RESULTS Cultivar 'Manuela' is characterized by the presence of 2C-8C and 'Dajana' 2C-16C nuclei. In general, the frequencies of nuclei only slightly changed during development. Endopolyploidy levels represented by endoreduplication index (EI) in the 'Manuela' sepals and stamens showed statistical differences between young and old stages, other organs of both cultivars between stages are not statistically different. Significant differences between 'Manuela' and 'Dajana' cultivars were found only in sepals of I. stage, and in petals and carpels of III. stage. Cultivars showed a similar pattern of endopolyploidy. However, a considerable decrease in EI 'Manuela' petals and carpels at III. stage was detected as opposed to 'Dajana'. Overall, a higher endoreduplication index is distinctive for organs of the 'Dajana' cultivar. CONCLUSIONS In this study we prove the permanent presence of endopolyploid cells in the floral organs of T. pratense throughout their development.
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Affiliation(s)
- Valéria Kocová
- Department of Botany, Faculty of Science, Institute of Biology and Ecology, P.J. Šafárik University, Mánesova 23, 04154 Košice, Slovakia
| | | | - Vladislav Kolarčik
- Department of Botany, Faculty of Science, Institute of Biology and Ecology, P.J. Šafárik University, Mánesova 23, 04154 Košice, Slovakia
| | - Albert Rákai
- Department of Botany, Faculty of Science, Institute of Biology and Ecology, P.J. Šafárik University, Mánesova 23, 04154 Košice, Slovakia
| | - Pavol Mártonfi
- Department of Botany, Faculty of Science, Institute of Biology and Ecology, P.J. Šafárik University, Mánesova 23, 04154 Košice, Slovakia
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Herrera J, Balao F. A test of phenotypic selection on petal form in the wild carnation, Dianthus inoxianus. PLANT BIOLOGY (STUTTGART, GERMANY) 2015; 17:1227-1232. [PMID: 26152531 DOI: 10.1111/plb.12366] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 07/02/2015] [Indexed: 06/04/2023]
Abstract
Floral phenotypes are considered a product of pollinator-mediated selection, which also has the side effect of decreasing floral variation within species. Correlates of flower visibility and function were studied in a carnation species (Dianthus inoxianus), which has crepuscular anthesis and scent-based pollination by the hawkmoth Hyles livornica. We also assessed constancy of flower form in nature and in cultivation and, using fruit set as an estimate of plant relative fitness, tested whether the main pollinator exerted phenotypic selection on floral traits. Petal claw, which is roughly equivalent to the average depth at which an insect's proboscis must be inserted to reach nectar, was remarkably constant among wild plants (coefficient of variation 8%). In contrast, the area of the visible part of the petal, and the intensity of a coloured dot pattern on the petal was very variable (respectively CV = 34% and 102%). Cultivation in a common environment revealed significant variation among genotypes as regards petal area, degree of laciniation and extension of the dot pattern, but not petal claw length, which remained steady. Petal area, shape and colour did not affect relative fitness during the year of study, but plants with intermediate petal claws (i.e. floral tubes) set significantly more fruit. Results are compatible with low response of the main pollinator to variation in visual traits (petal area, laciniation, colour) and high responsiveness to variation in other aspects (tube length). Inconsistent phenotypic selection by pollinators may add to other causes of floral variation in the genus Dianthus, the causes of which are discussed.
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Affiliation(s)
- J Herrera
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
| | - F Balao
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Sevilla, Spain
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Birlanga V, Villanova J, Cano A, Cano EA, Acosta M, Pérez-Pérez JM. Quantitative Analysis of Adventitious Root Growth Phenotypes in Carnation Stem Cuttings. PLoS One 2015; 10:e0133123. [PMID: 26230608 PMCID: PMC4521831 DOI: 10.1371/journal.pone.0133123] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Accepted: 06/26/2015] [Indexed: 12/21/2022] Open
Abstract
Carnation is one of the most important species on the worldwide market of cut flowers. Commercial carnation cultivars are vegetatively propagated from terminal stem cuttings that undergo a rooting and acclimation process. For some of the new cultivars that are being developed by ornamental breeders, poor adventitious root (AR) formation limits its commercial scaling-up, due to a significant increase in the production costs. We have initiated a genetical-genomics approach to determine the molecular basis of the differences found between carnation cultivars during adventitious rooting. The detailed characterization of AR formation in several carnation cultivars differing in their rooting losses has been performed (i) during commercial production at a breeders’ rooting station and (ii) on a defined media in a controlled environment. Our study reveals the phenotypic signatures that distinguishes the bad-rooting cultivars and provides the appropriate set-up for the molecular identification of the genes involved in AR development in this species.
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Affiliation(s)
- Virginia Birlanga
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Joan Villanova
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Antonio Cano
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain
| | - Emilio A. Cano
- Research and Development Department, Barberet & Blanc S.A., Puerto Lumbreras, Spain
| | - Manuel Acosta
- Departamento de Biología Vegetal (Fisiología Vegetal), Universidad de Murcia, Murcia, Spain
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Acosta-Motos JR, Diaz-Vivancos P, Álvarez S, Fernández-García N, Sánchez-Blanco MJ, Hernández JA. NaCl-induced physiological and biochemical adaptative mechanisms in the ornamental Myrtus communis L. plants. JOURNAL OF PLANT PHYSIOLOGY 2015; 183:41-51. [PMID: 26074356 DOI: 10.1016/j.jplph.2015.05.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/04/2015] [Accepted: 05/04/2015] [Indexed: 05/07/2023]
Abstract
Physiological and biochemical changes in Myrtus communis L. plants after being subjected to different solutions of NaCl (44, and 88 mM) for up to 30 days (Phase I) and after recovery from the salinity period (Phase II) were studied. Myrtle plants showed salinity tolerance by displaying a series of adaptative mechanisms to cope with salt-stress, including controlled ion homeostasis, the increase in root/shoot ratio, the reduction of water potentials and stomatal conductance to limit water loss. In addition, they displayed different strategies to protect the photosynthetic machinery, including limiting toxic ion accumulation in leaves, increase in chlorophyll content, and changes in chlorophyll fluorescence parameters, leaf anatomy and increases in catalase activity. Anatomical modifications in leaves, including a decrease in spongy parenchyma and increased intercellular spaces, allow CO2 diffusion in a situation of reduced stomatal aperture. In spite of all these changes, salinity produced oxidative stress in myrtle plants as monitored by increases in oxidative stress parameter values. The post-recovery period is perceived as a new stress situation, as observed through effects on plant growth and alterations in non-photochemical quenching parameters and lipid peroxidation values.
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Affiliation(s)
- José Ramón Acosta-Motos
- Irrigation Department, CEBAS-CSIC, Campus Universitario de Espinardo, P.O. Box 164, Murcia, E-30100, Spain
| | - Pedro Diaz-Vivancos
- Fruit Tree Biotechnology Group, Dept. of Plant Breeding, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, P.O. Box 164, E-30100, Spain
| | - Sara Álvarez
- Irrigation Department, CEBAS-CSIC, Campus Universitario de Espinardo, P.O. Box 164, Murcia, E-30100, Spain
| | | | - María Jesús Sánchez-Blanco
- Irrigation Department, CEBAS-CSIC, Campus Universitario de Espinardo, P.O. Box 164, Murcia, E-30100, Spain
| | - José Antonio Hernández
- Fruit Tree Biotechnology Group, Dept. of Plant Breeding, CEBAS-CSIC, Campus Universitario de Espinardo, Murcia, P.O. Box 164, E-30100, Spain.
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Agulló-Antón MÁ, Ferrández-Ayela A, Fernández-García N, Nicolás C, Albacete A, Pérez-Alfocea F, Sánchez-Bravo J, Pérez-Pérez JM, Acosta M. Early steps of adventitious rooting: morphology, hormonal profiling and carbohydrate turnover in carnation stem cuttings. PHYSIOLOGIA PLANTARUM 2014; 150:446-62. [PMID: 24117983 DOI: 10.1111/ppl.12114] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Revised: 09/06/2013] [Accepted: 09/26/2013] [Indexed: 05/21/2023]
Abstract
The rooting of stem cuttings is a common vegetative propagation practice in many ornamental species. A detailed analysis of the morphological changes occurring in the basal region of cultivated carnation cuttings during the early stages of adventitious rooting was carried out and the physiological modifications induced by exogenous auxin application were studied. To this end, the endogenous concentrations of five major classes of plant hormones [auxin, cytokinin (CK), abscisic acid, salicylic acid (SA) and jasmonic acid] and the ethylene precursor 1-aminocyclopropane-1-carboxylic acid were analyzed at the base of stem cuttings and at different stages of adventitious root formation. We found that the stimulus triggering the initiation of adventitious root formation occurred during the first hours after their excision from the donor plant, due to the breakdown of the vascular continuum that induces auxin accumulation near the wounding. Although this stimulus was independent of exogenously applied auxin, it was observed that the auxin treatment accelerated cell division in the cambium and increased the sucrolytic activities at the base of the stem, both of which contributed to the establishment of the new root primordia at the stem base. Further, several genes involved in auxin transport were upregulated in the stem base either with or without auxin application, while endogenous CK and SA concentrations were specially affected by exogenous auxin application. Taken together our results indicate significant crosstalk between auxin levels, stress hormone homeostasis and sugar availability in the base of the stem cuttings in carnation during the initial steps of adventitious rooting.
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Yagi M, Kosugi S, Hirakawa H, Ohmiya A, Tanase K, Harada T, Kishimoto K, Nakayama M, Ichimura K, Onozaki T, Yamaguchi H, Sasaki N, Miyahara T, Nishizaki Y, Ozeki Y, Nakamura N, Suzuki T, Tanaka Y, Sato S, Shirasawa K, Isobe S, Miyamura Y, Watanabe A, Nakayama S, Kishida Y, Kohara M, Tabata S. Sequence analysis of the genome of carnation (Dianthus caryophyllus L.). DNA Res 2013; 21:231-41. [PMID: 24344172 PMCID: PMC4060945 DOI: 10.1093/dnares/dst053] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The whole-genome sequence of carnation (Dianthus caryophyllus L.) cv. ‘Francesco’ was determined using a combination of different new-generation multiplex sequencing platforms. The total length of the non-redundant sequences was 568 887 315 bp, consisting of 45 088 scaffolds, which covered 91% of the 622 Mb carnation genome estimated by k-mer analysis. The N50 values of contigs and scaffolds were 16 644 bp and 60 737 bp, respectively, and the longest scaffold was 1 287 144 bp. The average GC content of the contig sequences was 36%. A total of 1050, 13, 92 and 143 genes for tRNAs, rRNAs, snoRNA and miRNA, respectively, were identified in the assembled genomic sequences. For protein-encoding genes, 43 266 complete and partial gene structures excluding those in transposable elements were deduced. Gene coverage was ∼98%, as deduced from the coverage of the core eukaryotic genes. Intensive characterization of the assigned carnation genes and comparison with those of other plant species revealed characteristic features of the carnation genome. The results of this study will serve as a valuable resource for fundamental and applied research of carnation, especially for breeding new carnation varieties. Further information on the genomic sequences is available at http://carnation.kazusa.or.jp.
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Affiliation(s)
- Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Shunichi Kosugi
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Akemi Ohmiya
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Koji Tanase
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Taro Harada
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Kyutaro Kishimoto
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Masayoshi Nakayama
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Kazuo Ichimura
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Takashi Onozaki
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Hiroyasu Yamaguchi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Nobuhiro Sasaki
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Taira Miyahara
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yuzo Nishizaki
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Yoshihiro Ozeki
- Tokyo University of Agriculture and Technology, 2-24-16 Naka-cho, Koganei, Tokyo 184-8588, Japan
| | - Noriko Nakamura
- Research Institute, Suntory Global Innovation Center, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan
| | - Takamasa Suzuki
- JST, ERATO, Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan
| | - Yoshikazu Tanaka
- Research Institute, Suntory Global Innovation Center, 1-1-1 Wakayamadai, Shimamoto, Mishima, Osaka 618-8503, Japan
| | - Shusei Sato
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Sachiko Isobe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yoshinori Miyamura
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Akiko Watanabe
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Shinobu Nakayama
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Yoshie Kishida
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Mitsuyo Kohara
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
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Chacón B, Ballester R, Birlanga V, Rolland-Lagan AG, Pérez-Pérez JM. A quantitative framework for flower phenotyping in cultivated carnation (Dianthus caryophyllus L.). PLoS One 2013; 8:e82165. [PMID: 24349209 PMCID: PMC3862579 DOI: 10.1371/journal.pone.0082165] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/21/2013] [Indexed: 11/26/2022] Open
Abstract
Most important breeding goals in ornamental crops are plant appearance and flower characteristics where selection is visually performed on direct offspring of crossings. We developed an image analysis toolbox for the acquisition of flower and petal images from cultivated carnation (Dianthus caryophyllus L.) that was validated by a detailed analysis of flower and petal size and shape in 78 commercial cultivars of D. caryophyllus, including 55 standard, 22 spray and 1 pot carnation cultivars. Correlation analyses allowed us to reduce the number of parameters accounting for the observed variation in flower and petal morphology. Convexity was used as a descriptor for the level of serration in flowers and petals. We used a landmark-based approach that allowed us to identify eight main principal components (PCs) accounting for most of the variance observed in petal shape. The effect and the strength of these PCs in standard and spray carnation cultivars are consistent with shared underlying mechanisms involved in the morphological diversification of petals in both subpopulations. Our results also indicate that neighbor-joining trees built with morphological data might infer certain phylogenetic relationships among carnation cultivars. Based on estimated broad-sense heritability values for some flower and petal features, different genetic determinants shall modulate the responses of flower and petal morphology to environmental cues in this species. We believe our image analysis toolbox could allow capturing flower variation in other species of high ornamental value.
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Affiliation(s)
- Borja Chacón
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Roberto Ballester
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
| | - Virginia Birlanga
- Instituto de Bioingeniería, Universidad Miguel Hernández, Elche, Spain
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Yagi M, Yamamoto T, Isobe S, Hirakawa H, Tabata S, Tanase K, Yamaguchi H, Onozaki T. Construction of a reference genetic linkage map for carnation (Dianthus caryophyllus L.). BMC Genomics 2013; 14:734. [PMID: 24160306 PMCID: PMC3870981 DOI: 10.1186/1471-2164-14-734] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 09/25/2013] [Indexed: 02/07/2023] Open
Abstract
Background Genetic linkage maps are important tools for many genetic applications including mapping of quantitative trait loci (QTLs), identifying DNA markers for fingerprinting, and map-based gene cloning. Carnation (Dianthus caryophyllus L.) is an important ornamental flower worldwide. We previously reported a random amplified polymorphic DNA (RAPD)-based genetic linkage map derived from Dianthus capitatus ssp. andrezejowskianus and a simple sequence repeat (SSR)-based genetic linkage map constructed using data from intraspecific F2 populations; however, the number of markers was insufficient, and so the number of linkage groups (LGs) did not coincide with the number of chromosomes (x = 15). Therefore, we aimed to produce a high-density genetic map to improve its usefulness for breeding purposes and genetic research. Results We improved the SSR-based genetic linkage map using SSR markers derived from a genomic library, expression sequence tags, and RNA-seq data. Linkage analysis revealed that 412 SSR loci (including 234 newly developed SSR loci) could be mapped to 17 linkage groups (LGs) covering 969.6 cM. Comparison of five minor LGs covering less than 50 cM with LGs in our previous RAPD-based genetic map suggested that four LGs could be integrated into two LGs by anchoring common SSR loci. Consequently, the number of LGs corresponded to the number of chromosomes (x = 15). We added 192 new SSRs, eight RAPD, and two sequence-tagged site loci to refine the RAPD-based genetic linkage map, which comprised 15 LGs consisting of 348 loci covering 978.3 cM. The two maps had 125 SSR loci in common, and most of the positions of markers were conserved between them. We identified 635 loci in carnation using the two linkage maps. We also mapped QTLs for two traits (bacterial wilt resistance and anthocyanin pigmentation in the flower) and a phenotypic locus for flower-type by analyzing previously reported genotype and phenotype data. Conclusions The improved genetic linkage maps and SSR markers developed in this study will serve as reference genetic linkage maps for members of the genus Dianthus, including carnation, and will be useful for mapping QTLs associated with various traits, and for improving carnation breeding programs.
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Affiliation(s)
- Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan.
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