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Bazakos C, Alexiou KG, Ramos-Onsins S, Koubouris G, Tourvas N, Xanthopoulou A, Mellidou I, Moysiadis T, Vourlaki IT, Metzidakis I, Sergentani C, Manolikaki I, Michailidis M, Pistikoudi A, Polidoros A, Kostelenos G, Aravanopoulos F, Molassiotis A, Ganopoulos I. Whole genome scanning of a Mediterranean basin hotspot collection provides new insights into olive tree biodiversity and biology. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:303-319. [PMID: 37164361 DOI: 10.1111/tpj.16270] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/29/2023] [Accepted: 04/29/2023] [Indexed: 05/12/2023]
Abstract
Olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important species of the Mediterranean region and one of the most ancient species domesticated. The availability of whole genome assemblies and annotations of olive tree cultivars and oleaster (O. europaea subsp. europaea var. sylvestris) has contributed to a better understanding of genetic and genomic differences between olive tree cultivars. However, compared to other plant species there is still a lack of genomic resources for olive tree populations that span the entire Mediterranean region. In the present study we developed the most complete genomic variation map and the most comprehensive catalog/resource of molecular variation to date for 89 olive tree genotypes originating from the entire Mediterranean basin, revealing the genetic diversity of this commercially significant crop tree and explaining the divergence/similarity among different variants. Additionally, the monumental ancient tree 'Throuba Naxos' was studied to characterize the potential origin or routes of olive tree domestication. Several candidate genes known to be associated with key agronomic traits, including olive oil quality and fruit yield, were uncovered by a selective sweep scan to be under selection pressure on all olive tree chromosomes. To further exploit the genomic and phenotypic resources obtained from the current work, genome-wide association analyses were performed for 23 morphological and two agronomic traits. Significant associations were detected for eight traits that provide valuable candidates for fruit tree breeding and for deeper understanding of olive tree biology.
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Affiliation(s)
- Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Thermi, 57001, Thessaloniki, Greece
- Joint Laboratory of Horticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Thermi, 57001, Thessaloniki, Greece
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829, Cologne, Germany
| | - Konstantinos G Alexiou
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona, Spain
| | - Sebastián Ramos-Onsins
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona, Spain
| | - Georgios Koubouris
- Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Chania, 73134, Greece
| | - Nikolaos Tourvas
- Laboratory of Forest Genetics, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Aliki Xanthopoulou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Thermi, 57001, Thessaloniki, Greece
- Joint Laboratory of Horticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Thermi, 57001, Thessaloniki, Greece
| | - Ifigeneia Mellidou
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Thermi, 57001, Thessaloniki, Greece
- Joint Laboratory of Horticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Thermi, 57001, Thessaloniki, Greece
| | - Theodoros Moysiadis
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Thermi, 57001, Thessaloniki, Greece
- Department of Computer Science, School of Sciences and Engineering, University of Nicosia, Nicosia, 2417, Cyprus
| | - Ioanna-Theoni Vourlaki
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries, Barcelona, Spain
| | - Ioannis Metzidakis
- Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Chania, 73134, Greece
| | - Chrysi Sergentani
- Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Chania, 73134, Greece
| | - Ioanna Manolikaki
- Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Chania, 73134, Greece
| | - Michail Michailidis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thermi, 57001, Thessaloniki, Greece
| | - Adamantia Pistikoudi
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Alexios Polidoros
- Laboratory of Genetics and Plant Breeding, School of Agriculture, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | | | - Filippos Aravanopoulos
- Laboratory of Forest Genetics, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thermi, 57001, Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Thermi, 57001, Thessaloniki, Greece
- Joint Laboratory of Horticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Thermi, 57001, Thessaloniki, Greece
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Sirangelo TM, Forgione I, Zelasco S, Benincasa C, Perri E, Vendramin E, Angilè F, Fanizzi FP, Sunseri F, Salimonti A, Carbone F. Combined Transcriptomic and Metabolomic Approach Revealed a Relationship between Light Control, Photoprotective Pigments, and Lipid Biosynthesis in Olives. Int J Mol Sci 2023; 24:14448. [PMID: 37833896 PMCID: PMC10572622 DOI: 10.3390/ijms241914448] [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: 07/17/2023] [Revised: 09/14/2023] [Accepted: 09/20/2023] [Indexed: 10/15/2023] Open
Abstract
Olive possesses excellent nutritional and economic values for its main healthy products. Among them, a high content of antioxidant compounds, balanced during the ripening process, are produced under genetic and environmental control, resulting in high variability among cultivars. The genes involved in these complex pathways are mainly known, but despite many studies which indicated the key role of light quality and quantity for the synthesis of many metabolites in plants, limited information on these topics is available in olive. We carried out a targeted gene expression profiling in three olive cultivars, Cellina di Nardò, Ruveia, and Salella, which were selected for their contrasting oleic acid and phenolic content. The -omics combined approach revealed a direct correlation between a higher expression of the main flavonoid genes and the high content of these metabolites in 'Cellina di Nardò'. Furthermore, it confirmed the key role of FAD2-2 in the linoleic acid biosynthesis. More interestingly, in all the comparisons, a co-regulation of genes involved in photoperception and circadian clock machinery suggests a key role of light in orchestrating the regulation of these pathways in olive. Therefore, the identified genes in our analyses might represent a useful tool to support olive breeding, although further investigations are needed.
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Affiliation(s)
- Tiziana Maria Sirangelo
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
| | - Ivano Forgione
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
| | - Samanta Zelasco
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
| | - Cinzia Benincasa
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
| | - Enzo Perri
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
| | - Elisa Vendramin
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via di Fioranello, 52, 00134 Rome, Italy
| | - Federica Angilè
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Lecce-Monteroni, 73100 Lecce, Italy
| | - Francesco Paolo Fanizzi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Via Lecce-Monteroni, 73100 Lecce, Italy
| | - Francesco Sunseri
- Department Agraria, University Mediterranea of Reggio Calabria, Località Feo di Vito, 89124 Reggio Calabria, Italy
| | - Amelia Salimonti
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
| | - Fabrizio Carbone
- Research Centre for Olive, Fruit and Citrus Crops, Council for Agricultural Research and Economics (CREA), Via Settimio Severo, 83, 87036 Rende, Italy
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Bullones A, Castro AJ, Lima-Cabello E, Fernandez-Pozo N, Bautista R, Alché JDD, Claros MG. Transcriptomic Insight into the Pollen Tube Growth of Olea europaea L. subsp. europaea Reveals Reprogramming and Pollen-Specific Genes Including New Transcription Factors. PLANTS (BASEL, SWITZERLAND) 2023; 12:2894. [PMID: 37631106 PMCID: PMC10459472 DOI: 10.3390/plants12162894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/01/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023]
Abstract
The pollen tube is a key innovation of land plants that is essential for successful fertilisation. Its development and growth have been profusely studied in model organisms, but in spite of the economic impact of olive trees, little is known regarding the genome-wide events underlying pollen hydration and growth in this species. To fill this gap, triplicate mRNA samples at 0, 1, 3, and 6 h of in vitro germination of olive cultivar Picual pollen were analysed by RNA-seq. A bioinformatics R workflow called RSeqFlow was developed contemplating the best practices described in the literature, covering from expression data filtering to differential expression and clustering, to finally propose hub genes. The resulting olive pollen transcriptome consisted of 22,418 reliable transcripts, where 5364 were differentially expressed, out of which 173 have no orthologue in plants and up to 3 of them might be pollen-specific transcription factors. Functional enrichment revealed a deep transcriptional reprogramming in mature olive pollen that is also dependent on protein stability and turnover to allow pollen tube emergence, with many hub genes related to heat shock proteins and F-box-containing proteins. Reprogramming extends to the first 3 h of growth, including processes consistent with studies performed in other plant species, such as global down-regulation of biosynthetic processes, vesicle/organelle trafficking and cytoskeleton remodelling. In the last stages, growth should be maintained from persistent transcripts. Mature pollen is equipped with transcripts to successfully cope with adverse environments, even though the in vitro growth seems to induce several stress responses. Finally, pollen-specific transcription factors were proposed as probable drivers of pollen germination in olive trees, which also shows an overall increased number of pollen-specific gene isoforms relative to other plants.
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Affiliation(s)
- Amanda Bullones
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain;
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-UMA-CSIC), 29010 Malaga, Spain;
| | - Antonio Jesús Castro
- Plant Reproductive Biology and Advanced Imaging Laboratory (BReMAP), Estación Experimental del Zaidín (EEZ-CSIC), 18008 Granada, Spain; (A.J.C.); (E.L.-C.); (J.d.D.A.)
| | - Elena Lima-Cabello
- Plant Reproductive Biology and Advanced Imaging Laboratory (BReMAP), Estación Experimental del Zaidín (EEZ-CSIC), 18008 Granada, Spain; (A.J.C.); (E.L.-C.); (J.d.D.A.)
| | - Noe Fernandez-Pozo
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-UMA-CSIC), 29010 Malaga, Spain;
| | - Rocío Bautista
- Plataforma Andaluza de Bioinformática, Supercomputing and Bioinnovation Center (SCBI), Universidad de Málaga, 29590 Malaga, Spain;
| | - Juan de Dios Alché
- Plant Reproductive Biology and Advanced Imaging Laboratory (BReMAP), Estación Experimental del Zaidín (EEZ-CSIC), 18008 Granada, Spain; (A.J.C.); (E.L.-C.); (J.d.D.A.)
- University Institute of Research on Olive Grove and Olive Oils (INUO), Universidad de Jaén, 23071 Jaen, Spain
| | - Manuel Gonzalo Claros
- Department of Molecular Biology and Biochemistry, Universidad de Málaga, 29010 Malaga, Spain;
- Institute for Mediterranean and Subtropical Horticulture “La Mayora” (IHSM-UMA-CSIC), 29010 Malaga, Spain;
- CIBER de Enfermedades Raras (CIBERER) U741, 29071 Malaga, Spain
- Institute of Biomedical Research in Málaga (IBIMA), IBIMA-RARE, 29010 Malaga, Spain
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Ferrari M, Muto A, Bruno L, Muzzalupo I, Chiappetta A. Modulation of Anthocyanin Biosynthesis-Related Genes during the Ripening of Olea europaea L. cvs Carolea and Tondina Drupes in Relation to Environmental Factors. Int J Mol Sci 2023; 24:ijms24108770. [PMID: 37240115 DOI: 10.3390/ijms24108770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/11/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Anthocyanins protect plants against various biotic and abiotic stresses, and anthocyanin-rich foods exert benefits on human health due to their antioxidant activity. Nevertheless, little information is available on the influence of genetic and environmental factors on the anthocyanin content in olive fruits. Based on this consideration, the total anthocyanin content, the genes involved in anthocyanin biosynthesis, and three putative R2R3-MYB transcription factors were evaluated at different ripening stages in the drupes of the Carolea and Tondina cultivars, sampled at different altitudes in the Calabria region, Italy. During drupe ripening, the total anthocyanin content and the transcript levels of analyzed genes gradually increased. In line with the anthocyanin content, a different level of expression of anthocyanin structural genes was observed in 'Carolea' compared to 'Tondina', and in relation to the cultivation area. Furthermore, we identified Oeu050989.1 as a putative R2R3-MYB involved in the regulation of anthocyanin structural genes correlated with the environmental temperature change response. We conclude that anthocyanin accumulation is strongly regulated by development, genotype, and also by environmental factors such as temperature, associated with the altitude gradient. The obtained results contribute to reducing the current information gap regarding the molecular mechanisms on anthocyanin biosynthesis regulation related to the environmental conditions in Olea europaea.
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Affiliation(s)
- Michele Ferrari
- Department of Biology, Ecology, and Earth Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Antonella Muto
- Department of Biology, Ecology, and Earth Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Leonardo Bruno
- Department of Biology, Ecology, and Earth Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Innocenzo Muzzalupo
- CREA-Council for Agricultural Research and Agricultural Economy Analysis, Forestry and Wood Research Center, 87036 Rende, Italy
| | - Adriana Chiappetta
- Department of Biology, Ecology, and Earth Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
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Skodra C, Michailidis M, Dasenaki M, Ganopoulos I, Thomaidis NS, Tanou G, Molassiotis A. Unraveling salt-responsive tissue-specific metabolic pathways in olive tree. PHYSIOLOGIA PLANTARUM 2021; 173:1643-1656. [PMID: 34537965 DOI: 10.1111/ppl.13565] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 06/13/2023]
Abstract
Salinity is a serious constraint that reduces olive crop productivity. Here, we defined metabolite and gene expression changes in various tissues of olive trees (cv. "Chondrolia Chalkidikis") exposed to 75 mM NaCl for 45 days. Results showed that salinity induced foliar symptoms and impaired growth and photosynthetic parameters. The content of Na+ and Cl- in roots, xylem, phloem and leaves increased, although the Na+ levels in old leaves and Cl- in young leaves remained unaffected. Mannitol was accumulated in roots and old leaves challenged by salinity. NaCl-treated trees have a decreased TCA-associated metabolites, such as citric and malic acid, as well as changes in phenylpropanoid-associated metabolites (i.e., pinoresinol and vanillic acid) and genes (OePLRTp2 and OeCA4H). Salt treatment resulted in hydroxyl-decarboxylmethyl eleuropein aglycone accumulation and OeGTF up-regulation in new leaves, possibly suggesting that oleuropein metabolism was modified by NaCl. Tyrosine metabolism, particularly verbascoside levels and OePPO and OehisC expressions, was modulated by salinity. Both genes (e.g., OeAtF3H and OeFNSII) and metabolites (e.g., apigenin and luteolin) involved in flavonoid biosynthesis were induced in old leaves exposed to NaCl. Based on these data, we constructed an interaction scheme of changes in metabolites and transcripts across olive tissues upon salinity. Particularly, several metabolites involved in carbohydrate metabolism were reduced in roots, while many sugars, carbohydrates and flavonoids were increased in leaves. This study provided a framework for better understanding the possible mechanisms that govern the tissue-specific response of olive tree to salinity stress, with insights into molecules that can be used for olive crop improvement projects.
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Affiliation(s)
- Christina Skodra
- Department of Horticulture, Laboratory of Pomology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Michail Michailidis
- Department of Horticulture, Laboratory of Pomology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Marilena Dasenaki
- Department of Chemistry, Laboratory of Analytical Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, ELGO-DEMETER, Thessaloniki, Greece
- Joint Laboratory of Horticulture, ELGO-DEMETER, Thessaloniki, Greece
| | - Nikolaos S Thomaidis
- Department of Chemistry, Laboratory of Analytical Chemistry, National and Kapodistrian University of Athens, Athens, Greece
| | - Georgia Tanou
- Joint Laboratory of Horticulture, ELGO-DEMETER, Thessaloniki, Greece
- Institute of Soil and Water Resources, ELGO-DEMETER, Thessaloniki, Greece
| | - Athanassios Molassiotis
- Department of Horticulture, Laboratory of Pomology, Aristotle University of Thessaloniki, Thessaloniki, Greece
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