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Servera-Vives G, Ricucci C, Snitker G. OLEAtool: An open-source software for morphopalynological research in Olea europaea L. pollen. OPEN RESEARCH EUROPE 2024; 3:29. [PMID: 38846176 PMCID: PMC11153994 DOI: 10.12688/openreseurope.15309.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Accepted: 03/07/2024] [Indexed: 06/09/2024]
Abstract
In this paper we present OLEAtool, a new software tool for palynological research to facilitate morphological analysis and measurements of Olea pollen. OLEAtool is a macro extension for use with ImageJ, an open-access and freely available image analysis software, and was developed as a component of the OLEA-project. This larger project examines olive tree expansion and mosaic landscape formation on the Balearic Islands. Pollen analysis of both fossil and modern grains has been proven useful for characterizing cultivars and therefore an important method for studying olive tree cultivation in the Mediterranean. However, these methods still struggle with distinguishing between wild and cultivated varieties. Traditional morphological analysis of pollen grains can be a difficult and time-consuming task. However, OLEAtool dramatically increases the speed of collecting data on pollen grains, expands the number of variables an analyst can measure, and greatly enhances the replicability of morphological analysis.
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Affiliation(s)
- Gabriel Servera-Vives
- ArqueoUIB, Department of Historical Sciences and Theory of Art, University of the Balearic Islands, Carretera de Valldemossa Km 7,5, CP07122 Palma, Mallorca, Spain
- Laboratory of Palynology and Palaeobotany, Department of Life Sciences, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Cristina Ricucci
- Laboratory of Palynology and Palaeobotany, Department of Life Sciences, Università degli Studi di Modena e Reggio Emilia, Modena, Italy
| | - Grant Snitker
- Cultural Resource Sciences, New Mexico Consortium, 4200 W. Jemez Rd. Suite 301, Los Alamos, New Mexico, 87544, USA
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2
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Guerrero C, Cerezo S, Feito I, Rodríguez L, Samach A, Mercado JA, Pliego-Alfaro F, Palomo-Ríos E. Effect of heterologous expression of FT gene from Medicago truncatula in growth and flowering behavior of olive plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1323087. [PMID: 38455727 PMCID: PMC10917891 DOI: 10.3389/fpls.2024.1323087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/31/2024] [Indexed: 03/09/2024]
Abstract
Olive (Olea europaea L. subsp. europaea) is one of the most important crops of the Mediterranean Basin and temperate areas worldwide. Obtaining new olive varieties adapted to climatic changing conditions and to modern agricultural practices, as well as other traits such as biotic and abiotic stress resistance and increased oil quality, is currently required; however, the long juvenile phase, as in most woody plants, is the bottleneck in olive breeding programs. Overexpression of genes encoding the 'florigen' Flowering Locus T (FT), can cause the loss of the juvenile phase in many perennials including olives. In this investigation, further characterization of three transgenic olive lines containing an FT encoding gene from Medicago truncatula, MtFTa1, under the 35S CaMV promoter, was carried out. While all three lines flowered under in vitro conditions, one of the lines stopped flowering after acclimatisation. In soil, all three lines exhibited a modified plant architecture; e.g., a continuous branching behaviour and a dwarfing growth habit. Gene expression and hormone content in shoot tips, containing the meristems from which this phenotype emerged, were examined. Higher levels of OeTFL1, a gene encoding the flowering repressor TERMINAL FLOWER 1, correlated with lack of flowering. The branching phenotype correlated with higher content of salicylic acid, indole-3-acetic acid and isopentenyl adenosine, and lower content of abscisic acid. The results obtained confirm that heterologous expression of MtFTa1 in olive induced continuous flowering independently of environmental factors, but also modified plant architecture. These phenotypical changes could be related to the altered hormonal content in transgenic plants.
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Affiliation(s)
- Consuelo Guerrero
- Departamento de Botánica y Fisiología Vegetal, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga, Spanish National Research Council (IHSM-UMA-CSIC), Málaga, Spain
| | - Sergio Cerezo
- Departamento de Botánica y Fisiología Vegetal, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga, Spanish National Research Council (IHSM-UMA-CSIC), Málaga, Spain
| | - Isabel Feito
- Servicio Regional de Investigación y Desarrollo Agroalimentario de Asturias, Finca Experimental “La Mata”, Grado, Spain
| | - Lucía Rodríguez
- Servicio Regional de Investigación y Desarrollo Agroalimentario de Asturias, Finca Experimental “La Mata”, Grado, Spain
| | - Alon Samach
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - José A. Mercado
- Departamento de Botánica y Fisiología Vegetal, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga, Spanish National Research Council (IHSM-UMA-CSIC), Málaga, Spain
| | - Fernando Pliego-Alfaro
- Departamento de Botánica y Fisiología Vegetal, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga, Spanish National Research Council (IHSM-UMA-CSIC), Málaga, Spain
| | - Elena Palomo-Ríos
- Departamento de Botánica y Fisiología Vegetal, Instituto de Hortofruticultura Subtropical y Mediterránea ‘La Mayora’, Universidad de Málaga, Spanish National Research Council (IHSM-UMA-CSIC), Málaga, Spain
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3
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Valverde P, Diez CM, Deger RE, Barranco D, Trapero C. Genotypic influence in the juvenile to adult transition in olive seedlings. FRONTIERS IN PLANT SCIENCE 2024; 15:1343589. [PMID: 38379947 PMCID: PMC10877029 DOI: 10.3389/fpls.2024.1343589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024]
Abstract
Olive breeding is a long process and any improvement in shortening the juvenile phase is highly desirable. In the present study, the effect of olive tree parents in different agronomic characteristics have been evaluated during four years in 520 olive genotypes generated from three different crosses in three different experimental fields, all located in Andalusia region, Spain. The crosses evaluated are 'Arbosana' x 'Sikitita' and its reciprocal, whose parents are characterized by being early bearers; and 'Frantoio' free pollinated, whose mother variety is characterized by having a long unproductive period. We studied plant height, distance and time to the first flowering, plant vigor and percentage of olive oil in the fruits. The findings reveal that progeny from 'Arbosana' and 'Sikitita' crosses, irrespective of the direction of the cross, exhibited a lower distance to flower, early bearing, reduced vigor and a lower percentage of olive oil in fruit compared to 'Frantoio' seedlings obtained from free pollination. Furthermore, no discernible differences were observed in the evaluated characteristics when comparing reciprocal crosses across the three fields in the four-years assessment period. Therefore, these results highlight the significance of planting height in reducing the evaluation period required in an olive breeding program and support the hypothesis that there is no maternal effect in the inheritance of the evaluated agronomic characteristics in olive trees.
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Affiliation(s)
- Pedro Valverde
- Department of Agricultural, Food and Environmental Sciences, Marche Polytechnic University, Ancona, Italy
- Department of Agronomy (Excellence Unit ‘María de Maeztu’ 2020-23), ETSIAM, University of Córdoba, Córdoba, Spain
| | - Concepción Munoz Diez
- Department of Agronomy (Excellence Unit ‘María de Maeztu’ 2020-23), ETSIAM, University of Córdoba, Córdoba, Spain
| | - Rustu Efe Deger
- Department of Agronomy (Excellence Unit ‘María de Maeztu’ 2020-23), ETSIAM, University of Córdoba, Córdoba, Spain
| | - Diego Barranco
- Department of Agronomy (Excellence Unit ‘María de Maeztu’ 2020-23), ETSIAM, University of Córdoba, Córdoba, Spain
| | - Carlos Trapero
- Department of Agronomy (Excellence Unit ‘María de Maeztu’ 2020-23), ETSIAM, University of Córdoba, Córdoba, Spain
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Zipser B, Scott AC, Allkin R, Gan P, Lardos A, Lazarou R, Lev E, Nesbitt M, Patmore K. Pharmaceutical Terminology in Ancient and Medieval Time - andrachne, chrysocolla and Others. STUDIA CERANEA 2023; 13:715-736. [PMID: 38524312 PMCID: PMC7615763 DOI: 10.18778/2084-140x.13.49] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Ancient and medieval pharmacological and medical texts contain a substantial amount of plant and mineral names. In some cases, the identification is straightforward. But for the majority of the data, we are unable to identify these ingredients with high certainty. In this paper, we discuss a selection of plant and mineral names both from a humanities and sciences point of view. In one case, the scientists were even able to examine a plant in situ. The conclusion of our paper is that a close collaboration between sciences and humanities is essential to avoid mistakes in the identification of materia medica.
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Affiliation(s)
- Barbara Zipser
- Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, United Kingdom
| | - Andrew C. Scott
- Royal Holloway, University of London, Egham Hill, Egham, Surrey, TW20 0EX, United Kingdom
| | - Robert Allkin
- Royal Botanic Gardens Kew, Kew, Richmond, London TW9 3AE, Great Britain
| | - Peretz Gan
- Al Alim Medicinal Herb Center, Moshav Zippori 49 Hamovil 1791000, Israel
| | - Andreas Lardos
- Zürcher Hochschule für Angewandte Wissenschaften, Gertrudstrasse 15, 8400 Winterthur, Switzerland
| | - Rebecca Lazarou
- Royal Botanic Gardens Kew, Kew, Richmond, London TW9 3AE, Great Britain
| | - Efraim Lev
- University of Haifa, 199 Aba Khoushy Ave. Mount Carmel, Haifa, Israel
| | - Mark Nesbitt
- Royal Botanic Gardens Kew, Kew, Richmond, London TW9 3AE, Great Britain
| | - Kristina Patmore
- Royal Botanic Gardens Kew, Kew, Richmond, London TW9 3AE, Great Britain
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Tourvas N, Ganopoulos I, Koubouris G, Kostelenos G, Manthos I, Bazakos C, Stournaras V, Molassiotis A, Aravanopoulos F. Wild and cultivated olive tree genetic diversity in Greece: a diverse resource in danger of erosion. Front Genet 2023; 14:1298565. [PMID: 38111682 PMCID: PMC10725918 DOI: 10.3389/fgene.2023.1298565] [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: 09/21/2023] [Accepted: 11/20/2023] [Indexed: 12/20/2023] Open
Abstract
The genetic relationships between Greek wild olive tree populations and cultivars were investigated. A total of 219 wild genotypes and 67 cultivar genotypes were analyzed by employing 10 SSR markers. Data evidenced that the wild populations exhibited high levels of genetic diversity and exclusively host 40% of the total number of alleles detected. Inbreeding was observed within populations, probably as a consequence of their fragmented spatial distribution. The genetic differentiation between cultivars and wild individuals, as well as within wild populations, was low. Nevertheless, three gene pools of wild trees were detected, corresponding to the geographical areas of Northeastern Greece, Peloponnese-Crete and Epirus. Most cultivars clustered in a separate group, while the rest of them formed a heterogenous group with membership coefficients akin to the three wild olive clusters. Regarding the history of olive cultivation in Greece, bidirectional gene flow was detected between populations of Peloponnese-Crete and the gene pool that composes some of Greece's most important cultivars, such as "Koroneiki" and "Mastoidis", which is inferred as an indication of a minor domestication event in the area. A strategy for the protection of Greek-oriented olive genetic resources is proposed, along with suggestions for the utilization of the genetically diverse wild resources with regard to the introgression of traits of agronomical interest to cultivars.
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Affiliation(s)
- Nikolaos Tourvas
- Laboratory of Forest Genetics, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ioannis Ganopoulos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Thessaloniki-Thermi, Greece
| | - Georgios Koubouris
- Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Chania, Greece
| | | | - Ioannis Manthos
- Department of Nut Trees, Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Neo Krikello-Lamia, Greece
| | - Christos Bazakos
- Institute of Plant Breeding and Genetic Resources, Hellenic Agricultural Organization (ELGO) DIMITRA, Thessaloniki-Thermi, Greece
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Vasileios Stournaras
- Department of Olive and Horticultural Crops, Institute of Olive Tree, Subtropical Crops and Viticulture, Hellenic Agricultural Organization (ELGO) DIMITRA, Kalamata, Greece
| | - Athanassios Molassiotis
- Laboratory of Pomology, Department of Horticulture, Aristotle University of Thessaloniki, Thessaloniki-Thermi, Greece
| | - Filippos Aravanopoulos
- Laboratory of Forest Genetics, Faculty of Agriculture, Forestry and Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, Greece
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Huang L, Zeng Y, Li J, Deng Y, Su G, Zhang J. One hundred single-copy nuclear sequence markers for olive variety identification: a case of fingerprinting database construction in China. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2023; 43:86. [PMID: 38028815 PMCID: PMC10678893 DOI: 10.1007/s11032-023-01434-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023]
Abstract
Olive is an ancient oil-producing tree, widely cultivated in Mediterranean countries, and now spread to other areas of the world, including China. Recently, several molecular databases were constructed in different countries and platforms for olive identification using simple sequence repeats (SSRs) or single-nucleotide polymorphisms (SNPs). However, comparing their results across laboratories was difficult. Herein, hundreds of polymorphic single-copy nuclear sequence markers were developed from the olive genome. Using the advantage of multiplex PCR amplification and high-throughput sequencing, a fingerprint database was constructed for the majority of olives cultivated in China. We used 100 high-quality sequence loci and estimated the genetic diversity and structure among all these varieties. We found that compared with that based on SSRs, the constructed fingerprint database based on these 100 sequences or a few of them, could provide a reliable olive variety identification platform in China, with high discrimination among different varieties using the principle of BLAST algorithm. An example of such identification platform based on this study was displayed on the web for the olive database in China (http://olivedb.cn/jianding). After resolving redundant genotypes, we identified 126 olive varieties with distinct genotypes in China. These varieties could be divided into two clusters, and it was revealed that the grouping of the varieties has a certain relationship with their origin. Herein, it is concluded that these single-copy orthologous nuclear sequences could be used to construct a universal fingerprint database of olives across different laboratories and platforms inexpensively. Based on such a database, variety identification can be performed easily by any laboratory, which would further facilitate olive breeding and variety exchange globally. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-023-01434-9.
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Affiliation(s)
- Lan Huang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
| | - Yanfei Zeng
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing, 100091 China
| | - Jinhua Li
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing, 100091 China
| | - Yu Deng
- Institute of Olive, Longnan Academy of Economic Forestry, Longnan, 746000 Gansu China
| | - Guangcan Su
- Liangshan Zhongze New Technology Development Co. Ltd., Xichang, 615042 Sichuan China
| | - Jianguo Zhang
- State Key Laboratory of Tree Genetics and Breeding & Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, No. 1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing, 100091 China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037 China
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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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Mariotti R, Belaj A, de la Rosa R, Muleo R, Cirilli M, Forgione I, Valeri MC, Mousavi S. Genealogical tracing of Olea europaea species and pedigree relationships of var. europaea using chloroplast and nuclear markers. BMC PLANT BIOLOGY 2023; 23:452. [PMID: 37749509 PMCID: PMC10521521 DOI: 10.1186/s12870-023-04440-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 09/04/2023] [Indexed: 09/27/2023]
Abstract
BACKGROUND Olive is one of the most cultivated species in the Mediterranean Basin and beyond. Despite being extensively studied for its commercial relevance, the origin of cultivated olive and the history of its domestication remain open questions. Here, we present a genealogical and kinship relationships analysis by mean of chloroplast and nuclear markers of different genera, subgenus, species, subspecies, ecotypes, cultivated, ancient and wild types, which constitutes one of the most inclusive research to date on the diversity within Olea europaea species. A complete survey of the variability across the nuclear and plastid genomes of different genotypes was studied through single nucleotide polymorphisms, indels (insertions and deletions), and length variation. RESULTS Fifty-six different chlorotypes were identified among the Oleaceae family including Olea europaea, other species and genera. The chloroplast genome evolution, within Olea europaea subspecies, probably started from subsp. cuspidata, which likely represents the ancestor of all the other subspecies and therefore of wild types and cultivars. Our study allows us to hypothesize that, inside the subspecies europaea containing cultivars and the wild types, the ancestral selection from var. sylvestris occurred both in the eastern side of the Mediterranean and in the central-western part of Basin. Moreover, it was elucidated the origin of several cultivars, which depends on the introduction of eastern cultivars, belonging to the lineage E1, followed by crossing and replacement of the autochthonous olive germplasm of central-western Mediterranean Basin. In fact, our study highlighted that two main 'founders' gave the origin to more than 60% of analyzed olive cultivars. Other secondary founders, which strongly contributed to give origin to the actual olive cultivar diversity, were already detected. CONCLUSIONS The application of comparative genomics not only paves the way for a better understanding of the phylogenetic relationships within the Olea europaea species but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance and parentage inside olive cultivars, opening new scenarios for further research such as the association studies and breeding programs.
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Affiliation(s)
- Roberto Mariotti
- Institute of Biosciences and Bioresources, National Research Council, Perugia, 06128, Italy.
| | | | | | - Rosario Muleo
- Department of Agricultural and Forestry Sciences (DAFNE), University of Tuscia, Viterbo, 01100, Italy
| | - Marco Cirilli
- Department of Agricultural and Environmental Sciences (DiSAA), University of Milan, Milan, Italy
| | - Ivano Forgione
- Department of Agricultural and Forestry Sciences (DAFNE), University of Tuscia, Viterbo, 01100, Italy
| | - Maria Cristina Valeri
- Institute of Biosciences and Bioresources, National Research Council, Perugia, 06128, Italy
| | - Soraya Mousavi
- Institute of Biosciences and Bioresources, National Research Council, Perugia, 06128, Italy.
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Passeri V, Sammut C, Mifsud D, Domesi A, Stanzione V, Baldoni L, Mousavi S, Mariotti R, Pandolfi S, Cinosi N, Famiani F, Bufacchi M. The Ancient Olive Trees ( Olea europaea L.) of the Maltese Islands: A Rich and Unexplored Patrimony to Enhance Oliviculture. PLANTS (BASEL, SWITZERLAND) 2023; 12:1988. [PMID: 37653905 PMCID: PMC10221224 DOI: 10.3390/plants12101988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 09/02/2023]
Abstract
A prospecting campaign in the Maltese Islands has ensured the survival of several ancient olive trees (Olea europaea L.), genetically distant from known cultivars. Most of these plants were abandoned or partially cultivated. A two-year evaluation of fruit characteristics and compositions was performed on samples collected from the main representatives of these indigenous genotypes. Analyses were carried out using Gas Chromatography, High-Performance Liquid Chromatography and Near Infrared Spectrometry. Among the fruit samples, a wide range of variations was observed. Some of the genotypes showed fruit traits suitable for table olive production. This is the case of samples with a pulp/pit ratio higher than four, such as 1Wardija, 1Caritas, 1Plattini, 1Bingemma Malta and 3Loretu, whilst 1Bidni, 1Mellieha, 2Qnotta, 3Loretu, 1Bingemma Malta and 1Caritas were suitable for dual purpose. The total phenol content ranged from 6.3 (1Wardija) to 117.9 (2Mtarfa) g/kg of fresh pulp. The average percentage of MUFA was quite low for most of the varieties. These genotypes, which presumably originated in the Maltese Islands and are well adapted to the local pedo-climatic conditions, are being propagated for the following evaluation of their bio-agronomical performance (production, suitability to intensive cultivation, environmental sustainability, product quality, etc.). The purpose is to select, among these local genotypes, the most outstanding varieties, in terms of phenolic and FA profile and agronomical potential, to spread into cultivation, thereby contributing to an increase in the quality of the local table and olive oil production, strongly linked to the territory.
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Affiliation(s)
- Valentina Passeri
- Institute for Agricultural and Forest Systems in the Mediterranean, National Research Council, 06128 Perugia, Italy
| | - Clayton Sammut
- Institute of Earth Systems, Division of Rural Sciences and Food Systems, University of Malta, 2080 Msida, MSD, Malta
| | - David Mifsud
- Institute of Earth Systems, Division of Rural Sciences and Food Systems, University of Malta, 2080 Msida, MSD, Malta
| | - Andrea Domesi
- Institute for Agricultural and Forest Systems in the Mediterranean, National Research Council, 06128 Perugia, Italy
| | - Vitale Stanzione
- Institute for Agricultural and Forest Systems in the Mediterranean, National Research Council, 06128 Perugia, Italy
| | - Luciana Baldoni
- Institute of Biosciences and Bioresources, National Research Council, 06128 Perugia, Italy
| | - Soraya Mousavi
- Institute of Biosciences and Bioresources, National Research Council, 06128 Perugia, Italy
| | - Roberto Mariotti
- Institute of Biosciences and Bioresources, National Research Council, 06128 Perugia, Italy
| | - Saverio Pandolfi
- Institute of Biosciences and Bioresources, National Research Council, 06128 Perugia, Italy
| | - Nicola Cinosi
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 06121 Perugia, Italy (F.F.)
| | - Franco Famiani
- Department of Agricultural, Food and Environmental Sciences, University of Perugia, Borgo XX Giugno, 06121 Perugia, Italy (F.F.)
| | - Marina Bufacchi
- Institute for Agricultural and Forest Systems in the Mediterranean, National Research Council, 06128 Perugia, Italy
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10
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Julca I, Vargas P, Gabaldón T. Phylogenomics of the Olea europaea complex using 15 whole genomes supports recurrent genetic admixture together with differentiation into seven subspecies. BMC Biol 2023; 21:85. [PMID: 37069619 PMCID: PMC10111821 DOI: 10.1186/s12915-023-01583-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The last taxonomic account of Olea recognises six subspecies within Olea europaea L., including the Mediterranean olive tree (subsp. europaea) and five other subspecies (laperrinei, guanchica, maroccana, cerasiformis, and cuspidata) distributed across the Old World, including Macaronesian islands. The evolutionary history of this monophyletic group (O. europaea complex) has revealed a reticulated scenario involving hybridization and polyploidization events, leading to the presence of a polyploid series associated with the subspecies. However, how the polyploids originated, and how the different subspecies contributed to the domestication of the cultivated olive are questions still debated. Tracing the recent evolution and genetic diversification of the species is key for the management and preservation of its genetic resources. To study the recent history of the O. europaea complex, we compared newly sequenced and available genomes for 27 individuals representing the six subspecies. RESULTS Our results show discordance between current subspecies distributions and phylogenomic patterns, which support intricate biogeographic patterns. The subspecies guanchica, restricted to the Canary Islands, is closely related to subsp. europaea, and shows a high genetic diversity. The subsp. laperrinei, restricted now to high mountains of the Sahara desert, and the Canarian subsp. guanchica contributed to the formation of the allotetraploid subsp. cerasiformis (Madeira islands) and the allohexaploid subsp. maroccana (western Sahara region). Our phylogenomic data support the recognition of one more taxon (subsp. ferruginea) for the Asian populations, which is clearly segregated from the African subsp. cuspidata. CONCLUSIONS In sum, the O. europaea complex underwent several processes of hybridization, polyploidy, and geographical isolation resulting in seven independent lineages with certain morphological traits recognised into subspecies.
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Affiliation(s)
- Irene Julca
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Pablo Vargas
- Department of Biodiversity and Conservation, Real Jardín Botánico de Madrid, Calle Claudio Moyano 1, 28014, Madrid, Spain
| | - Toni Gabaldón
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain.
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain.
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain.
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11
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Barazani O, Dag A, Dunseth Z. The history of olive cultivation in the southern Levant. FRONTIERS IN PLANT SCIENCE 2023; 14:1131557. [PMID: 36909452 PMCID: PMC9996078 DOI: 10.3389/fpls.2023.1131557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
The olive tree (Olea europaea L. subsp. europaea var. europaea) is one of the most important crops across the Mediterranean, particularly the southern Levant. Its regional economic importance dates at least to the Early Bronze Age (~3600 BCE) and its cultivation contributed significantly to the culture and heritage of ancient civilizations in the region. In the southern Levant, pollen, pits and wood remains of wild olives (O. europaea subsp. europaea var. sylvestris) has been found in Middle Pleistocene sediments dating to approximately 780 kya, and are present in numerous palynological sequences throughout the Pleistocene and into the Holocene. Archeological evidence indicates the olive oil production from at least the Pottery Neolithic to Chalcolithic transition (~7600-7000 BP), and clear evidence for cultivation by, 7000 BP. It is hypothesized that olive cultivation began through the selection of local genotypes of the wild var. sylvestris. Local populations of naturally growing trees today have thus been considered wild relatives of the olive. However, millennia of cultivation raises questions about whether genuine populations of var. sylvestris remain in the region. Ancient olive landraces might thus represent an ancient genetic stock closer to the ancestor gene pool. This review summarizes the evidence supporting the theory that olives were first cultivated in the southern Levant and reviews our genetic work characterizing local ancient cultivars. The significance and importance of old cultivars and wild populations are discussed, given the immediate need to adapt agricultural practices and crops to environmental degradation and global climate change.
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Affiliation(s)
- Oz Barazani
- Agricultural Research Organization, Institute of Plant Sciences, Department of Vegetables and Field Crops, Rishon LeZion, Israel
| | - Arnon Dag
- Agricultural Research Organization, Institute of Plant Sciences, Department of Fruit Tree Sciences, Gilat Research Center, Gilat, Israel
| | - Zachary Dunseth
- Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, RI, United States
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12
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Manetti G, Brunetti A, Lumia V, Sciarroni L, Marangi P, Cristella N, Faggioli F, Reverberi M, Scortichini M, Pilotti M. Identification and Characterization of Neofusicoccum stellenboschiana in Branch and Twig Dieback-Affected Olive Trees in Italy and Comparative Pathogenicity with N. mediterraneum. J Fungi (Basel) 2023; 9:jof9030292. [PMID: 36983460 PMCID: PMC10053632 DOI: 10.3390/jof9030292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 02/18/2023] [Accepted: 02/19/2023] [Indexed: 02/26/2023] Open
Abstract
For about a decade, olive groves in Apulia (Southern Italy) have been progressively destroyed by Olive Quick Decline Syndrome (OQDS), a disease caused by the bacterium Xylella fastidiosa subsp. pauca (Xfp). Recently, we described an additional wilting syndrome affecting olive trees in that area. The botryosphaeriaceous fungus Neofusicoccum mediterraneum was found associated with the diseased trees, and its high virulence toward olive trees was demonstrated. Given the common features with Branch and Twig Dieback (BTD) of olive tree, occurring in Spain and California, we suggested that the observed syndrome was BTD. During our first survey, we also found a botryosphaeriaceous species other than N. mediterraneum. In the present article, we report the morphological and molecular characterization of this fungal species which we identified as Neofusicoccum stellenboschiana. In the study, we also included for comparison additional N. stellenboschiana isolates obtained from olive trees in Latium and Tuscany region (Central Italy). The occurrence of N. stellenboschiana in olive trees is reported here for the first time in the northern hemisphere. The pathogenicity and virulence were tested in nine inoculation trials, where the Apulian N. stellenboschiana isolate was compared with the isolate from Latium and with the Apulian isolate of N. mediterraneum. Both isolates of N. stellenboschiana proved pathogenic to olive trees. They caused evident bark canker and wood discolouration when inoculated at the base of the stem of two/three-year-old trees and on one-year-old twigs. However, virulence of N. stellenboschiana was significantly lower, though still remarkable, compared with N. mediterraneum in term of necrosis progression in the bark and the wood and capacity of wilting the twigs. Virulence of N. stellenboschiana and N. mediterraneum did not substantially change when inoculations were performed in spring/summer and in autumn, suggesting that these fungal species have the potential to infect and damage olive trees in all seasons. The high thermotolerance of N. stellenboschiana was also revealed with in vitro growth and survival tests. The high virulence of these Botryosphaeriaceae species highlights their contribution in BTD aetiology and the necessity to investigate right away their diffusion and, possibly, the role of additional factors other than Xfp in the general decline of olive groves in Apulia. Hence the importance of assessing the degree of overlap of BTD/Botryosphariaceae with OQDS/Xfp is discussed.
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Affiliation(s)
- Giuliano Manetti
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Angela Brunetti
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Valentina Lumia
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Lorenzo Sciarroni
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Paolo Marangi
- Terranostra S.r.l.s., 72021 Francavilla Fontana, Italy
| | | | - Francesco Faggioli
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 00156 Rome, Italy
| | - Massimo Reverberi
- Department of Environmental Biology, University Sapienza, 00165 Rome, Italy
| | - Marco Scortichini
- Research Centre for Olive, Fruit trees and Citrus Crops, Council for Agricultural Research and Economics (CREA) (CREA-OFA), 00134 Rome, Italy
| | - Massimo Pilotti
- Research Centre for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, 00156 Rome, Italy
- Correspondence: ; Tel.: +39-06-8207-0357
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13
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Kaniewski D, Marriner N, Morhange C, Khater C, Terral JF, Besnard G, Otto T, Luce F, Couillebault Q, Tsitsou L, Pourkerman M, Cheddadi R. Climate change threatens olive oil production in the Levant. NATURE PLANTS 2023; 9:219-227. [PMID: 36702932 DOI: 10.1038/s41477-022-01339-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
The olive tree (Olea europaea L.) is one of the species best adapted to a Mediterranean-type climate1-8. Nonetheless, the Mediterranean Basin is deemed to be a climate change 'hotspot' by the Intergovernmental Panel on Climate Change9,10 because future model projections suggest considerable warming and drying11,12. Within this context, new environmental challenges will arise in the coming decades, which will both weaken and threaten olive-growing areas, leading to a loss of productivity and changes in fruit and oil quality13-15. Olive growing, a core of the Mediterranean economy, might soon be under stress. To probe the link between climate and olive trees, we here report 5,400 years of olive tree dynamics from the ancient city of Tyre, Lebanon. We show that optimal fruiting scales closely with temperature. Present-day and palaeo data define an optimal annual average temperature of 16.9 ± 0.3 °C for olive flowering that has existed at least since the Neolithic period. According to our projections, during the second half of the twenty-first century, temperature increases in Lebanon will have detrimental consequences on olive tree growth and olive oil production, especially in the country's southern regions, which will become too hot for optimal flowering and fruiting. These data provide a template to understand present and future thresholds of olive production under climate change.
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Affiliation(s)
- David Kaniewski
- TRACES, UMR 5608 CNRS, Université Toulouse Jean Jaurès, Toulouse, France.
- Département de Biologie et Géosciences, Université Paul Sabatier - Toulouse III, Toulouse, France.
| | - Nick Marriner
- CNRS, ThéMA, Université de Franche-Comté, UMR 6049, MSHE Ledoux, Besançon, France
| | - Christophe Morhange
- Aix Marseille Université, CNRS, IRD, INRA, Collège de France, CEREGE, Aix-en-Provence, France
- EPHE-Section des Sciences Historiques et Philologiques, AOROC, UMR 8546, CNRS/PSL, École Normale Supérieure, Paris, France
| | - Carla Khater
- Center for Remote Sensing, National Council for Scientific Research - Lebanon, Beirut, Lebanon
| | | | - Guillaume Besnard
- Laboratoire Évolution & Diversité Biologique (EDB UMR 5174), Université de Toulouse, CNRS, UPS, IRD, Toulouse, France
| | - Thierry Otto
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, INP, UPS, Toulouse, France
| | - Frédéric Luce
- Laboratoire Ecologie Fonctionnelle et Environnement, Université de Toulouse, CNRS, INP, UPS, Toulouse, France
| | - Quentin Couillebault
- TRACES, UMR 5608 CNRS, Université Toulouse Jean Jaurès, Toulouse, France
- Aix Marseille Université, CNRS, CCJ, Aix en Provence, France
| | - Labrini Tsitsou
- Aix Marseille Université, CNRS, IRD, INRA, Collège de France, CEREGE, Aix-en-Provence, France
| | - Majid Pourkerman
- Iranian National Institute for Oceanography and Atmospheric Sciences (INIOAS), Tehran, Iran
| | - Rachid Cheddadi
- Université Montpellier II, CNRS-UM-IRD, ISEM, Montpellier, France
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14
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Salmona J, Dresen A, Ranaivoson AE, Manzi S, Le Pors B, Hong-Wa C, Razanatsoa J, Andriaholinirina NV, Rasoloharijaona S, Vavitsara ME, Besnard G. How ancient forest fragmentation and riparian connectivity generate high levels of genetic diversity in a microendemic Malagasy tree. Mol Ecol 2023; 32:299-315. [PMID: 36320175 PMCID: PMC10100191 DOI: 10.1111/mec.16759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 10/13/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
Understanding landscape changes is central to predicting evolutionary trajectories and defining conservation practices. While human-driven deforestation is intense throughout Madagascar, exceptions in areas such as the Loky-Manambato region (north) raise questions regarding the causes and age of forest fragmentation. The Loky-Manambato region also harbours a rich and endemic flora, whose evolutionary origin remains poorly understood. We assessed the genetic diversity of an endangered microendemic Malagasy olive species (Noronhia spinifolia Hong-Wa) to better understand the vegetation dynamics in the Loky-Manambato region and its influence on past evolutionary processes. We characterized 72 individuals sampled across eight forests through nuclear and mitochondrial restriction-associated DNA sequencing data and chloroplast microsatellites. Combined population and landscape genetics analyses indicate that N. spinifolia diversity is largely explained by the current forest cover, highlighting a long-standing habitat mosaic in the region. This sustains a major and long-term role of riparian corridors in maintaining connectivity across these antique mosaic habitats, calling for the study of organismal interactions that promote gene flow.
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Affiliation(s)
- Jordi Salmona
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Axel Dresen
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | - Anicet E Ranaivoson
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France.,Faculté des Sciences, Université de Mahajanga, Mahajanga, Madagascar
| | - Sophie Manzi
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
| | | | - Cynthia Hong-Wa
- Claude E. Phillips Herbarium, Delaware State University, Dover, Delaware, USA
| | - Jacqueline Razanatsoa
- Herbier, Département Flore, Parc Botanique et Zoologique de Tsimbazaza, Antananarivo, Madagascar
| | | | | | | | - Guillaume Besnard
- CNRS-UPS-IRD, UMR5174, Laboratoire Évolution & Diversité Biologique, Université Paul Sabatier, Toulouse, France
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15
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Global ecological niche conservatism and evolution in Olea species. Saudi J Biol Sci 2022; 30:103500. [DOI: 10.1016/j.sjbs.2022.103500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 10/25/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022] Open
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16
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Wu T, Ma T, Xu T, Pan L, Zhang Y, Li Y, Ning D. The De Novo Genome Assembly of Olea europaea subsp. cuspidate, a Widely Distributed Olive Close Relative. Front Genet 2022; 13:868540. [PMID: 36092936 PMCID: PMC9454953 DOI: 10.3389/fgene.2022.868540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 05/09/2022] [Indexed: 11/13/2022] Open
Abstract
The olive complex, comprising six subspecies, is a valuable plant for global trade, human health, and food safety. However, only one subspecies (Olea europaea subsp. europaea, OE) and its wild relative (Olea europaea subsp. europaea var. sylvestris, OS) have genomic references, hindering our understanding of the evolution of this species. Using a hybrid approach by incorporating Illumina, MGI, Nanopore, and Hi-C technologies, we obtained a 1.20-Gb genome assembly for the olive subspecies, Olea europaea subsp. cuspidate (OC), with contig and scaffold N50 values of 5.33 and 50.46 Mb, respectively. A total of 43,511 protein-coding genes were predicted from the genome. Interestingly, we observed a large region (37.5 Mb) of “gene-desert” also called “LTR-hotspot” on chromosome 17. The gene origination analyses revealed a substantial outburst (19.5%) of gene transposition events in the common ancestor of olive subspecies, suggesting the importance of olive speciation in shaping the new gene evolution of OC subspecies. The divergence time between OC and the last common ancestor of OE and OS was estimated to be 4.39 Mya (95% CI: 2.58–6.23 Mya). The pathways of positively selected genes of OC are related to the metabolism of cofactors and vitamins, indicating the potential medical and economic values of OC for further research and utilization. In summary, we constructed the de novo genome assembly and protein-coding gene pool for Olea europaea subsp. cuspidate (OC) in this study, which may facilitate breeding applications of improved olive varieties from this widely distributed olive close relative.
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Affiliation(s)
| | | | | | | | | | - Yongjie Li
- *Correspondence: Yongjie Li, ; Delu Ning,
| | - Delu Ning
- *Correspondence: Yongjie Li, ; Delu Ning,
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Morphological and Eco-Geographic Variation in Algerian Wild Olives. PLANTS 2022; 11:plants11141803. [PMID: 35890437 PMCID: PMC9319472 DOI: 10.3390/plants11141803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/24/2022] [Accepted: 07/06/2022] [Indexed: 11/20/2022]
Abstract
Algerian wild olives can represent an important resource for cultivated olive breeding, since they are characterized by great morphological variability. Moreover, they grow in different bioclimatic environments, including dry and hot climates, making the collections of wild olives a good source of abiotic stress resistance traits. Our study aimed to investigate the morphological diversity of 175 wild olive trees collected in North Algeria along with a wide range of different bioclimatic habitats for studying traits of olive accessions in relation to their different ecogeographical parameters. Wild olive trees were found in five different bioclimates areas spanning from humid to Saharan areas. They showed high variation in all traits, in particular fruit and stone weight, which expressed the highest coefficient of variation, and a high positive correlation between fruit weight/width. Cluster analysis separated the samples into two groups mostly based on fruit and stone size, while no relationship was observed with the area of sampling. Only the Saharan samples showed significantly different foliar and fruit characteristics compared to samples from other bioclimatic areas.
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18
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Anguita-Maeso M, Haro C, Navas-Cortés JA, Landa BB. Primer Choice and Xylem-Microbiome-Extraction Method Are Important Determinants in Assessing Xylem Bacterial Community in Olive Trees. PLANTS (BASEL, SWITZERLAND) 2022; 11:1320. [PMID: 35631745 PMCID: PMC9144944 DOI: 10.3390/plants11101320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 06/15/2023]
Abstract
Understanding the unique and unexplored microbial environment of xylem sap is starting to be of relevant importance for plant health, as it could include microbes that may protect plants against xylem-limited pathogens, such as Verticillium dahliae and Xylella fastidiosa. In this study, we evaluated the effects that the method for extracting the xylem bacterial communities, the plant age and the PCR primers may have on characterizing the xylem-bacterial-community composition by using an NGS approach. Xylem sap was extracted from xylem vessels by using a Scholander pressure chamber, or by macerating wood shavings that were obtained from xylem tissues by using branches from 10-year-old olive trees, or the entire canopy of 1-year-old olive plantlets. Additionally, we compared four different PCR-primer pairs that target 16S rRNA for their efficacy to avoid the coamplification of mitochondria and chloroplast 16S rRNA, as this represents an important drawback in metabarcoding studies. The highest amplifications in the mitochondria and chloroplast reads were obtained when using xylem woody chips with the PCR1-799F/1062R (76.05%) and PCR3-967F/1391R (99.96%) primer pairs. To the contrary, the PCR2-799F/1115R and PCR4-799F/1193R primer pairs showed the lowest mitochondria 16S rRNA amplification (<27.48%), no chloroplast sequences and the highest numbers of bacterial OTUs identified (i.e., 254 and 266, respectively). Interestingly, only 73 out of 172 and 46 out of 181 genera were shared between the xylem sap and woody chips after amplification with PCR2 or PCR4 primers, respectively, which indicates a strong bias of the bacterial-community description, depending on the primers used. Globally, the most abundant bacterial genera (>60% of reads) included Anoxybacillus, Cutibacterium, Pseudomonas, Spirosoma, Methylobacterium-Methylorubrum and Sphingomonas; however, their relative importance varied, depending on the matrix that was used for the DNA extraction and the primer pairs that were used, with the lowest effect due to plant age. These results will help to optimize the analysis of xylem-inhabiting bacteria, depending on whether whole xylematic tissue or xylem sap is used for the DNA extraction. More importantly, it will help to better understand the driving and modifying factors that shape the olive-xylem-bacterial-community composition.
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Utility of EST-SNP Markers for Improving Management and Use of Olive Genetic Resources: A Case Study at the Worldwide Olive Germplasm Bank of Córdoba. PLANTS 2022; 11:plants11070921. [PMID: 35406901 PMCID: PMC9002360 DOI: 10.3390/plants11070921] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 01/11/2023]
Abstract
Olive, the emblematic Mediterranean fruit crop, owns a great varietal diversity, which is maintained in ex situ field collections, such as the World Olive Germplasm Bank of Córdoba (WOGBC), Spain. Accurate identification of WOGBC, one of the world’s largest collections, is essential for efficient management and use of olive germplasm. The present study is the first report of the use of a core set of 96 EST-SNP markers for the fingerprinting of 1273 accessions from 29 countries, including both field and new acquired accessions. The EST-SNP fingerprinting made possible the accurate identification of 668 different genotypes, including 148 detected among the new acquired accessions. Despite the overall high genetic diversity found at WOGBC, the EST-SNPs also revealed the presence of remarkable redundant germplasm mostly represented by synonymy cases within and between countries. This finding, together with the presence of homonymy cases, may reflect a continuous interchange of olive cultivars, as well as a common and general approach for their naming. The structure analysis revealed a certain geographic clustering of the analysed germplasm. The EST-SNP panel under study provides a powerful and accurate genotyping tool, allowing for the foundation of a common strategy for efficient safeguarding and management of olive genetic resources.
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Fanelli V, Mascio I, Falek W, Miazzi MM, Montemurro C. Current Status of Biodiversity Assessment and Conservation of Wild Olive (Olea europaea L. subsp. europaea var. sylvestris). PLANTS 2022; 11:plants11040480. [PMID: 35214813 PMCID: PMC8877956 DOI: 10.3390/plants11040480] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 02/08/2022] [Accepted: 02/09/2022] [Indexed: 12/31/2022]
Abstract
Oleaster (Olea europaea L. subsp. europaea var. sylvestris) is the ancestor of cultivated olive (Olea europaea L. subsp. europaea var. europaea) and it is spread through the whole Mediterranean Basin, showing an overlapping distribution with cultivated olive trees. Climate change and new emerging diseases are expected to severely affect the cultivations of olive in the future. Oleaster presents a higher genetic variability compared to the cultivated olive and some wild trees were found adapted to particularly harsh conditions; therefore, the role of oleaster in the future of olive cultivation may be crucial. Despite the great potential, only recently the need to deeply characterize and adequately preserve the wild olive resources drew the attention of researchers. In this review, we summarized the most important morphological and genetic studies performed on oleaster trees collected in different countries of the Mediterranean Basin. Moreover, we reviewed the strategies introduced so far to preserve and manage the oleaster germplasm collections, giving a future perspective on their role in facing the future agricultural challenges posed by climatic changes and new emerging diseases.
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Affiliation(s)
- Valentina Fanelli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70125 Bari, Italy; (I.M.); (C.M.)
- Correspondence: (V.F.); (M.M.M.)
| | - Isabella Mascio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70125 Bari, Italy; (I.M.); (C.M.)
| | - Wahiba Falek
- Ecole Nationale Superieure de Biotechnologie, Constantine 251000, Algeria;
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70125 Bari, Italy; (I.M.); (C.M.)
- Correspondence: (V.F.); (M.M.M.)
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70125 Bari, Italy; (I.M.); (C.M.)
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, 70125 Bari, Italy
- Support Unit Bari, Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), 70125 Bari, Italy
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Prediction scenarios of past, present, and future environmental suitability for the Mediterranean species Arbutus unedo L. Sci Rep 2022; 12:84. [PMID: 34997024 PMCID: PMC8742115 DOI: 10.1038/s41598-021-03996-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 12/08/2021] [Indexed: 12/02/2022] Open
Abstract
Climate change is a challenge for forests in the coming decades, with a major impact on species adaptation and distribution. The Mediterranean Basin is one of the most vulnerable hotspots for biodiversity conservation under climate change in the world. This research aimed at studying a Mediterranean species well adapted to the region: the Arbutus unedo L. (strawberry tree). The MaxEnt, a presence-only species-distribution software, was used to model A. unedo’s environmental suitability. The current species potential distribution was accessed based on actual occurrences and selected environmental variables and subsequently projected for the Last Glacial Maximum (LGM), the Mid-Holocene (MH), and the years 2050 and 2070, considering the two Representative Concentration Pathways: RCP4.5 and RCP8.5. Results from the LGM projection suggest the presence of refugia in the core of the Mediterranean Basin, in particular the Iberian Peninsula (IP). The projections for the MH indicate increasing climatic suitability for the species and an eastward expansion, relatively to LGM. The predicted future environmental changes will most likely act as a catalyst for suitable habitat loss and a range shift towards the North is likely to occur.
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Brunetti A, Matere A, Lumia V, Pasciuta V, Fusco V, Sansone D, Marangi P, Cristella N, Faggioli F, Scortichini M, Pilotti M. Neofusicoccum mediterraneum Is Involved in a Twig and Branch Dieback of Olive Trees Observed in Salento (Apulia, Italy). Pathogens 2022; 11:53. [PMID: 35056001 PMCID: PMC8780778 DOI: 10.3390/pathogens11010053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 12/30/2021] [Accepted: 12/30/2021] [Indexed: 12/04/2022] Open
Abstract
Olive trees are infected and damaged by Botryosphaeriaceae fungi in various countries. The botryosphaeriaceous fungus Neofusicoccum mediterraneum is highly aggressive and is a major concern for olive groves in Spain and California (USA), where it causes 'branch and twig dieback' characterized by wood discoloration, bark canker, and canopy blight. During surveys of olive groves in Apulia (southern Italy), we noticed that-in some areas-trees were heavily affected by severe branch and twig dieback. In addition, chlorosis and the appearance of red-bronze patches on the leaf preceded the wilting of the foliage, with necrotic leaves persisting on the twigs. Given the severity of the manifestation in zones also subject to olive quick decline syndrome (OQDS) caused by Xylella fastidiosa subsp. pauca, we investigated the etiology and provide indications for differentiating the symptoms from OQDS. Isolation from diseased wood samples revealed a mycete, which was morphologically and molecularly identified as N. mediterraneum. The pathogenicity tests clearly showed that this fungus is able to cause the natural symptoms. Therefore, also considering the low number of tested samples, N. mediterraneum is a potential causal agent of the observed disease. Specifically, inoculation of the twigs caused complete wilting in two to three weeks, while inoculation at the base of the stem caused severe girdling wedge-shaped cankers. The growth rate of the fungus in in vitro tests was progressively higher from 10 to 30 °C, failing to grow at higher temperatures, but keeping its viability even after prolonged exposure at 50 °C. The capacity of the isolate to produce catenulate chlamydospores, which is novel for the species, highlights the possibility of a new morphological strain within N. mediterraneum. Further investigations are ongoing to verify whether additional fungal species are involved in this symptomatology.
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Affiliation(s)
- Angela Brunetti
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Via C.G. Bertero, 22, 00156 Roma, Italy; (A.B.); (A.M.); (V.L.); (V.P.); (V.F.); (D.S.); (F.F.)
| | - Antonio Matere
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Via C.G. Bertero, 22, 00156 Roma, Italy; (A.B.); (A.M.); (V.L.); (V.P.); (V.F.); (D.S.); (F.F.)
| | - Valentina Lumia
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Via C.G. Bertero, 22, 00156 Roma, Italy; (A.B.); (A.M.); (V.L.); (V.P.); (V.F.); (D.S.); (F.F.)
| | - Vittorio Pasciuta
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Via C.G. Bertero, 22, 00156 Roma, Italy; (A.B.); (A.M.); (V.L.); (V.P.); (V.F.); (D.S.); (F.F.)
| | - Valeria Fusco
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Via C.G. Bertero, 22, 00156 Roma, Italy; (A.B.); (A.M.); (V.L.); (V.P.); (V.F.); (D.S.); (F.F.)
| | - Domenico Sansone
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Via C.G. Bertero, 22, 00156 Roma, Italy; (A.B.); (A.M.); (V.L.); (V.P.); (V.F.); (D.S.); (F.F.)
| | - Paolo Marangi
- Terranostra S.r.l.s., Via Monte Grappa, 48, 72021 Francavilla Fontana, Italy; (P.M.); (N.C.)
| | - Nicola Cristella
- Terranostra S.r.l.s., Via Monte Grappa, 48, 72021 Francavilla Fontana, Italy; (P.M.); (N.C.)
| | - Francesco Faggioli
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Via C.G. Bertero, 22, 00156 Roma, Italy; (A.B.); (A.M.); (V.L.); (V.P.); (V.F.); (D.S.); (F.F.)
| | - Marco Scortichini
- Council for Agricultural Research and Economics (CREA)-Research Centre for Olive, Fruit Trees and Citrus Crops (CREA-OFA), Via di Fioranello, 52, 00134 Roma, Italy;
| | - Massimo Pilotti
- Council for Agricultural Research and Economics (CREA)-Research Centre for Plant Protection and Certification (CREA-DC), Via C.G. Bertero, 22, 00156 Roma, Italy; (A.B.); (A.M.); (V.L.); (V.P.); (V.F.); (D.S.); (F.F.)
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Fusco V, Pasciuta V, Lumia V, Matere A, Battaglia V, Bertinelli G, Sansone D, Brunetti A, Pilotti M. Root and stem rot, and wilting of olive tree caused by Dematophora necatrix and associated with Emmia lacerata in Central Italy. EUROPEAN JOURNAL OF PLANT PATHOLOGY 2022; 163:71-96. [PMID: 35095205 PMCID: PMC8783780 DOI: 10.1007/s10658-022-02458-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/31/2021] [Indexed: 05/14/2023]
Abstract
UNLABELLED Lethal wilting was observed on young olive trees cv Favolosa in a grove in central Italy. White mycelial strands wrapped the basal portion of the stems that had been buried during planting. The bark was rotted and the xylem was discoloured. A fungal morphotype was strictly associated with symptomatic plants and identified as Dematophora (ex Rosellinia) necatrix. Pathogenicity tests on cvs Favolosa, Leccino and Ogliarola demonstrated that D. necatrix was the causal agent of the disease. Our investigations revealed that infections occurring during autumn and winter greatly favour the disease. By applying a marcottage to the inoculation point, we accelerated the course of the disease and mimicked the lethal outcome observed in the field. In in vitro tests, seven systemic (potential) fungicides strongly inhibited D. necatrix. Dentamet, Al-phosphite and Thiophanate methyl were selected to be tested in planta with a curative and preventive modality. Only Thiophanate methyl, in preventive modality, fully protected the plants from disease progression throughout the observation period. An additional fungal species was strictly associated with both diseased and apparently healthy plants. Morphological and molecular features identified the fungus as Emmia lacerata, a polypore species within the Irpicaceae, which is the agent of white rot on dead woody substrates. To our knowledge, this is the first time that E. lacerata has been reported in Italy and worldwide on olive trees. Inoculation of ‛Favolosa' trees revealed that it colonizes the xylem without causing visible alterations. The possible role of E. lacerata in the olive tree-D. necatrix pathosystem is discussed. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10658-022-02458-1.
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Affiliation(s)
- Valeria Fusco
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Vittorio Pasciuta
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Valentina Lumia
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Antonio Matere
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Valerio Battaglia
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Giorgia Bertinelli
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Domenico Sansone
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Angela Brunetti
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
| | - Massimo Pilotti
- Research Center for Plant Protection and Certification (CREA-DC), Council for Agricultural Research and Economics, Via C. G. Bertero 22, 00156 Rome, Italy
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Friel J, Bombarely A, Fornell CD, Luque F, Fernández-Ocaña AM. Comparative Analysis of Genotyping by Sequencing and Whole-Genome Sequencing Methods in Diversity Studies of Olea europaea L. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112514. [PMID: 34834877 PMCID: PMC8622120 DOI: 10.3390/plants10112514] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 10/27/2021] [Accepted: 11/11/2021] [Indexed: 05/11/2023]
Abstract
Olive, Olea europaea L., is a tree of great economic and cultural importance in the Mediterranean basin. Thousands of cultivars have been described, of which around 1200 are conserved in the different olive germplasm banks. The genetic characterisation of these cultivars can be performed in different ways. Whole-genome sequencing (WGS) provides more information than the reduced representation methods such as genotype by sequencing (GBS), but at a much higher cost. This may change as the cost of sequencing continues to drop, but, currently, genotyping hundreds of cultivars using WGS is not a realistic goal for most research groups. Our aim is to systematically compare both methodologies applied to olive genotyping and summarise any possible recommendations for the geneticists and molecular breeders of the olive scientific community. In this work, we used a selection of 24 cultivars from an olive core collection from the World Olive Germplasm Collection of the Andalusian Institute of Agricultural and Fisheries Research and Training (WOGBC), which represent the most of the cultivars present in cultivated fields over the world. Our results show that both methodologies deliver similar results in the context of phylogenetic analysis and popular population genetic analysis methods such as clustering. Furthermore, WGS and GBS datasets from different experiments can be merged in a single dataset to perform these analytical methodologies with proper filtering. We also tested the influence of the different olive reference genomes in this type of analysis, finding that they have almost no effect when estimating genetic relationships. This work represents the first comparative study between both sequencing techniques in olive. Our results demonstrate that the use of GBS is a perfectly viable option for replacing WGS and reducing research costs when the goal of the experiment is to characterise the genetic relationship between different accessions. Besides this, we show that it is possible to combine variants from GBS and WGS datasets, allowing the reuse of publicly available data.
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Affiliation(s)
- James Friel
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20122 Milan, Italy; (J.F.); (A.B.)
| | - Aureliano Bombarely
- Dipartimento di Bioscienze, Università degli Studi di Milano, 20122 Milan, Italy; (J.F.); (A.B.)
- Instituto de Biologıa Molecular y Celular de Plantas (IBMCP), CSIC, Universitat Politecnica de Valencia, 46011 Valencia, Spain
| | - Carmen Dorca Fornell
- Departamento de Didáctica de las Matemáticas y las Ciencias Experimentales, Facultad de Educación, Universidad Internacional de la Rioja (UNIR), 26006 Logroño, Spain;
| | - Francisco Luque
- Instituto Universitario de Investigación en Olivar y Aceites de Oliva (INUO), Universidad de Jaén, 23071 Jaén, Spain;
| | - Ana Maria Fernández-Ocaña
- Departamento de Biología Animal, Biologia Vegetal y Ecología, Facultad de Ciencias Experimentales, Campus de Las Lagunillas s/n, Universidad de Jaén UJA, 23071 Jaén, Spain
- Correspondence:
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25
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Assessment of population structure, genetic diversity and relationship of Mediterranean olive accessions using SSR markers and computational tools. Biotechnol Lett 2021; 44:113-127. [PMID: 34761348 DOI: 10.1007/s10529-021-03204-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 10/09/2021] [Indexed: 01/09/2023]
Abstract
Olive tree is an emblematic crop of the Mediterranean region, mainly renowned for its fruit oil, although the species provides several industrial purposes. The Mediterranean basin constitutes the origin of olive species diversification and represents a valuable source of genetic variability of olive germplasm. Therefore, the evaluation of the diversity and the population structure of this Mediterranean germplasm is a challenge for olive species preservation, crop breeding and genetic improvement. In this context, our study aims to analyze the genetic diversity and the population structure of 79 Mediterranean olive accessions using 15 genomic SSRs and by applying computational model-based approaches. The used SSRs revealed a total number of 225 alleles with a mean of 15 alleles per locus. Observed and expected heterozygosity (Ho = 0.79, He = 0.805) with a Polymorphism Information Content value of 0.775 indicate high level of genetic diversity. All results of the Unweighted Pair Group Method with Arithmetic (UPGMA), Jaccard similarity index, Principal Coordinate Analysis (PCoA) and the Bayesian analyses supported the separation of the Mediterranean varieties in two sub-populations, one of which mainly composed by Spanish accessions.
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26
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Nobre T. Olive fruit fly and its obligate symbiont Candidatus Erwinia dacicola: Two new symbiont haplotypes in the Mediterranean basin. PLoS One 2021; 16:e0256284. [PMID: 34495983 PMCID: PMC8425570 DOI: 10.1371/journal.pone.0256284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/03/2021] [Indexed: 11/19/2022] Open
Abstract
The olive fruit fly, specialized to become monophagous during several life stages, remains the most important olive tree pest with high direct production losses, but also affecting the quality, composition, and inherent properties of the olives. Thought to have originated in Africa is nowadays present wherever olive groves are grown. The olive fruit fly evolved to harbor a vertically transmitted and obligate bacterial symbiont -Candidatus Erwinia dacicola- leading thus to a tight evolutionary history between olive tree, fruit fly and obligate, vertical transmitted symbiotic bacterium. Considering this linkage, the genetic diversity (at a 16S fragment) of this obligate symbiont was added in the understanding of the distribution pattern of the holobiont at nine locations throughout four countries in the Mediterranean Basin. This was complemented with mitochondrial (four mtDNA fragments) and nuclear (ten microsatellites) data of the host. We focused on the previously established Iberian cluster for the B. oleae structure and hypothesised that the Tunisian samples would fall into a differentiated cluster. From the host point of view, we were unable to confirm this hypothesis. Looking at the symbiont, however, two new 16S haplotypes were found exclusively in the populations from Tunisia. This finding is discussed in the frame of host-symbiont specificity and transmission mode. To understand olive fruit fly population diversity and dispersion, the dynamics of the symbiont also needs to be taken into consideration, as it enables the fly to, so efficiently and uniquely, exploit the olive fruit resource.
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Affiliation(s)
- Tânia Nobre
- MED - Mediterranean Institute for Agriculture, Environment and Development, Instituto de Investigação e Formação Avançada, Universidade de Évora, Pólo da Mitra, Évora, Portugal
- * E-mail:
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Arenas-Castro S, Gonçalves J. SDM-CropProj - A model-assisted framework to forecast crop environmental suitability and fruit production. MethodsX 2021; 8:101394. [PMID: 34430290 PMCID: PMC8374490 DOI: 10.1016/j.mex.2021.101394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 05/21/2021] [Indexed: 11/20/2022] Open
Abstract
The effects of climate change (CC) will impact species ranges, and crops are no exception. Anticipating these changes through forecasting the environmentally suitable area of crops would help to reduce or mitigate the impact and adapt ecological and economic strategies. To forecast the CC effects on crops, we describe here a model-assisted framework (hereafter SDM-CropProj) that combines two modelling steps to be implemented in sequence: i) a multi-technique calibration process and ensemble-forecasting approach to predict the current and future environmental suitability of target crops; ii) a parsimonious univariate log-log linear model to relate the average total annual production to the current SDM-based suitable area. Different metrics for assessing the model's predictive performance showed that:Crop production is related to model-predicted suitable area, thus allowing to obtain future projections of total fruit production based on climate scenarios. The SDM-CropProj framework can assess potential pathways and trends in annual production due to changes in the environmental suitability and the distribution of multiple crop varieties/types as a consequence of CC, offering insights to other areas and crop types.
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Affiliation(s)
- Salvador Arenas-Castro
- Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Praça Gen. Barbosa 44, 4900-347 Viana do Castelo, Portugal
- Área de Ecología, Dpto. de Botánica, Ecología y Fisiología Vegetal, Facultad de Ciencias, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, España
- InBIO/CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal
- Corresponding author.
| | - João Gonçalves
- Escola Superior Agrária, Instituto Politécnico de Viana do Castelo, Praça Gen. Barbosa 44, 4900-347 Viana do Castelo, Portugal
- InBIO/CIBIO - Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Rua Padre Armando Quintas, 4485-601 Vairão, Portugal
- proMetheus - Instituto Politécnico de Viana do Castelo, Rua Escola Industrial e Comercial Nun’Álvares, 4900-347 Viana do Castelo, Portugal
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Badad O, Lakhssassi N, Zaid N, El Baze A, Zaid Y, Meksem J, Lightfoot DA, Tombuloglu H, Zaid EH, Unver T, Meksem K. Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil. PLANTS 2021; 10:plants10071405. [PMID: 34371608 PMCID: PMC8309279 DOI: 10.3390/plants10071405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/31/2022]
Abstract
Secondary metabolites are particularly important to humans due to their pharmaceutical properties. Moreover, secondary metabolites are key compounds in climate change adaptation in long-living trees. Recently, it has been described that the domestication of Olea subspecies had no major selection signature on coding variants and was mainly related to changes in gene expression. In addition, the phenotypic plasticity in Olea subspecies was linked to the activation of transposable elements in the genes neighboring. Here, we investigated the imprint of DNA methylation in the unassigned fraction of the phenotypic plasticity of the Olea subspecies, using methylated DNA immuno-precipitation sequencing (MeDIP-seq) for a high-resolution genome-wide DNA methylation profiling of leaves and fruits during fruit development in wild and cultivated olives from Turkey. Notably, the methylation profiling showed a differential DNA methylation in secondary metabolism responsible for the sensory quality of olive oil. Here, we highlight for the first time the imprint of DNA methylation in modulating the activity of the Linoleate 9S lipoxygenase in the biosynthesis of volatile aromatic compounds. Unprecedently, the current study reveals the methylation status of the olive genome during fruit ripening.
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Affiliation(s)
- Oussama Badad
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
| | - Nabil Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
| | - Younes Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
- Research Center, Abulcasis University of Health Sciences, Rabat 10000, Morocco
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA;
| | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia;
| | - El Houcine Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
| | - Turgay Unver
- Ficus Biotechnology, Ostim OSB Mah, 100. Yil Blv, No:55, Yenimahalle, Ankara 06000, Turkey
- Correspondence: (T.U.); (K.M.)
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
- Correspondence: (T.U.); (K.M.)
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29
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The Monumental Olive Trees as Biocultural Heritage of Mediterranean Landscapes: The Case Study of Sicily. SUSTAINABILITY 2021. [DOI: 10.3390/su13126767] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Monumental olive trees, with their longevity and their remarkable size, represent an important information source for the comprehension of the territory where they grow and the human societies that have kept them through time. Across the centuries, olive trees are the only cultivated plants that tell the story of Mediterranean landscapes. The same as stone monuments, these green monuments represent a real Mediterranean natural and cultural heritage. The aim of this paper is to discuss the value of monumental trees as “biocultural heritage” elements and the role they play in the interpretation of the historical stratification of the landscape. We present the results of a survey of the most significant olive trees growing in Sicily. The selection was based on the “monumentality” aspects of trees, taking into account dendrometric parameters and environmental contexts. The collected dataset constitutes a heterogeneous sample of 367 specimens of considerable size that, in some cases, reach a circumference of about 19 m. Starting from the data presented here, the whole Sicilian territory shows a historical relationship between human and olive. The presence of these plant monuments is, therefore, evidence of long-term, often centennial, landscapes as a result of sustainable use of the territory.
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Early production of table olives at a mid-7th millennium BP submerged site off the Carmel coast (Israel). Sci Rep 2021; 11:2218. [PMID: 33500447 PMCID: PMC7838305 DOI: 10.1038/s41598-020-80772-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 12/23/2020] [Indexed: 11/25/2022] Open
Abstract
We present here the earliest evidence for large-scale table olive production from the mid-7th millennium BP inundated site of Hishuley Carmel on the northern Mediterranean coast of Israel. Olive pit size and fragmentation patterns, pollen as well as the architecture of installations associated with pits from this site, were compared to finds from the nearby and slightly earlier submerged Kfar Samir site. Results indicate that at Kfar Samir olive oil was extracted, while at Hishuley Carmel the data showed that large quantities of table olives, the oldest reported to date, were prepared. This process was most probably facilitated by the site’s proximity to the Mediterranean Sea, which served as a source of both sea water and salt required for debittering/pickling/salting the fruit, as experimentally demonstrated in this study. Comparison of pit morphometry from modern cultivars, wild-growing trees and the archaeological sites, intimates that in pit morphology the ancient pits resemble wild olives, but we cannot totally exclude the possibility that they derive from early cultivated trees. Our findings demonstrate that in this region, olive oil production may have predated table olive preparation, with each development serving as a milestone in the early exploitation of the olive.
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Sales H, Šatović Z, Alves ML, Fevereiro P, Nunes J, Vaz Patto MC. Accessing Ancestral Origin and Diversity Evolution by Net Divergence of an Ongoing Domestication Mediterranean Olive Tree Variety. FRONTIERS IN PLANT SCIENCE 2021; 12:688214. [PMID: 34249057 PMCID: PMC8265600 DOI: 10.3389/fpls.2021.688214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 05/17/2021] [Indexed: 05/17/2023]
Abstract
Olea europaea 'Galega vulgar' variety is a blend of West and Central Mediterranean germplasm with cultivated-wild admixture characteristics. 'Galega vulgar' is known for its high rusticity and superior-quality olive oil, being the main Portuguese variety with high impact for bioeconomy. Nevertheless, it has been replaced by higher-yielding and more adapted to intensive production foreign varieties. To clarify the potential ancestral origin, genetic diversity evolution, and existing genetic relationships within the national heritage of 'Galega vulgar', 595 trees, belonging to ancient and centenary age groups and prospected among ten traditional production regions, were characterized using 14 SSR markers after variety validation by endocarp measurements. Ninety-five distinguishable genets were identified, revealing the presence of a reasonable amount of intra-genetic and morphological variability. A minimum spanning tree, depicting the complete genealogy of all identified genets, represented the 'Galega vulgar' intra-varietal diversity, with 94% of the trees showing only a two-allele difference from the most frequent genet (C001). Strong correlations between the number of differentiating alleles from C001, the clonal size, and their net divergence suggested an ancestral monoclonal origin of the 'Galega vulgar', with the most frequent genet identified as the most likely origin of all the genets and phenotypic diversification occurring through somatic mutations. Genetic erosion was detected through the loss of some allele combinations across time. This work highlights the need to recover the lost diversity in this traditional olive variety by including ancient private genets (associated with potential adaptation traits) in future breeding programs and investing in the protection of these valuable resources in situ by safeguarding the defined region of origin and dispersion of 'Galega vulgar'. Furthermore, this approach proved useful on a highly diverse olive variety and thus applicable to other diverse varieties due either to their intermediate nature between different gene pools or to the presence of a mixture of cultivated and wild traits (as is the case of 'Galega vulgar').
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Affiliation(s)
- Hélia Sales
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- Centre Bio R&D Unit, Association BLC3 – Technology and Innovation Campus, Lagares, Oliveira do Hospital, Portugal
- *Correspondence: Hélia Sales
| | - Zlatko Šatović
- Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia
| | - Mara Lisa Alves
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Pedro Fevereiro
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
- InnovPlantProtect - Collaborative Laboratory, Estrada de Gil Vaz, Elvas, Portugal
| | - João Nunes
- Centre Bio R&D Unit, Association BLC3 – Technology and Innovation Campus, Lagares, Oliveira do Hospital, Portugal
| | - Maria Carlota Vaz Patto
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
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Julca I, Marcet-Houben M, Cruz F, Gómez-Garrido J, Gaut BS, Díez CM, Gut IG, Alioto TS, Vargas P, Gabaldón T. Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.). BMC Biol 2020; 18:148. [PMID: 33100219 PMCID: PMC7586694 DOI: 10.1186/s12915-020-00881-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 09/27/2020] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework. RESULTS We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)-and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000-14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place. CONCLUSIONS Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin.
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Affiliation(s)
- Irene Julca
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Universitat Autònoma de Barcelona (UAB), 08193, Barcelona, Spain
| | - Marina Marcet-Houben
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- Present address: Barcelona Supercomputing Centre (BSC-CNS), and Institute for Research in Biomedicine (IRB), Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Jèssica Gómez-Garrido
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Brandon S Gaut
- Department Ecology and Evolutionary Biology, University of California Irvine, Irvine, CA, 92697, USA
| | | | - Ivo G Gut
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Tyler S Alioto
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Pablo Vargas
- Royal Botanical Garden of Madrid. Consejo Superior de Investigaciones Científicas (CSIC), 28014, Madrid, Spain
| | - Toni Gabaldón
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003, Barcelona, Spain.
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.
- Present address: Barcelona Supercomputing Centre (BSC-CNS), and Institute for Research in Biomedicine (IRB), Barcelona, Spain.
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010, Barcelona, Spain.
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Genetic Resources of Olea europaea L. in the Garda Trentino Olive Groves Revealed by Ancient Trees Genotyping and Parentage Analysis of Drupe Embryos. Genes (Basel) 2020; 11:genes11101171. [PMID: 33036264 PMCID: PMC7600466 DOI: 10.3390/genes11101171] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 09/18/2020] [Accepted: 10/03/2020] [Indexed: 11/17/2022] Open
Abstract
The area of the Garda Lake within the Trentino province (north of Italy) is the northernmost part of Europe where the Mediterranean species Olea europaea L. is traditionally cultivated. ‘Casaliva’ is claimed as the main variety traditionally grown in the Garda Trentino area (GT) from which a world renowned niche extra virgin olive oil is produced. Since a dominant presence of ‘Casaliva’ would link the fruit set success and yield to a self-pollination compatibility system, a deep genetic survey of the olive tree population in the GT has been performed with the aim of establishing the actual varietal composition and of understanding from which pollen donor the ‘Casaliva’ olives originate. Forty-four different genetic profiles were observed among the 205 leaf samples collected from 106 ancient trees through the analysis of 20 nuclear microsatellite markers. The varietal composition in modern orchards was also explored and the vast majority of the additional 151 trees analyzed showed the same genotype as the ancient accessions of ‘Casaliva’. The results support the long historical link of ‘Casaliva’ with the GT and, besides a high varietal homogeneity, they also revealed the presence of olive genetic resources essential to fruit production. In fact, the parentage analysis of 550 embryos from drupes of ‘Casaliva’ evidenced that a cross-fertilization system is favored and a list of candidate cultivars most suitable as local pollinizers of ‘Casaliva’ was identified.
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Mariotti R, Belaj A, De La Rosa R, Leòn L, Brizioli F, Baldoni L, Mousavi S. EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives. Genes (Basel) 2020; 11:E916. [PMID: 32785094 PMCID: PMC7465833 DOI: 10.3390/genes11080916] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 08/04/2020] [Accepted: 08/07/2020] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers. METHODS In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms. RESULTS Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported. CONCLUSION This deep EST-SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation.
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Affiliation(s)
- Roberto Mariotti
- CNR—Institute of Biosciences and Bioresources, Via Madonna Alta 130, 06128 Perugia, Italy; (R.M.); (F.B.); (S.M.)
| | - Angjelina Belaj
- IFAPA—Centro Alameda del Obispo, Avda Menendez Pidal, s/n, E-14004 Cordoba, Spain; (A.B.); (R.D.L.R.); (L.L.)
| | - Raul De La Rosa
- IFAPA—Centro Alameda del Obispo, Avda Menendez Pidal, s/n, E-14004 Cordoba, Spain; (A.B.); (R.D.L.R.); (L.L.)
| | - Lorenzo Leòn
- IFAPA—Centro Alameda del Obispo, Avda Menendez Pidal, s/n, E-14004 Cordoba, Spain; (A.B.); (R.D.L.R.); (L.L.)
| | - Federico Brizioli
- CNR—Institute of Biosciences and Bioresources, Via Madonna Alta 130, 06128 Perugia, Italy; (R.M.); (F.B.); (S.M.)
| | - Luciana Baldoni
- CNR—Institute of Biosciences and Bioresources, Via Madonna Alta 130, 06128 Perugia, Italy; (R.M.); (F.B.); (S.M.)
| | - Soraya Mousavi
- CNR—Institute of Biosciences and Bioresources, Via Madonna Alta 130, 06128 Perugia, Italy; (R.M.); (F.B.); (S.M.)
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Díaz-Rueda P, Franco-Navarro JD, Messora R, Espartero J, Rivero-Núñez CM, Aleza P, Capote N, Cantos M, García-Fernández JL, de Cires A, Belaj A, León L, Besnard G, Colmenero-Flores JM. SILVOLIVE, a Germplasm Collection of Wild Subspecies With High Genetic Variability as a Source of Rootstocks and Resistance Genes for Olive Breeding. FRONTIERS IN PLANT SCIENCE 2020; 11:629. [PMID: 32547577 PMCID: PMC7270354 DOI: 10.3389/fpls.2020.00629] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
Wild subspecies of Olea europaea constitute a source of genetic variability with huge potential for olive breeding to face global changes in Mediterranean-climate regions. We intend to identify wild olive genotypes with optimal adaptability to different environmental conditions to serve as a source of rootstocks and resistance genes for olive breeding. The SILVOLIVE collection includes 146 wild genotypes representative of the six O. europaea subspecies and early-generations hybrids. These genotypes came either from olive germplasm collections or from direct prospection in Spain, continental Africa and the Macaronesian archipelago. The collection was genotyped with plastid and nuclear markers, confirming the origin of the genotypes and their high genetic variability. Morphological and architectural parameters were quantified in 103 genotypes allowing the identification of three major groups of correlative traits including vigor, branching habits and the belowground-to-aboveground ratio. The occurrence of strong phenotypic variability in these traits within the germplasm collection has been shown. Furthermore, wild olive relatives are of great significance to be used as rootstocks for olive cultivation. Thus, as a proof of concept, different wild genotypes used as rootstocks were shown to regulate vigor parameters of the grafted cultivar "Picual" scion, which could improve the productivity of high-density hedgerow orchards.
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Affiliation(s)
- Pablo Díaz-Rueda
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Juan D. Franco-Navarro
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Rita Messora
- Plant Physiology Laboratory, Dipartimento Sci Vita, Univ Modena & Reggio Emilia, Modena, Italy
| | - Joaquín Espartero
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Carlos M. Rivero-Núñez
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Pablo Aleza
- Centro de Citricultura y Producción Vegetal, Instituto Valenciano de Investigaciones Agrarias, Moncada, Spain
| | - Nieves Capote
- Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA) Centro Las Torres, Seville, Spain
| | - Manuel Cantos
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Jose L. García-Fernández
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
| | - Alfonso de Cires
- Departamento de Biología Vegetal y Ecología, Fac Biología, Univ de Sevilla, Seville, Spain
| | - Angjelina Belaj
- Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA) Centro Alameda del Obispo, Córdoba, Spain
| | - Lorenzo León
- Andalusian Institute of Agricultural and Fisheries Research and Training (IFAPA) Centro Alameda del Obispo, Córdoba, Spain
| | - Guillaume Besnard
- CNRS-UPS-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse, France
| | - Jose M. Colmenero-Flores
- Instituto de Recursos Naturales y Agrobiología, Spanish National Research Council (CSIC), Seville, Spain
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Bourguiba H, Scotti I, Sauvage C, Zhebentyayeva T, Ledbetter C, Krška B, Remay A, D’Onofrio C, Iketani H, Christen D, Krichen L, Trifi-Farah N, Liu W, Roch G, Audergon JM. Genetic Structure of a Worldwide Germplasm Collection of Prunus armeniaca L. Reveals Three Major Diffusion Routes for Varieties Coming From the Species' Center of Origin. FRONTIERS IN PLANT SCIENCE 2020; 11:638. [PMID: 32523597 PMCID: PMC7261834 DOI: 10.3389/fpls.2020.00638] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/24/2020] [Indexed: 05/22/2023]
Abstract
The characterization of the largest worldwide representative data set of apricot (Prunus armeniaca L.) germplasm was performed using molecular markers. Genetic diversity and structure of the cultivated apricot genetic resources were analyzed to decipher the history of diffusion of this species around the world. A common set of 25 microsatellite markers was used for genotyping a total of 890 apricot accessions in different collections from the center of origin to the more recent regions of apricot culture. Using a Bayesian model-based clustering approach, the apricot genotypes can be structured into five different genetic clusters (FST = 0.174), correlated with the geographical regions of origin of the accessions. Accessions from China and Central Asia were clustered together and exhibited the highest levels of diversity, confirming an origin in this region. A loss of genetic diversity was observed from the center of origin to both western and eastern zones of recent apricot culture. Altogether, our results revealed that apricot spread from China and Central Asia, defined as the center of origin, following three major diffusion routes with a decreasing gradient of genetic variation in each geographical group. The identification of specific alleles outside the center of origin confirmed the existence of different secondary apricot diversification centers. The present work provides more understanding of the worldwide history of apricot species diffusion as well as the field of conservation of the available genetic resources. Data have been used to define an apricot core collection based on molecular marker diversity which will be useful for further identification of genomic regions associated with commercially important horticultural traits through genome-wide association studies to sustain apricot breeding programs.
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Affiliation(s)
- Hedia Bourguiba
- LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Ivan Scotti
- INRA Centre PACA, UR 629 URFM, Avignon, France
| | | | - Tetyana Zhebentyayeva
- Schatz Center for Tree Molecular Genetics, The Pennsylvania State University, University Park, PA, United States
| | - Craig Ledbetter
- San Joaquin Valley Agricultural Sciences Center, Crop Diseases, Pests & Genetics, Parlier, CA, United States
| | - Boris Krška
- Department of Fruit Growing, Faculty of Horticulture, Mendel University, Lednice, Czechia
| | | | - Claudio D’Onofrio
- Dipartimento di Scienze Agrarie, Alimentari e Agro-Ambientali, Università di Pisa, Pisa, Italy
| | - Hiroyuki Iketani
- National Agriculture and Food Research Organization (NARO) Institute of Fruit Tree Science, Tsukuba, Japan
| | - Danilo Christen
- Département Fédéral de L’économie DFE, Station de Recherche Agroscope Changins-Wädenswil ACW, Centre de Recherche Conthey, Conthey, Switzerland
| | - Lamia Krichen
- LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Neila Trifi-Farah
- LR99ES12, Laboratoire de Génétique Moléculaire, Immunologie et Biotechnologie, Faculté des Sciences de Tunis, Université Tunis El Manar, Tunis, Tunisia
| | - Weisheng Liu
- Liaoning Institute of Pomology, Yingkou City, China
| | - Guillaume Roch
- INRA Centre PACA, UR 1052 GAFL, Montfavet, France
- CEP Innovation, Lyon, France
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Haddad B, Gristina AS, Mercati F, Saadi AE, Aiter N, Martorana A, Sharaf A, Carimi F. Molecular Analysis of the Official Algerian Olive Collection Highlighted a Hotspot of Biodiversity in the Central Mediterranean Basin. Genes (Basel) 2020; 11:E303. [PMID: 32183122 PMCID: PMC7140851 DOI: 10.3390/genes11030303] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Revised: 03/04/2020] [Accepted: 03/09/2020] [Indexed: 12/20/2022] Open
Abstract
Genetic diversity and population structure studies of local olive germplasm are important to safeguard biodiversity, for genetic resources management and to improve the knowledge on the distribution and evolution patterns of this species. In the present study Algerian olive germplasm was characterized using 16 nuclear (nuSSR) and six chloroplast (cpSSR) microsatellites. Algerian varieties, collected from the National Olive Germplasm Repository (ITAFV), 10 of which had never been genotyped before, were analyzed. Our results highlighted the presence of an exclusive genetic core represented by 13 cultivars located in a mountainous area in the North-East of Algeria, named Little Kabylie. Comparison with published datasets, representative of the Mediterranean genetic background, revealed that the most Algerian varieties showed affinity with Central and Eastern Mediterranean cultivars. Interestingly, cpSSR phylogenetic analysis supported results from nuSSRs, highlighting similarities between Algerian germplasm and wild olives from Greece, Italy, Spain and Morocco. This study sheds light on the genetic relationship of Algerian and Mediterranean olive germplasm suggesting possible events of secondary domestication and/or crossing and hybridization across the Mediterranean area. Our findings revealed a distinctive genetic background for cultivars from Little Kabylie and support the increasing awareness that North Africa represents a hotspot of diversity for crop varieties and crop wild relative species.
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Affiliation(s)
- Benalia Haddad
- Département de Productions Végétales, Laboratoire Amélioration Intégrative Des Productions Végétales (AIPV, C2711100), Ecole Nationale Supérieure Agronomique (ENSA), Hassan Badi, El Harrach, Algiers 16000, Algeria;
| | - Alessandro Silvestre Gristina
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
| | - Francesco Mercati
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
| | - Abd Elkader Saadi
- University Hassiba Benbouali, Faculty of Science of Nature and Life, Plant Biotechnology Laboratory, BP 151, Chlef 02000, Algeria;
| | - Nassima Aiter
- Université Saad Dahleb-Blida 1, Faculté des Sciences de la Nature et de la Vie, Laboratoire de Biotechnologie des Productions Végétales, Département de Biotechnologies, Blida 09000, Algeria
- Laboratoire de culture in vitro, Département central, Institut Technique de l’Arboriculture Fruitière et de la Vigne, ITAFV, Algiers 16000, Algeria
| | - Adriana Martorana
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
| | - Abdoallah Sharaf
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
- Institute of Molecular Biology of Plants, Biology Centre, CAS, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Francesco Carimi
- Institute of Biosciences and BioResources, National Research Council (CNR), Research Division of Palermo, Corso Calatafimi 414, 90129 Palermo, Italy; (F.M.); (A.M.); (A.S.); (F.C.)
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Jiménez-Ruiz J, Ramírez-Tejero JA, Fernández-Pozo N, Leyva-Pérez MDLO, Yan H, Rosa RDL, Belaj A, Montes E, Rodríguez-Ariza MO, Navarro F, Barroso JB, Beuzón CR, Valpuesta V, Bombarely A, Luque F. Transposon activation is a major driver in the genome evolution of cultivated olive trees (Olea europaea L.). THE PLANT GENOME 2020; 13:e20010. [PMID: 33016633 DOI: 10.1002/tpg2.20010] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Accepted: 01/15/2020] [Indexed: 05/25/2023]
Abstract
The primary domestication of olive (Olea europaea L.) in the Levant dates back to the Neolithic period, around 6,000-5,500 BC, as some archeological remains attest. Cultivated olive trees are reproduced clonally, with sexual crosses being the sporadic events that drive the development of new varieties. In order to determine the genomic changes which have occurred in a modern olive cultivar, the genome of the Picual cultivar, one of the most popular olive varieties, was sequenced. Additional 40 cultivated and 10 wild accessions were re-sequenced to elucidate the evolution of the olive genome during the domestication process. It was found that the genome of the 'Picual' cultivar contains 79,667 gene models, of which 78,079 were protein-coding genes and 1,588 were tRNA. Population analyses support two independent events in olive domestication, including an early possible genetic bottleneck. Despite genetic bottlenecks, cultivated accessions showed a high genetic diversity driven by the activation of transposable elements (TE). A high TE gene expression was observed in presently cultivated olives, which suggests a current activity of TEs in domesticated olives. Several TEs families were expanded in the last 5,000 or 6,000 years and produced insertions near genes that may have been involved in selected traits during domestication as reproduction, photosynthesis, seed development, and oil production. Therefore, a great genetic variability has been found in cultivated olive as a result of a significant activation of TEs during the domestication process.
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Affiliation(s)
- Jaime Jiménez-Ruiz
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Jorge A Ramírez-Tejero
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Noé Fernández-Pozo
- Plant Cell Biology, Faculty of Biology, University of Marburg, Marburg, Germany
| | - María de la O Leyva-Pérez
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Haidong Yan
- School of Plants and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
| | - Raúl de la Rosa
- Centro de Investigación y Formación Agraria de Alameda del Obispo, Instituto de Investigación y Formación Agraria y Pesquera (IFAPA), Córdoba, Spain
| | - Angjelina Belaj
- Centro de Investigación y Formación Agraria de Alameda del Obispo, Instituto de Investigación y Formación Agraria y Pesquera (IFAPA), Córdoba, Spain
| | - Eva Montes
- Instituto Universitario de Investigación en Arqueología Ibérica, University. Jaén, Jaén, 23071, Spain
| | - Mª Oliva Rodríguez-Ariza
- Instituto Universitario de Investigación en Arqueología Ibérica, University. Jaén, Jaén, 23071, Spain
| | - Francisco Navarro
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Juan Bautista Barroso
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
| | - Carmen R Beuzón
- Departamento de Biología Celular, Genética y Fisiología, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - Victoriano Valpuesta
- Departamento de Biología Molecular y Bioquímica, Facultad de Ciencias, Instituto de Hortofruticultura Subtropical y Mediterránea, Universidad de Málaga - Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - Aureliano Bombarely
- School of Plants and Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- present address, Department of Bioscience, Universita degli Studi di Milano, Milan, 20133, Italy
| | - Francisco Luque
- Center for Advanced Studies in Olive Grove and Olive Oils, Department of Experimental Biology, University. Jaén, Jaén, 23071, Spain
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Hernández-Rosales HS, Castellanos-Morales G, Sánchez-de la Vega G, Aguirre-Planter E, Montes-Hernández S, Lira-Saade R, Eguiarte LE. Phylogeographic and population genetic analyses of Cucurbita moschata reveal divergence of two mitochondrial lineages linked to an elevational gradient. AMERICAN JOURNAL OF BOTANY 2020; 107:510-525. [PMID: 32072632 DOI: 10.1002/ajb2.1424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
PREMISE Domestication usually involves local adaptation to environmental conditions. Cucurbita species are a promising model for studying these processes. Cucurbita moschata is the third major crop in the genus because of its economic value and because it displays high landrace diversity, but research about its genetic diversity, population structure, and phylogeography is limited. We aimed at understanding how geography and elevation shape the distribution of genetic diversity in C. moschata landraces in Mexico. METHODS We sampled fruits from 24 localities throughout Mexico. We assessed 11 nuclear microsatellite loci, one mtDNA region, and three cpDNA regions but found no variation in cpDNA. We explored genetic structure with cluster analysis, and phylogeographic relationships with haplotype network analysis. RESULTS Mitochondrial genetic diversity was high, and nuclear genetic differentiation among localities was intermediate compared to other domesticated Cucurbita. We found high levels of inbreeding. We recovered two mitochondrial lineages: highland (associated with the Trans-Mexican Volcanic Belt) and lowland. Nuclear microsatellites show that localities from the Yucatan Peninsula constitute a well-differentiated group. CONCLUSIONS Mexico is an area of high diversity for C. moschata, and these landraces represent important plant genetic resources. In Mexico this species is characterized by divergence processes linked to an elevational gradient, which could be related to adaptation and may be of value for applications in agriculture. The Isthmus of Tehuantepec may be a partial barrier to gene flow. Morphological variation, agricultural management, and cultural differences may be related to this pattern of genetic structure, but further studies are needed.
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Affiliation(s)
- Helena S Hernández-Rosales
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
- Programa de Doctorado en Ciencias Biomédicas, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Gabriela Castellanos-Morales
- Departamento de Conservación de la Biodiversidad, El Colegio de la Frontera Sur, Villahermosa, Carretera Villahermosa-Reforma km 15.5 Ranchería El Guineo 2ª sección, 86280, Villahermosa, Tabasco, Mexico
| | - Guillermo Sánchez-de la Vega
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Erika Aguirre-Planter
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
| | - Salvador Montes-Hernández
- Campo Experimental Bajío, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarías, Km 6.5 carretera Celaya-San Miguel de Allende, C.P. 38110, Celaya, Guanajuato, México, Mexico
| | - Rafael Lira-Saade
- UBIPRO, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Av. de los Barrios #1, Col. Los Reyes Iztacala, 54090, Tlanepantla, Edo. de Mex, Mexico
| | - Luis E Eguiarte
- Departamento de Ecología Evolutiva, Instituto de Ecología, Universidad Nacional Autónoma de México, Circuito Exterior s/n Anexo al Jardín Botánico, 04510, Ciudad de México, Mexico
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Cavaca LA, López-Coca IM, Silvero G, Afonso CA. The olive-tree leaves as a source of high-added value molecules: Oleuropein. BIOACTIVE NATURAL PRODUCTS 2020. [DOI: 10.1016/b978-0-12-817903-1.00005-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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Khadari B, El Bakkali A, Essalouh L, Tollon C, Pinatel C, Besnard G. Cultivated Olive Diversification at Local and Regional Scales: Evidence From the Genetic Characterization of French Genetic Resources. FRONTIERS IN PLANT SCIENCE 2019; 10:1593. [PMID: 31921243 PMCID: PMC6937215 DOI: 10.3389/fpls.2019.01593] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 11/13/2019] [Indexed: 05/11/2023]
Abstract
Molecular characterization of crop genetic resources is a powerful approach to elucidate the origin of varieties and facilitate local cultivar management. Here we aimed to decipher the origin and diversification of French local olive germplasm. The 113 olive accessions of the ex situ collection of Porquerolles were characterized with 20 nuclear microsatellites plus their plastid haplotype. We then compared this collection to Mediterranean olive varieties from the Worldwide Olive Germplasm Bank of Marrakech, Morocco. High genetic diversity was observed within local French varieties, indicating a high admixture level, with an almost equal contribution from the three main Mediterranean gene pools. Nearly identical and closely related genotypes were observed among French and Italian/Spanish varieties. A high number of parent-offspring relationships were also detected among French varieties and between French and two Italian varieties ('Frantoio' and 'Moraiolo') and the Spanish variety ('Gordal Sevillana'). Our investigations indicated that French olive germplasm resulted from the diffusion of material from multiple origins followed by diversification based on parentage relationships between varieties. We strongly suggest that farmers have been actively selecting olives based on local French varieties. French olive agroecosystems more affected by unexpected frosts than southernmost regions could also be seen as incubators and as a bridge between Italy and Spain that has enhanced varietal olive diversification.
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Affiliation(s)
- Bouchaib Khadari
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- Conservatoire Botanique National Méditerranéen de Porquerolles (CBNMed), UMR AGAP, Montpellier, France
| | - Ahmed El Bakkali
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phytogénétiques, Meknès, Morocco
| | - Laila Essalouh
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- Établissement Public Local d’Enseignement et de Formation Professionnelle Agricoles Nîmes-Rodilhan-CFPPA du Gard, Rodilhan, France
| | - Christine Tollon
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Christian Pinatel
- Centre Technique de l’Olivier, Maison des Agriculteurs, Aix-en-Provence, France
| | - Guillaume Besnard
- CNRS-IRD-UPS EDB, UMR 5174, Université Paul Sabatier, Toulouse, France
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El Bakkali A, Essalouh L, Tollon C, Rivallan R, Mournet P, Moukhli A, Zaher H, Mekkaoui A, Hadidou A, Sikaoui L, Khadari B. Characterization of Worldwide Olive Germplasm Banks of Marrakech (Morocco) and Córdoba (Spain): Towards management and use of olive germplasm in breeding programs. PLoS One 2019; 14:e0223716. [PMID: 31622375 PMCID: PMC6797134 DOI: 10.1371/journal.pone.0223716] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/26/2019] [Indexed: 11/09/2022] Open
Abstract
Olive (Olea europaea L.) is a major fruit crop in the Mediterranean Basin. Ex-situ olive management is essential to ensure optimal use of genetic resources in breeding programs. The Worldwide Olive Germplasm Bank of Córdoba (WOGBC), Spain, and Marrakech (WOGBM), Morocco, are currently the largest existing olive germplasm collections. Characterization, identification, comparison and authentication of all accessions in both collections could thus provide useful information for managing olive germplasm for its preservation, exchange within the scientific community and use in breeding programs. Here we applied 20 microsatellite markers (SSR) and 11 endocarp morphological traits to discriminate and authenticate 1091 olive accessions belonging to WOGBM and WOGBC (554 and 537, respectively). Of all the analyzed accessions, 672 distinct SSR profiles considered as unique genotypes were identified, but only 130 were present in both collections. Combining SSR markers and endocarp traits led to the identification of 535 cultivars (126 in common) and 120 authenticated cultivars. No significant differences were observed between collections regarding the allelic richness and diversity index. We concluded that the genetic diversity level was stable despite marked contrasts in varietal composition between collections, which could be explained by their different collection establishment conditions. This highlights the extent of cultivar variability within WOGBs. Moreover, we detected 192 mislabeling errors, 72 of which were found in WOGBM. A total of 228 genotypes as molecular variants of 74 cultivars, 79 synonyms and 39 homonyms as new cases were identified. Both collections were combined to define the nested core collections of 55, 121 and 150 sample sizes proposed for further studies. This study was a preliminary step towards managing and mining the genetic diversity in both collections while developing collaborations between olive research teams to conduct association mapping studies by exchanging and phenotyping accessions in contrasted environmental sites.
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Affiliation(s)
- Ahmed El Bakkali
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phyto-génétiques, Meknès, Morocco
| | - Laila Essalouh
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- EPLEFPA de Nîmes-CFPPA du Gard, Rodilhan, France
| | - Christine Tollon
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Ronan Rivallan
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | - Pierre Mournet
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
| | | | - Hayat Zaher
- INRA, UR Amélioration des Plantes, Marrakech, Morocco
| | - Abderrahmane Mekkaoui
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phyto-génétiques, Meknès, Morocco
| | - Amal Hadidou
- INRA, UR Amélioration des Plantes et Conservation des Ressources Phyto-génétiques, Meknès, Morocco
| | | | - Bouchaib Khadari
- AGAP, University Montpellier, CIRAD, INRA, Montpellier SupAgro, Montpellier, France
- Conservatoire Botanique National Méditerranéen de Porquerolles (CBNMed), UMR AGAP, Montpellier, France
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Gros‐Balthazard M, Besnard G, Sarah G, Holtz Y, Leclercq J, Santoni S, Wegmann D, Glémin S, Khadari B. Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:143-157. [PMID: 31192486 PMCID: PMC6851578 DOI: 10.1111/tpj.14435] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 05/29/2019] [Accepted: 06/03/2019] [Indexed: 05/11/2023]
Abstract
The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio-economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA-sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two-step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits.
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Affiliation(s)
- Muriel Gros‐Balthazard
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Present address:
New York University Abu Dhabi (NYUAD), Center for Genomics and Systems BiologySaadiyat IslandAbu DhabiUnited Arab Emirates
| | | | - Gautier Sarah
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Yan Holtz
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Julie Leclercq
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Sylvain Santoni
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
| | - Daniel Wegmann
- Department of BiologyUniversity of FribourgFribourgSwitzerland
- Swiss Institute of BioinformaticsFribourgSwitzerland
| | - Sylvain Glémin
- CNRSUniversité de RennesECOBIO (Ecosystèmes, biodiversité, évolution) − UMR 6553F‐35000RennesFrance
- Department of Ecology and GeneticsEvolutionary Biology CentreUppsala UniversityUppsalaSweden
| | - Bouchaib Khadari
- AGAP, University Montpellier, CIRAD, INRAMontpellier SupAgroMontpellierFrance
- Conservatoire Botanique National MéditerranéenUMR AGAPMontpellierFrance
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Grilo F, Novara ME, D'Oca MC, Rubino S, Lo Bianco R, Di Stefano V. Quality evaluation of extra-virgin olive oils from Sicilian genotypes grown in a high-density system. Int J Food Sci Nutr 2019; 71:397-409. [PMID: 31530051 DOI: 10.1080/09637486.2019.1666806] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Studying the sensory profile and chemical composition of monovarietal extra-virgin olive oils (EVOOs) is important to define and manage their quality and uniqueness. Chemical and sensory traits of olive oils from 14 minor Sicilian olive genotypes in comparison with oils from six major Sicilian and three international cultivars were analysed. Oils were extracted in 2015 from fruit of the 23 genotypes grown in an experimental orchard at a planting density of 1140 trees ha-1. Fatty acid composition, phenol composition, carotenoid content and antioxidant power were determined and analysed using univariate and multivariate procedures, in particular Nocellara Etnea along with carotenoid, phenol content and good sensory attributes, producing the best quality EVOO among the genotypes in trial. These results show that some Sicilian accessions used in this study may represent valid alternatives to produce high-quality EVOOs in modern, hedgerow planting systems.
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Affiliation(s)
- Filipa Grilo
- Department of Food Science and Technology, University of California, Davis, CA, USA
| | - Maria Eugenia Novara
- Department of Biological Chemistry and Pharmaceutical Science and Technology (STEBICEF), University of Palermo, Palermo, Italy
| | - Maria Cristina D'Oca
- Department of Physics and Chemistry (DiFC), University of Palermo, Palermo, Italy
| | - Simona Rubino
- Department of Biological Chemistry and Pharmaceutical Science and Technology (STEBICEF), University of Palermo, Palermo, Italy
| | - Riccardo Lo Bianco
- Department of Agricultural, Food, and Forest Sciences, University of Palermo, Palermo, Italy
| | - Vita Di Stefano
- Department of Biological Chemistry and Pharmaceutical Science and Technology (STEBICEF), University of Palermo, Palermo, Italy
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Sion S, Taranto F, Montemurro C, Mangini G, Camposeo S, Falco V, Gallo A, Mita G, Debbabi OS, Amar FB, Pavan S, Roseti V, Miazzi MM. Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs. PLANTS (BASEL, SWITZERLAND) 2019; 8:E268. [PMID: 31387331 PMCID: PMC6724140 DOI: 10.3390/plants8080268] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/30/2019] [Accepted: 07/31/2019] [Indexed: 11/17/2022]
Abstract
The olive is a fruit tree species with a century-old history of cultivation in theMediterranean basin. In Apulia (Southern Italy), the olive is of main social, cultural and economicimportance, and represents a hallmark of the rural landscape. However, olive cultivation in thisregion is threatened by the recent spread of the olive quick decline syndrome (OQDS) disease, thusthere is an urgent need to explore biodiversity and search for genetic sources of resistance. Herein,a genetic variation in Apulian olive germplasm was explored, as a first step to identify genotypeswith enhanced bio-agronomic traits, including resistance to OQDS. A preselected set of nuclearmicrosatellite markers allowed the acquisition of genotypic profiles, and to define geneticrelationships between Apulian germplasm and widespread cultivars. The analysis highlighted thebroad genetic variation in Apulian accessions and the presence of different unique genetic profiles.The results of this study lay a foundation for the organization of new breeding programs for olivegenetic improvement.
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Affiliation(s)
- S Sion
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - F Taranto
- Research Centre for Cereal and Industrial Crops, (CREA-CI), S.S. 71122 Foggia, Italy.
| | - C Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy.
| | - G Mangini
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - S Camposeo
- Department of Agricultural and Environmental Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - V Falco
- CNR Institute of Sciences of Food Production, Unit of Lecce, 73100 Lecce, Italy
| | - A Gallo
- CNR Institute of Sciences of Food Production, Unit of Lecce, 73100 Lecce, Italy
| | - G Mita
- CNR Institute of Sciences of Food Production, Unit of Lecce, 73100 Lecce, Italy
| | | | - F Ben Amar
- Institut de l'Olivier, Route de l'aéroport, BP 1087, Sfax 3000, Tunisia
| | - S Pavan
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - V Roseti
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
| | - M M Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, 70121 Bari, Italy
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Cultrera NGM, Sarri V, Lucentini L, Ceccarelli M, Alagna F, Mariotti R, Mousavi S, Ruiz CG, Baldoni L. High Levels of Variation Within Gene Sequences of Olea europaea L. FRONTIERS IN PLANT SCIENCE 2019; 9:1932. [PMID: 30671076 PMCID: PMC6331486 DOI: 10.3389/fpls.2018.01932] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 12/12/2018] [Indexed: 05/08/2023]
Abstract
Gene sequence variation in cultivated olive (Olea europaea L. subsp. europaea var. europaea), the most important oil tree crop of the Mediterranean basin, has been poorly evaluated up to now. A deep sequence analysis of fragments of four genes, OeACP1, OeACP2, OeLUS and OeSUT1, in 90 cultivars, revealed a wide range of polymorphisms along all recognized allele forms and unexpected allele frequencies and genotype combinations. High linkage values among most polymorphisms were recorded within each gene fragment. The great sequence variability corresponded to a low number of alleles and, surprisingly, to a small fraction of genotype combinations. The distribution, frequency, and combination of the different alleles at each locus is possibly due to natural and human pressures, such as selection, ancestrality, or fitness. Phylogenetic analyses of allele sequences showed distant and complex patterns of relationships among cultivated olives, intermixed with other related forms, highlighting an evolutionary connection between olive cultivars and the O. europaea subspecies cuspidata and cerasiformis. This study demonstrates how a detailed and complete sequence analysis of a few gene portions and a thorough genotyping on a representative set of cultivars can clarify important issues related to sequence polymorphisms, reconstructing the phylogeny of alleles, as well as the genotype combinations. The identification of regions representing blocks of recombination could reveal polymorphisms that represent putatively functional markers. Indeed, specific mutations found on the analyzed OeACP1 and OeACP2 fragments seem to be correlated to the fruit weight.
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Affiliation(s)
- Nicolò G. M. Cultrera
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Vania Sarri
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Livia Lucentini
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Marilena Ceccarelli
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Fiammetta Alagna
- ENEA Italian National Agency for New Technologies Energy and Sustainable Economic Development, Trisaia Research Center, Rotondella, Italy
| | - Roberto Mariotti
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | - Soraya Mousavi
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
| | | | - Luciana Baldoni
- Institute of Biosciences and Bioresources, National Research Council, Perugia, Italy
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D'Agostino N, Taranto F, Camposeo S, Mangini G, Fanelli V, Gadaleta S, Miazzi MM, Pavan S, di Rienzo V, Sabetta W, Lombardo L, Zelasco S, Perri E, Lotti C, Ciani E, Montemurro C. GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars. Sci Rep 2018; 8:15877. [PMID: 30367101 PMCID: PMC6203791 DOI: 10.1038/s41598-018-34207-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/12/2018] [Indexed: 11/08/2022] Open
Abstract
Information on the distribution of genetic variation is essential to preserve olive germplasm from erosion and to recover alleles lost through selective breeding. In addition, knowledge on population structure and genotype-phenotype associations is crucial to support modern olive breeding programs that must respond to new environmental conditions imposed by climate change and novel biotic/abiotic stressors. To further our understanding of genetic variation in the olive, we performed genotype-by-sequencing on a panel of 94 Italian olive cultivars. A reference-based and a reference-independent SNP calling pipeline generated 22,088 and 8,088 high-quality SNPs, respectively. Both datasets were used to model population structure via parametric and non parametric clustering. Although the two pipelines yielded a 3-fold difference in the number of SNPs, both described wide genetic variability among our study panel and allowed individuals to be grouped based on fruit weight and the geographical area of cultivation. Multidimensional scaling analysis on identity-by-state allele-sharing values as well as inference of population mixtures from genome-wide allele frequency data corroborated the clustering pattern we observed. These findings allowed us to formulate hypotheses about geographical relationships of Italian olive cultivars and to confirm known and uncover novel cases of synonymy.
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Affiliation(s)
- Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano Faiano, Italy.
| | - Francesca Taranto
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy.
| | - Salvatore Camposeo
- Department of Agricultural and Environmental sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Giacomo Mangini
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Valentina Fanelli
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Susanna Gadaleta
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Valentina di Rienzo
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Wilma Sabetta
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Luca Lombardo
- Center for Agriculture, Food ad Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Samanta Zelasco
- CREA Research Centre for Olive, Citrus and Tree Fruit, Rende, Italy
| | - Enzo Perri
- CREA Research Centre for Olive, Citrus and Tree Fruit, Rende, Italy
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Foggia, Italy
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Cinzia Montemurro
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
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di Rienzo V, Sion S, Taranto F, D'Agostino N, Montemurro C, Fanelli V, Sabetta W, Boucheffa S, Tamendjari A, Pasqualone A, Zammit-Mangion M, Miazzi MM. Genetic flow among olive populations within the Mediterranean basin. PeerJ 2018; 6:e5260. [PMID: 30018865 PMCID: PMC6045921 DOI: 10.7717/peerj.5260] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 06/28/2018] [Indexed: 11/30/2022] Open
Abstract
Background The olive tree is a typical crop of the Mediterranean basin where it shows a wide diversity, accounting for more than 2,600 cultivars. The ability to discriminate olive cultivars and determine their genetic variability is pivotal for an optimal exploitation of olive genetic resources. Methods We investigated the genetic diversity within 128 olive accessions belonging to four countries in the Mediterranean Basin (Italy, Algeria, Syria, and Malta), with the purpose of better understanding the origin and spread of the olive genotypes across Mediterranean Basin countries. Eleven highly polymorphic simple sequence repeat (SSR) markers were used and proved to be very informative, producing a total of 179 alleles. Results Cluster analysis distinguished three main groups according to their geographical origin, with the current sample of Maltese accessions included in the Italian group. Phylogenetic analysis further differentiated Italian and Maltese olive accessions, clarifying the intermediate position of Maltese accessions along the x/y-axes of principal coordinate analysis (PCoA). Model-based and neighbor clustering, PCoA, and migration analysis suggested the existence of two different gene pools (Algerian and Syrian) and that the genetic exchange occurred between the Syrian, Italian and Maltese populations. Discussion The close relationship between Syrian and Italian and Maltese olives was consistent with the historical domestication and migration of olive tree from the North Levant to eastern Mediterranean basin. This study lays the foundations for a better understanding of olive genetic diversity in the Mediterranean basin and represents a step toward an optimal conservation and exploitation of olive genetic resources.
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Affiliation(s)
- Valentina di Rienzo
- Department of Soil, Plant and Food Sciences (DISSPA), University of Bari, Bari, Italy.,Sinagri s.r.l. Spin-off, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Sara Sion
- Department of Soil, Plant and Food Sciences (DISSPA), University of Bari, Bari, Italy
| | - Francesca Taranto
- Department of Soil, Plant and Food Sciences (DISSPA), University of Bari, Bari, Italy
| | - Nunzio D'Agostino
- Research Centre for Vegetable and Ornamental Crops, CREA, Pontecagnano Faiano (SA), Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences (DISSPA), University of Bari, Bari, Italy.,Sinagri s.r.l. Spin-off, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Sciences (DISSPA), University of Bari, Bari, Italy
| | - Wilma Sabetta
- Sinagri s.r.l. Spin-off, Università degli Studi di Bari Aldo Moro, Bari, Italy
| | - Saliha Boucheffa
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algérie
| | - Abderezak Tamendjari
- Laboratoire de Biochimie Appliquée, Faculté des Sciences de la Nature et de la Vie, Université de Bejaia, Bejaia, Algérie
| | - Antonella Pasqualone
- Department of Soil, Plant and Food Sciences (DISSPA), University of Bari, Bari, Italy
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Miho H, Díez CM, Mena-Bravo A, Sánchez de Medina V, Moral J, Melliou E, Magiatis P, Rallo L, Barranco D, Priego-Capote F. Cultivar influence on variability in olive oil phenolic profiles determined through an extensive germplasm survey. Food Chem 2018; 266:192-199. [PMID: 30381176 DOI: 10.1016/j.foodchem.2018.06.002] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 05/25/2018] [Accepted: 06/03/2018] [Indexed: 11/16/2022]
Abstract
Despite the evident influence of the cultivar on olive oil composition, few studies have been devoted to exploring the variability of phenols in a representative number of monovarietal olive oils. In this study, oil samples from 80 cultivars selected for their impact on worldwide oil production were analyzed to compare their phenolic composition by using a method based on LC-MS/MS. Secoiridoid derivatives were the most concentrated phenols in virgin olive oil, showing high variability that was significantly due to the cultivar. Multivariate analysis allowed discrimination between four groups of cultivars through their phenolic profiles: (i) richer in aglycon isomers of oleuropein and ligstroside; (ii) richer in oleocanthal and oleacein; (iii) richer in flavonoids; and (iv) oils with balanced but reduced phenolic concentrations. Additionally, correlation analysis showed no linkage among aglycon isomers and oleocanthal/oleacein, which can be explained by the enzymatic pathways involved in the metabolism of both oleuropein and ligstroside.
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Affiliation(s)
- H Miho
- Department of Agronomy, Campus of Rabanales, University of Cordoba, Spain
| | - C M Díez
- Department of Agronomy, Campus of Rabanales, University of Cordoba, Spain
| | - A Mena-Bravo
- Department of Analytical Chemistry, Campus of Rabanales, University of Cordoba, Spain; Agroalimentary Excellence Campus (ceiA3), Campus of Rabanales, University of Cordoba, Spain; Maimonides Institute of Biomedical Research (IMIBIC), Reina Sofia University Hospital, Spain
| | - V Sánchez de Medina
- Department of Analytical Chemistry, Campus of Rabanales, University of Cordoba, Spain
| | - J Moral
- Department of Agronomy, Campus of Rabanales, University of Cordoba, Spain; Plant Pathology Department, University of California Davis, Davis, USA
| | - E Melliou
- Laboratory of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, University of Athens, Greece
| | - P Magiatis
- Laboratory of Pharmacognosy and Natural Products Chemistry, Faculty of Pharmacy, University of Athens, Greece
| | - L Rallo
- Department of Agronomy, Campus of Rabanales, University of Cordoba, Spain
| | - D Barranco
- Department of Agronomy, Campus of Rabanales, University of Cordoba, Spain
| | - F Priego-Capote
- Department of Analytical Chemistry, Campus of Rabanales, University of Cordoba, Spain; Agroalimentary Excellence Campus (ceiA3), Campus of Rabanales, University of Cordoba, Spain; Maimonides Institute of Biomedical Research (IMIBIC), Reina Sofia University Hospital, Spain.
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50
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Besnard G, Terral JF, Cornille A. On the origins and domestication of the olive: a review and perspectives. ANNALS OF BOTANY 2018; 121:385-403. [PMID: 29293871 PMCID: PMC5838823 DOI: 10.1093/aob/mcx145] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 10/12/2017] [Indexed: 05/18/2023]
Abstract
Background Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. Scope The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. Conclusion The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.
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Affiliation(s)
- Guillaume Besnard
- CNRS-UPS-ENSFEA-IRD, EDB, UMR 5174, Université Paul Sabatier, Toulouse Cedex , France
| | - Jean-Frédéric Terral
- ISEM, UMR 5554, CNRS-Université de Montpellier-IRD-EPHE, Equipe Dynamique de la Biodiversité, Anthropo-écologie, Montpellier Cedex, France
- International Associated Laboratory (LIA, CNRS) EVOLea, Zürich, Switzerland
| | - Amandine Cornille
- Center for Adaptation to a Changing Environment, ETH Zürich, Zürich, Switzerland
- GQE - Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
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