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Al-Kilani MA, Taranto F, D’Agostino N, Montemurro C, Belaj A, Ayoub S, Albdaiwi R, Hasan S, Al-Abdallat AM. Evaluation of genetic diversity among olive trees ( Olea europaea L.) from Jordan. FRONTIERS IN PLANT SCIENCE 2024; 15:1437055. [PMID: 39166249 PMCID: PMC11333458 DOI: 10.3389/fpls.2024.1437055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/15/2024] [Indexed: 08/22/2024]
Abstract
This study aimed to identify and evaluate the genetic diversity of olive trees in Jordan, a country located in the eastern Mediterranean, where olive domestication originated. For this purpose, a total of 386 olive trees were analyzed, including 338 collected from two surveys (JOCC-1 and JOCC-2) across seven regions, and 48 selected accessions from the Olive Germplasm Bank of Jordan (JGBOC). These trees underwent comprehensive phenotypic and molecular characterization using different tools. Significant differences in morphological traits were detected among tested regions using the Chi-square test. Principal components analysis revealed that fruit color change and growth habit as the most discriminating traits, segregating the trees into two groups, with the first group including the Kanabisi cultivar and the second group including the Kfari Baladi cultivar. Utilizing Kompetitive Allele Specific PCR assay, two sets of informative SNPs were used for the genetic diversity analysis. Cladograms were constructed using the maximum likelihood method, revealing a consistent pattern where two clades containing identical genotypes were observed to cluster with the Kfari Baladi or Kanabisi. In addition, the SNP data was used to perform a comparative analysis with the Worldwide Olive Germplasm Bank of Córdoba, which revealed 73 unreported olive genotypes from Jordan. Genetic structure analyses using Discriminant Analysis of Principal Components (DAPC) identified four clusters with distinctive patterns of relatedness among 149 unique accessions, including 52 olive accessions from various Mediterranean countries (IOCC-3). ADMIXTURE analysis revealed four genetic clusters, consistent with the clustering observed in DAPC and cladogram analysis, indicating a high level of genetic admixture among Jordanian olive germplasm. In conclusion, the results show that olive trees in Jordan are highly diverse, providing valuable information for future conservation and management plans.
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Affiliation(s)
| | - Francesca Taranto
- Institute of Biosciences and Bioresources, National Research Council (CNR-IBBR), Bari, Italy
| | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Cinzia Montemurro
- Department of Soil: Plant and Food Sciences (DiSSPA), University of Bari Aldo Moro, Bari, Italy
| | - Angjelina Belaj
- Centro “Alameda del Obispo”, Instituto Andaluz de Investigación y Formación Agraria, Pesquera, Alimentaria y de la Producción Ecológica (IFAPA), Córdoba, Spain
| | - Salam Ayoub
- National Center for Agriculture Research (NARC), Amman, Jordan
| | - Randa Albdaiwi
- Department of Allied Medical Sciences, Zarqa University College, Al-Balqa Applied University, Al-Salt, Jordan
| | - Shireen Hasan
- Hamdi Mango Center for Scientific Research, The University of Jordan, Amman, Jordan
| | - Ayed M. Al-Abdallat
- Department of Horticulture and Crop Science, School of Agriculture, The University of Jordan, Amman, Jordan
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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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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: 3] [Impact Index Per Article: 3.0] [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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Characterization of Differentially Expressed Genes under Salt Stress in Olive. Int J Mol Sci 2021; 23:ijms23010154. [PMID: 35008580 PMCID: PMC8745295 DOI: 10.3390/ijms23010154] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/15/2021] [Accepted: 12/21/2021] [Indexed: 12/29/2022] Open
Abstract
Climate change, currently taking place worldwide and also in the Mediterranean area, is leading to a reduction in water availability and to groundwater salinization. Olive represents one of the most efficient tree crops to face these scenarios, thanks to its natural ability to tolerate moderate salinity and drought. In the present work, four olive cultivars (Koroneiki, Picual, Royal de Cazorla and Fadak86) were exposed to high salt stress conditions (200 mM of NaCl) in greenhouse, in order to evaluate their tolerance level and to identify key genes involved in salt stress response. Molecular and physiological parameters, as well as plant growth and leaves’ ions Na+ and K+ content were measured. Results of the physiological measurements showed Royal de Cazorla as the most tolerant cultivar, and Fadak86 and Picual as the most susceptible ones. Ten candidate genes were analyzed and their complete genomic, CDS and protein sequences were identified. The expression analysis of their transcripts through reverse transcriptase quantitative PCR (RT-qPCR) demonstrated that only OeNHX7, OeP5CS, OeRD19A and OePetD were upregulated in tolerant cultivars, thus suggesting their key role in the activation of a salt tolerance mechanism.
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How to Choose a Good Marker to Analyze the Olive Germplasm ( Olea europaea L.) and Derived Products. Genes (Basel) 2021; 12:genes12101474. [PMID: 34680869 PMCID: PMC8535536 DOI: 10.3390/genes12101474] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/08/2021] [Accepted: 09/16/2021] [Indexed: 12/30/2022] Open
Abstract
The olive tree (Olea europaea L.) is one of the most cultivated crops in the Mediterranean basin. Its economic importance is mainly due to the intense production of table olives and oil. Cultivated varieties are characterized by high morphological and genetic variability and present a large number of synonyms and homonyms. This necessitates the introduction of a rapid and accurate system for varietal identification. In the past, the recognition of olive cultivars was based solely on analysis of the morphological traits, however, these are highly influenced by environmental conditions. Therefore, over the years, several methods based on DNA analysis were developed, allowing a more accurate and reliable varietal identification. This review aims to investigate the evolving history of olive tree characterization approaches, starting from the earlier morphological methods to the latest technologies based on molecular markers, focusing on the main applications of each approach. Furthermore, we discuss the impact of the advent of next generation sequencing and the recent sequencing of the olive genome on the strategies used for the development of new molecular markers.
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Mariotti R, Pandolfi S, De Cauwer I, Saumitou‐Laprade P, Vernet P, Rossi M, Baglivo F, Baldoni L, Mousavi S. Diallelic self-incompatibility is the main determinant of fertilization patterns in olive orchards. Evol Appl 2021; 14:983-995. [PMID: 33897815 PMCID: PMC8061272 DOI: 10.1111/eva.13175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 11/13/2020] [Accepted: 11/19/2020] [Indexed: 01/28/2023] Open
Abstract
Self-incompatibility (SI) in flowering plants potentially represents a major obstacle for sexual reproduction, especially when the number of S-alleles is low. The situation is extreme in the commercially important olive tree, where in vitro pollination assays suggested the existence of a diallelic SI (DSI) system involving only two groups (G1 and G2). Varieties belonging to the same SI group cannot fertilize each other, such that successful fruit production is predicted to require pollination between varieties of different groups. To test this prediction, we explored the extent to which the DSI system determines fertilization patterns under field conditions. One hundred and seventeen olive cultivars were first genotyped using 10 highly polymorphic dinucleotide Simple Sequence Repeat (SSR) markers to ascertain varietal identity. Cultivars were then phenotyped through controlled pollination tests to assign each of them to one of the two SI groups. We then collected and genotyped 1440 open pollinated embryos from five different orchards constituted of seven local cultivars with known group of incompatibility groups. Embryos genotype information were used: (i) to assign embryos to the most likely pollen donor genotype in the neighbourhood using paternity analysis, and (ii) to compare the composition of the pollen cloud genetic among recipient trees in the five sites. The paternity analysis showed that the DSI system is the main determinant of fertilization success under field open pollination conditions: G1 cultivars sired seeds exclusively on G2 cultivars, and reciprocally. No self-fertilization events were observed. Our results demonstrate that DSI is a potent force determining pollination success among varieties within olive orchards used for production. They have the potential to improve management practices by guiding the selection of compatible varieties to avoid planting orchards containing sets of varieties with strongly unbalanced SI groups, as these would lead to suboptimal olive production.
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Affiliation(s)
| | | | | | | | | | - Martina Rossi
- Institute of Biosciences and BioresourcesCNRPerugiaItaly
| | | | | | - Soraya Mousavi
- Institute of Biosciences and BioresourcesCNRPerugiaItaly
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Bettaieb I, Hamdi J, Bouktila D. Genome-wide analysis of HSP90 gene family in the Mediterranean olive ( Olea europaea subsp. europaea) provides insight into structural patterns, evolution and functional diversity. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2301-2318. [PMID: 33268931 PMCID: PMC7688888 DOI: 10.1007/s12298-020-00888-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/01/2020] [Accepted: 09/22/2020] [Indexed: 05/09/2023]
Abstract
Plants regularly experience multiple abiotic and biotic pressures affecting their normal development. The 90-kDa heat shock protein (HSP90) plays a dynamic role in countering abiotic and biotic stresses via a plethora of functional mechanisms. The HSP90 has been investigated in many plant species. However, there is little information available about this gene family in the cultivated Mediterranean olive tree, Olea europaea subsp. europaea var. europaea. In the current study, we systematically performed genome-wide identification and characterization of the HSP90 gene family in O. europaea var. europaea (OeHSP90s). Twelve regular OeHSP90s were identified, which were phylogenetically grouped into two major clusters and four sub-clusters, showing five paralogous gene pairs evolving under purifying selection. All of the 12 proteins contained a Histidine kinase-like ATPase (HATPase_c) domain, justifying the role played by HSP90 proteins in ATP binding and hydrolysis. The predicted 3D structure of OeHSP90 proteins provided information to understand their functions at the biochemical level. Consistent with their phylogenetic relationships, OeHSP90 members were predicted to be localized in different cellular compartments, suggesting their involvement in various subcellular processes. In consonance with their spatial organization, olive HSP90 family members were found to share similar motif arrangements and similar number of exons. We found that OeHSP90 promoters contained various cis-acting elements associated with light responsiveness, hormone signaling pathways and reaction to various stress conditions. In addition, expression sequence tags (ESTs) analysis offered a view of OeHSP90 tissue- and developmental stage specific pattern of expression. Proteins interacting with OeHSP90s were predicted and their potential roles were discussed. Overall, our results offer premises for further investigation of the implication of HSP90 genes in the physiological processes of the olive and its adaptation to stresses.
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Affiliation(s)
- Inchirah Bettaieb
- Laboratoire LR11ES41 Génétique, Biodiversité & Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Monastir, Tunisia
| | - Jihen Hamdi
- Laboratoire LR11ES41 Génétique, Biodiversité & Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Monastir, Tunisia
| | - Dhia Bouktila
- Laboratoire LR11ES41 Génétique, Biodiversité & Valorisation des Bioressources, Institut Supérieur de Biotechnologie de Monastir, Université de Monastir, Monastir, Tunisia
- Institut Supérieur de Biotechnologie de Béja, Université de Jendouba, Béja, Tunisia
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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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ChooChuay C, Pongpiachan S, Tipmanee D, Deelaman W, Iadtem N, Suttinun O, Wang Q, Xing L, Li G, Han Y, Hashmi MZ, Palakun J, Poshyachinda S, Aukkaravittayapun S, Surapipith V, Cao J. Effects of Agricultural Waste Burning on PM2.5-Bound Polycyclic Aromatic Hydrocarbons, Carbonaceous Compositions, and Water-Soluble Ionic Species in the Ambient Air of Chiang-Mai, Thailand. Polycycl Aromat Compd 2020. [DOI: 10.1080/10406638.2020.1750436] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Chomsri ChooChuay
- Faculty of Environmental Management, Prince of Songkla University Hat-Yai Campus, Songkla, Thailand
| | - Siwatt Pongpiachan
- NIDA Center for Research & Development of Disaster Prevention & Management, School of Social and Environmental Development, National Institute of Development Administration (NIDA), Bangkapi, Bangkok, Thailand
| | - Danai Tipmanee
- Faculty of Technology and Environment, Prince of Songkla University Phuket, Phuket, Thailand
| | - Woranuch Deelaman
- Faculty of Environmental Management, Prince of Songkla University Hat-Yai Campus, Songkla, Thailand
| | - Natthapong Iadtem
- Faculty of Environmental Management, Prince of Songkla University Hat-Yai Campus, Songkla, Thailand
| | - Oramas Suttinun
- Faculty of Environmental Management, Prince of Songkla University Hat-Yai Campus, Songkla, Thailand
| | - Qiyuan Wang
- SKLLQG and Key Lab of Aerosol Chemistry & Physics, Institute of Earth Environment, Chinese Academy of Sciences (IEECAS), Xi’an, China
| | - Li Xing
- SKLLQG and Key Lab of Aerosol Chemistry & Physics, Institute of Earth Environment, Chinese Academy of Sciences (IEECAS), Xi’an, China
| | - Guohui Li
- SKLLQG and Key Lab of Aerosol Chemistry & Physics, Institute of Earth Environment, Chinese Academy of Sciences (IEECAS), Xi’an, China
| | - Yongming Han
- SKLLQG and Key Lab of Aerosol Chemistry & Physics, Institute of Earth Environment, Chinese Academy of Sciences (IEECAS), Xi’an, China
| | | | - Jittree Palakun
- Faculty of Education, Valaya Alongkorn Rajabhat University under the Royal Patronage (VRU), Pathumthani, Thailand
| | - Saran Poshyachinda
- National Astronomical Research Institute of Thailand (Public Organization, Chiang-Mai, Thailand
| | | | - Vanisa Surapipith
- National Astronomical Research Institute of Thailand (Public Organization, Chiang-Mai, Thailand
| | - Junji Cao
- SKLLQG and Key Lab of Aerosol Chemistry & Physics, Institute of Earth Environment, Chinese Academy of Sciences (IEECAS), Xi’an, China
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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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11
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Miazzi MM, di Rienzo V, Mascio I, Montemurro C, Sion S, Sabetta W, Vivaldi GA, Camposeo S, Caponio F, Squeo G, Difonzo G, Loconsole G, Bottalico G, Venerito P, Montilon V, Saponari A, Altamura G, Mita G, Petrontino A, Fucilli V, Bozzo F. Re.Ger.O.P.: An Integrated Project for the Recovery of Ancient and Rare Olive Germplasm. FRONTIERS IN PLANT SCIENCE 2020; 11:73. [PMID: 32153605 PMCID: PMC7044272 DOI: 10.3389/fpls.2020.00073] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
The olive tree is one of the most important economic, cultural, and environmental resources for Italy, in particular for the Apulian region, where it shows a wide diversity. The increasing attention to the continuous loss of plant genetic diversity due to social, economic and climatic changes, has favored a renewed interest in strategies aimed at the recovery and conservation of these genetic resources. In the frame of a project for the valorization of the olive Apulian biodiversity (Re.Ger.O.P. project), 177 minor genotypes were recovered in different territories of the region. They were submitted to morphological, molecular, technological and phytosanitary status analysis in comparison with reference cultivars, then they were propagated and transferred in an ex situ field. All the available information was stored in an internal regional database including photographic documentation and geographic position. The work allowed obtaining information about the genetic diversity of Apulian germplasm, to clarify cases of homonymy and synonymy, to check the sanitary status, and to identify candidate genotypes useful both to set up breeding programs and to enrich the panel of olive cultivars available to farmers for commercial exploitation.
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Affiliation(s)
| | | | - Isabella Mascio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- SINAGRI S.r.l.—Spin Off of the University of Bari Aldo Moro, Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- SINAGRI S.r.l.—Spin Off of the University of Bari Aldo Moro, Bari, Italy
| | - Sara Sion
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Wilma Sabetta
- SINAGRI S.r.l.—Spin Off of the University of Bari Aldo Moro, Bari, Italy
- Unit of Bari CNR Institute of Biosciences and Bioresources, Bari, Italy
| | | | - Salvatore Camposeo
- Department of Agricultural and Environmental Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Caponio
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Giacomo Squeo
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Graziana Difonzo
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Guiliana Loconsole
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- SINAGRI S.r.l.—Spin Off of the University of Bari Aldo Moro, Bari, Italy
| | - Giovanna Bottalico
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- SINAGRI S.r.l.—Spin Off of the University of Bari Aldo Moro, Bari, Italy
| | - Pasquale Venerito
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura, “Basile Caramia” Locorotondo, Bari, Italy
| | - Vito Montilon
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Antonella Saponari
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura, “Basile Caramia” Locorotondo, Bari, Italy
| | - Giuseppe Altamura
- CRSFA-Centro Ricerca, Sperimentazione e Formazione in Agricoltura, “Basile Caramia” Locorotondo, Bari, Italy
| | - Giovanni Mita
- Unit of Lecce, CNR Institute of Sciences of Food Production, Lecce, Italy
| | | | - Vincenzo Fucilli
- SINAGRI S.r.l.—Spin Off of the University of Bari Aldo Moro, Bari, Italy
- Department of Agricultural and Environmental Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Francesco Bozzo
- SINAGRI S.r.l.—Spin Off of the University of Bari Aldo Moro, Bari, Italy
- Department of Agricultural and Environmental Sciences, University of Bari Aldo Moro, Bari, Italy
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12
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Mousavi S, de la Rosa R, Moukhli A, El Riachy M, Mariotti R, Torres M, Pierantozzi P, Stanzione V, Mastio V, Zaher H, El Antari A, Ayoub S, Dandachi F, Youssef H, Aggelou N, Contreras C, Maestri D, Belaj A, Bufacchi M, Baldoni L, Leon L. Plasticity of fruit and oil traits in olive among different environments. Sci Rep 2019; 9:16968. [PMID: 31740728 PMCID: PMC6861299 DOI: 10.1038/s41598-019-53169-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 10/26/2019] [Indexed: 01/12/2023] Open
Abstract
Olive is a long-living perennial species with a wide geographical distribution, showing a large genetic and phenotypic variation in its growing area. There is an urgent need to uncover how olive phenotypic traits and plasticity can change regardless of the genetic background. A two-year study was conducted, based on the analysis of fruit and oil traits of 113 cultivars from five germplasm collections established in Mediterranean Basin countries and Argentina. Fruit and oil traits plasticity, broad-sense heritability and genotype by environment interaction were estimated. From variance and heritability analyses, it was shown that fruit fresh weight was mainly under genetic control, whereas oleic/(palmitic + linoleic) acids ratio was regulated by the environment and genotype by environment interaction had the major effect on oil content. Among the studied cultivars, different level of stability was observed, which allowed ranking the cultivars based on their plasticity for oil traits. High thermal amplitude, the difference of low and high year values of temperature, negatively affected the oil content and the oleic acid percentage. Information derived from this work will help to direct the selection of cultivars with the highest global fitness averaged over the environments rather than the highest fitness in each environment separately.
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Affiliation(s)
- Soraya Mousavi
- CNR - Institute for Agricultural and Forest Systems of the Mediterranean, 06128, Perugia, Italy
- CNR - Institute of Biosciences and Bioresources, 06128, Perugia, Italy
| | | | | | - Milad El Riachy
- LARI - Lebanese Agricultural Research Institute Tal Amara, Bekaa, Lebanon
| | - Roberto Mariotti
- CNR - Institute of Biosciences and Bioresources, 06128, Perugia, Italy
| | - Mariela Torres
- Estación Experimental Agropecuaria San Juan (EEA INTA San Juan), and CONICET. Ing. Marcos Zalazar (Calle 11) y Vidart. Villa Aberastain, Pocito, 5427, San Juan, Argentina
| | - Pierluigi Pierantozzi
- Estación Experimental Agropecuaria San Juan (EEA INTA San Juan), and CONICET. Ing. Marcos Zalazar (Calle 11) y Vidart. Villa Aberastain, Pocito, 5427, San Juan, Argentina
| | - Vitale Stanzione
- CNR - Institute for Agricultural and Forest Systems of the Mediterranean, 06128, Perugia, Italy
| | - Valerio Mastio
- CNR - Institute for Agricultural and Forest Systems of the Mediterranean, 06128, Perugia, Italy
| | - Hayat Zaher
- INRA - CRRA, Marrakech-Safi, BP 533, Marrakech, Morocco
| | | | - Salam Ayoub
- National Agricultural Research Center (NARC), Baqa, 19381, Jordan
| | - Faten Dandachi
- LARI - Lebanese Agricultural Research Institute Tal Amara, Bekaa, Lebanon
| | - Hiyam Youssef
- LARI - Lebanese Agricultural Research Institute Tal Amara, Bekaa, Lebanon
| | - Nikolas Aggelou
- MAICh - Department of Horticultural Genetics and Biotechnology, 73100, Chania-Crete, Greece
| | - Cibeles Contreras
- Estación Experimental Agropecuaria San Juan (EEA INTA San Juan), and CONICET. Ing. Marcos Zalazar (Calle 11) y Vidart. Villa Aberastain, Pocito, 5427, San Juan, Argentina
| | - Damián Maestri
- Instituto Multidisciplinario de Biología Vegetal (IMBIV, CONICET-UNC). Av. Vélez Sarsfield 1611, X5016GCA, Córdoba, Argentina
| | | | - Marina Bufacchi
- CNR - Institute for Agricultural and Forest Systems of the Mediterranean, 06128, Perugia, Italy.
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources, 06128, Perugia, Italy
| | - Lorenzo Leon
- IFAPA - Centro Alameda del Obispo, Córdoba, Spain
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13
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Temporal Variation and Statistical Assessment of the b Value off the Pacific Coast of Tokachi, Hokkaido, Japan. ENTROPY 2019; 21:e21030249. [PMID: 33266964 PMCID: PMC7514730 DOI: 10.3390/e21030249] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 02/18/2019] [Accepted: 02/26/2019] [Indexed: 11/21/2022]
Abstract
The Gutenberg-Richter Law describes the frequency-magnitude distribution of earthquakes. A number of studies have shown that the slope (b value) of the relationship between frequency and magnitude decreased before large earthquakes. In this paper, we investigate the temporal variation of the b value off the Pacific coast of Tokachi, Hokkaido, Japan, during 1990–2014. The magnitude of completeness (Mc) in the catalog is evaluated by combining the maximum curvature (MAXC) technique and the bootstrap approach. Then, the b value, and its uncertainty, is computed by using the maximum likelihood estimation. The Akaike Information Criterion (AIC) with the bootstrap approach is introduced to statistically assess the temporal variation of b values and quantify the significance level. The results show a decrease in trends of the b value prior to two large earthquakes (26 September 2003 (M8.0) and 11 September 2008 (M7.1)) in the analyzed area. In addition, the decrease of b values shows certain statistical significance three months before the 2003 Earthquake off the Pacific coast of Tokachi (M8.0). It is concluded that the b value with statistical assessment may contain potential information for future large earthquake preparation off the Pacific coast of Tokachi, Hokkaido, Japan.
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14
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Mousavi S, Regni L, Bocchini M, Mariotti R, Cultrera NGM, Mancuso S, Googlani J, Chakerolhosseini MR, Guerrero C, Albertini E, Baldoni L, Proietti P. Physiological, epigenetic and genetic regulation in some olive cultivars under salt stress. Sci Rep 2019; 9:1093. [PMID: 30705308 PMCID: PMC6355907 DOI: 10.1038/s41598-018-37496-5] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/30/2018] [Indexed: 12/20/2022] Open
Abstract
Cultivated olive, a typical fruit crop species of the semi-arid regions, could successfully face the new scenarios driven by the climate change through the selection of tolerant varieties to salt and drought stresses. In the present work, multidisciplinary approaches, including physiological, epigenetic and genetic studies, have been applied to clarify the salt tolerance mechanisms in olive. Four varieties (Koroneiki, Royal de Cazorla, Arbequina and Picual) and a related form (O. europaea subsp. cuspidata) were grown in a hydroponic system under different salt concentrations from zero to 200 mM. In order to verify the plant response under salt stress, photosynthesis, gas exchange and relative water content were measured at different time points, whereas chlorophyll and leaf concentration of Na+, K+ and Ca2+ ions, were quantified at 43 and 60 days after treatment, when stress symptoms became prominent. Methylation sensitive amplification polymorphism (MSAP) technique was used to assess the effects of salt stress on plant DNA methylation. Several fragments resulted differentially methylated among genotypes, treatments and time points. Real time quantitative PCR (RT-qPCR) analysis revealed significant expression changes related to plant response to salinity. Four genes (OePIP1.1, OePetD, OePI4Kg4 and OeXyla) were identified, as well as multiple retrotransposon elements usually targeted by methylation under stress conditions.
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Affiliation(s)
- Soraya Mousavi
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
- CNR - Institute of Biosciences and Bioresources, Perugia, Italy
| | - Luca Regni
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| | - Marika Bocchini
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| | | | | | - Stefano Mancuso
- Università degli Studi di Firenze, Dept. Agrifood Production and Environmental Sciences, Florence, Italy
| | - Jalaladdin Googlani
- Università degli Studi di Firenze, Dept. Agrifood Production and Environmental Sciences, Florence, Italy
| | | | | | - Emidio Albertini
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources, Perugia, Italy.
| | - Primo Proietti
- Università degli Studi di Perugia, Dept. Agricultural, Food and Environmental Sciences, Perugia, Italy
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15
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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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16
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Alagna F, Caceres ME, Pandolfi S, Collani S, Mousavi S, Mariotti R, Cultrera NGM, Baldoni L, Barcaccia G. The Paradox of Self-Fertile Varieties in the Context of Self-Incompatible Genotypes in Olive. FRONTIERS IN PLANT SCIENCE 2019; 10:725. [PMID: 31293602 PMCID: PMC6606695 DOI: 10.3389/fpls.2019.00725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/16/2019] [Indexed: 05/09/2023]
Abstract
Olive, representing one of the most important fruit crops of the Mediterranean area, is characterized by a general low fruit yield, due to numerous constraints, including alternate bearing, low flower viability, male-sterility, inter-incompatibility, and self-incompatibility (SI). Early efforts to clarify the genetic control of SI in olive gave conflicting results, and only recently, the genetic control of SI has been disclosed, revealing that olive possesses an unconventional homomorphic sporophytic diallelic system of SI, dissimilar from other described plants. This system, characterized by the presence of two SI groups, prevents self-fertilization and regulates inter-compatibility between cultivars, such that cultivars bearing the same incompatibility group are incompatible. Despite the presence of a functional SI, some varieties, in particular conditions, are able to set seeds following self-fertilization, a mechanism known as pseudo-self-compatibility (PSC), as widely reported in previous literature. Here, we summarize the results of previous works on SI in olive, particularly focusing on the occurrence of self-fertility, and offer a new perspective in view of the recent elucidation of the genetic architecture of the SI system in olive. Recent advances in research aimed at unraveling the molecular bases of SI and its breakdown in olive are also presented. The clarification of these mechanisms may have a huge impact on orchard management and will provide fundamental information for the future of olive breeding programs.
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Affiliation(s)
- F. Alagna
- Dipartimento Tecnologie Energetiche (DTE), Centro Ricerche Trisaia, ENEA Agenzia nazionale per le nuove tecnologie, l’energia e lo sviluppo economico sostenibile, Rotondella, Italy
| | - M. E. Caceres
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - S. Pandolfi
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - S. Collani
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - S. Mousavi
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - R. Mariotti
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - N. G. M. Cultrera
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
| | - L. Baldoni
- Dipartimento di Scienze Bio Agroalimentari (DiSBA), Istituto di Bioscienze e Biorisorse (IBBR), Consiglio Nazionale Delle Ricerche (CNR), Perugia, Italy
- *Correspondence: L. Baldoni,
| | - G. Barcaccia
- Laboratorio di Genomica, Dipartimento di Agronomia, Animali, Alimenti, Risorse naturali e Ambiente (DAFNAE), Università di Padova, Legnaro, Italy
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17
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Mariotti R, Fornasiero A, Mousavi S, Cultrera NG, Brizioli F, Pandolfi S, Passeri V, Rossi M, Magris G, Scalabrin S, Scaglione D, Di Gaspero G, Saumitou-Laprade P, Vernet P, Alagna F, Morgante M, Baldoni L. Genetic Mapping of the Incompatibility Locus in Olive and Development of a Linked Sequence-Tagged Site Marker. FRONTIERS IN PLANT SCIENCE 2019; 10:1760. [PMID: 32117338 PMCID: PMC7025539 DOI: 10.3389/fpls.2019.01760] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 12/16/2019] [Indexed: 05/20/2023]
Abstract
The genetic control of self-incompatibility (SI) has been recently disclosed in olive. Inter-varietal crossing confirmed the presence of only two incompatibility groups (G1 and G2), suggesting a simple Mendelian inheritance of the trait. A double digest restriction associated DNA (ddRAD) sequencing of a biparental population segregating for incompatibility groups has been performed and high-density linkage maps were constructed in order to map the SI locus and identify gene candidates and linked markers. The progeny consisted of a full-sib family of 229 individuals derived from the cross 'Leccino' (G1) × 'Dolce Agogia' (G2) varieties, segregating 1:1 (G1:G2), in accordance with a diallelic self-incompatibility (DSI) model. A total of 16,743 single nucleotide polymorphisms was identified, 7,006 in the female parent 'Leccino' and 9,737 in the male parent 'Dolce Agogia.' Each parental map consisted of 23 linkage groups and showed an unusual large size (5,680 cM in 'Leccino' and 3,538 cM in 'Dolce Agogia'). Recombination was decreased across all linkage groups in pollen mother cells of 'Dolce Agogia,' the parent with higher heterozygosity, compared to megaspore mother cells of 'Leccino,' in a context of a species that showed exceptionally high recombination rates. A subset of 109 adult plants was assigned to either incompatibility group by a stigma test and the diallelic self-incompatibility (DSI) locus was mapped to an interval of 5.4 cM on linkage group 18. This region spanned a size of approximately 300 Kb in the olive genome assembly. We developed a sequence-tagged site marker in the DSI locus and identified five haplotypes in 57 cultivars with known incompatibility group assignment. A combination of two single-nucleotide polymorphisms (SNPs) was sufficient to predict G1 or G2 phenotypes in olive cultivars, enabling early marker-assisted selection of compatible genotypes and allowing for a rapid screening of inter-compatibility among cultivars in order to guarantee effective fertilization and increase olive production. The construction of high-density linkage maps has led to the development of the first functional marker in olive and provided positional candidate genes in the SI locus.
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Affiliation(s)
- Roberto Mariotti
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Alice Fornasiero
- Institute of Applied Genomics, Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Soraya Mousavi
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | | | - Federico Brizioli
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Saverio Pandolfi
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Valentina Passeri
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Martina Rossi
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
| | - Gabriele Magris
- Institute of Applied Genomics, Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | | | | | | | | | - Philippe Vernet
- University of Lille, CNRS, UMR 8198 - Evo-Eco-Paleo, F-59000, Lille, France
| | | | - Michele Morgante
- Institute of Applied Genomics, Udine, Italy
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Luciana Baldoni
- CNR - Institute of Biosciences and Bioresources (IBBR), Perugia, Italy
- *Correspondence: Luciana Baldoni,
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18
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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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Biochemical and molecular profiling of unknown olive genotypes from central Italy: determination of major and minor components. Eur Food Res Technol 2018. [DOI: 10.1007/s00217-018-3142-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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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: 66] [Impact Index Per Article: 11.0] [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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Belaj A, de la Rosa R, Lorite IJ, Mariotti R, Cultrera NGM, Beuzón CR, González-Plaza JJ, Muñoz-Mérida A, Trelles O, Baldoni L. Usefulness of a New Large Set of High Throughput EST-SNP Markers as a Tool for Olive Germplasm Collection Management. FRONTIERS IN PLANT SCIENCE 2018; 9:1320. [PMID: 30298075 PMCID: PMC6160578 DOI: 10.3389/fpls.2018.01320] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Accepted: 08/22/2018] [Indexed: 05/08/2023]
Abstract
Germplasm collections are basic tools for conservation, characterization, and efficient use of olive genetic resources. The identification of the olive cultivars maintained in the collections is an important ongoing task which has been performed by both, morphological and molecular markers. In the present study, based on the sequencing results of previous genomic projects, a new set of 1,043 EST-SNP markers has been identified. In order to evaluate its discrimination capacity and utility in diversity studies, this set of markers was used in a representative number of accessions from 20 different olive growing countries and maintained at the World Olive Germplasm Collection of IFAPA Centre 'Alameda del Obispo' (Córdoba, Spain), one of the world's largest olive germplasm bank. Thus, the cultivated material included: cultivars belonging to previously defined core collections by means of SSR markers and agronomical traits, well known homonymy cases, possible redundancies previously identified in the collection, and recently introduced accessions. Marker stability was tested in repeated analyses of a selected number of accessions, as well as in different trees and accessions belonging to the same cultivar. In addition, 15 genotypes from a cross 'Picual' × 'Arbequina' cultivars from the IFAPA olive breeding program and a set of 89 wild genotypes were also included in the study. Our results indicate that, despite their relatively wide variability, the new set of EST-SNPs displayed lower levels of genetic diversity than SSRs in the set of olive core collections tested. However, the EST-SNP markers displayed consistent and reliable results from different plant material sources and plant propagation events. The EST-SNPs revealed a clear cut off between inter- and intra-cultivar variation in olive. Besides, they were able to reliably discriminate among different accessions, to detect possible homonymy cases as well as efficiently ascertain the presence of redundant germplasm in the collection. Additionally, these markers were highly transferable to the wild genotypes. These results, together with the low genotyping error rates and the easy and fully automated procedure used to get the genotyping data, validate the new set of EST-SNPs as possible markers of choice for olive cultivar identification.
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Affiliation(s)
- Angjelina Belaj
- IFAPA Centro Alameda del Obispo, Córdoba, Spain
- *Correspondence: Angjelina Belaj,
| | | | | | | | | | - Carmen R. Beuzón
- Instituto de Hortofruticultura Subtropical y Mediterranea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
| | - J. J. González-Plaza
- Instituto de Hortofruticultura Subtropical y Mediterranea, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Málaga, Spain
- Present address: J. J. González-Plaza, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences, Prague, Czechia
| | - A. Muñoz-Mérida
- CIBIO, InBIO – Research Network in Biodiversity and Evolutionary Biology, University of Porto, Porto, Portugal
| | - O. Trelles
- Department of Integrated Bioinformatics, National Institute for Bioinformatics, Universidad de Málaga, Málaga, Spain
| | - Luciana Baldoni
- CNR – Institute of Biosciences and Bioresources, Perugia, Italy
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Mousavi S, Mariotti R, Regni L, Nasini L, Bufacchi M, Pandolfi S, Baldoni L, Proietti P. The First Molecular Identification of an Olive Collection Applying Standard Simple Sequence Repeats and Novel Expressed Sequence Tag Markers. FRONTIERS IN PLANT SCIENCE 2017; 8:1283. [PMID: 28769972 PMCID: PMC5515915 DOI: 10.3389/fpls.2017.01283] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 07/07/2017] [Indexed: 05/10/2023]
Abstract
Germplasm collections of tree crop species represent fundamental tools for conservation of diversity and key steps for its characterization and evaluation. For the olive tree, several collections were created all over the world, but only few of them have been fully characterized and molecularly identified. The olive collection of Perugia University (UNIPG), established in the years' 60, represents one of the first attempts to gather and safeguard olive diversity, keeping together cultivars from different countries. In the present study, a set of 370 olive trees previously uncharacterized was screened with 10 standard simple sequence repeats (SSRs) and nine new EST-SSR markers, to correctly and thoroughly identify all genotypes, verify their representativeness of the entire cultivated olive variation, and validate the effectiveness of new markers in comparison to standard genotyping tools. The SSR analysis revealed the presence of 59 genotypes, corresponding to 72 well known cultivars, 13 of them resulting exclusively present in this collection. The new EST-SSRs have shown values of diversity parameters quite similar to those of best standard SSRs. When compared to hundreds of Mediterranean cultivars, the UNIPG olive accessions were splitted into the three main populations (East, Center and West Mediterranean), confirming that the collection has a good representativeness of the entire olive variability. Furthermore, Bayesian analysis, performed on the 59 genotypes of the collection by the use of both sets of markers, have demonstrated their splitting into four clusters, with a well balanced membership obtained by EST respect to standard SSRs. The new OLEST (Olea expressed sequence tags) SSR markers resulted as effective as the best standard markers. The information obtained from this study represents a high valuable tool for ex situ conservation and management of olive genetic resources, useful to build a common database from worldwide olive cultivar collections, also based on recently developed markers.
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Affiliation(s)
- Soraya Mousavi
- Consiglio Nazionale delle Ricerche – Institute for Agricultural and Forest Systems in the MediterraneanPerugia, Italy
| | - Roberto Mariotti
- Consiglio Nazionale delle Ricerche – Institute of Biosciences and BioresourcesPerugia, Italy
| | - Luca Regni
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di PerugiaPerugia, Italy
| | - Luigi Nasini
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di PerugiaPerugia, Italy
| | - Marina Bufacchi
- Consiglio Nazionale delle Ricerche – Institute for Agricultural and Forest Systems in the MediterraneanPerugia, Italy
| | - Saverio Pandolfi
- Consiglio Nazionale delle Ricerche – Institute of Biosciences and BioresourcesPerugia, Italy
| | - Luciana Baldoni
- Consiglio Nazionale delle Ricerche – Institute of Biosciences and BioresourcesPerugia, Italy
| | - Primo Proietti
- Department of Agricultural, Food and Environmental Sciences, Università degli Studi di PerugiaPerugia, Italy
- *Correspondence: Primo Proietti,
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