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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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Carvalho J, Yadav S, Garrido-Maestu A, Azinheiro S, Trujillo I, Barros-Velázquez J, Prado M. Evaluation of simple sequence repeats (SSR) and single nucleotide polymorphism (SNP)-based methods in olive varieties from the Northwest of Spain and potential for miniaturization. FOOD CHEMISTRY: MOLECULAR SCIENCES 2021; 3:100038. [PMID: 35415648 PMCID: PMC8991621 DOI: 10.1016/j.fochms.2021.100038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 07/10/2021] [Accepted: 07/31/2021] [Indexed: 11/17/2022]
Abstract
SSR- and SNP-based methods were evaluated for the identification of olive varieties. SNP identification was performed for the first time for two autochthonous varieties. The potential for future miniaturization of the genotyping methods was evaluated. Allele-specific PCR provided the best results for the tested olive varieties.
Miniaturization of DNA-based techniques can bring interesting advantages for food analysis, such as portability of complex analytical procedures. In the olive oil industry, miniaturization can be particularly interesting for authenticity and traceability applications, through in situ control of raw materials before production and/or the final products. However, variety identification is challenging, and implementation on miniaturized settings must be carefully evaluated, starting from the selected analytical approach. In this work, SSR- and SNP-based genotyping strategies were investigated for the identification and differentiation of two olive varieties from the Northwest of Spain. For the selected SNPs two genotyping methods were tested: real-time allele-specific PCR and high resolution melting analysis. These methods were compared and evaluated regarding their potential for integration in a microfluidic device. Both SNP-based methods proved to be successful for identification of the selected varieties, however real-time allele-specific PCR was the one that achieved the best results when analyzing mixtures, allowing the identification of both monovarietal samples and mixtures of the varieties tested with up to 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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Vuletin Selak G, Baruca Arbeiter A, Cuevas J, Perica S, Pujic P, Raboteg Božiković M, Bandelj D. Seed Paternity Analysis Using SSR Markers to Assess Successful Pollen Donors in Mixed Olive Orchards. PLANTS 2021; 10:plants10112356. [PMID: 34834719 PMCID: PMC8624852 DOI: 10.3390/plants10112356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/19/2021] [Accepted: 10/28/2021] [Indexed: 11/22/2022]
Abstract
The olive tree (Olea europaea L.) is a wind-pollinated crop that exhibits an extreme alternate bearing habit. To improve fruit set, several methods have been used to determine the most successful compatible combinations of cultivars. In this study, priority is given to seed paternity analysis based on simple sequence repeats (SSRs), microsatellite markers used for the identification of potential pollen donors of cultivar ‘Oblica’ in a mixed olive orchard during two consecutive years. Seven microsatellite primers were successfully used to examine the paternity of olive embryos from ‘Oblica’ mother trees. Embryos were considered as a product of self-fertilization if only maternal alleles were present, but not a single case of self-fertilization was found among all the embryos analyzed. Two dominant pollen donors were not the closest nor the cultivars with the highest number of trees in the orchard, suggesting that cross-compatibility may have a key role in determining pollen donor success. In our earlier studies, pollen tube growth and fertilization success correlated with fruit set when controlled crosses between cultivars were performed; however, some discrepancy might appear compared to paternity analyses when mother trees have a free choice among different pollen sources from cultivars growing in their surroundings.
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Affiliation(s)
- Gabriela Vuletin Selak
- Department of Plant Sciences, Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia; (S.P.); (M.R.B.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska Cesta 25, 10000 Zagreb, Croatia
- Correspondence: ; Tel.: +385-21-434-436
| | - Alenka Baruca Arbeiter
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia; (A.B.A.); (D.B.)
| | - Julián Cuevas
- Department of Agronomy, University of Almería, CeiA3, La Cañada de San Urbano, s/n, 04120 Almería, Spain;
| | - Slavko Perica
- Department of Plant Sciences, Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia; (S.P.); (M.R.B.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Petar Pujic
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, F-69622 Villeurbanne, France;
| | - Marina Raboteg Božiković
- Department of Plant Sciences, Institute for Adriatic Crops and Karst Reclamation, 21000 Split, Croatia; (S.P.); (M.R.B.)
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Svetošimunska Cesta 25, 10000 Zagreb, Croatia
| | - Dunja Bandelj
- Faculty of Mathematics, Natural Sciences and Information Technologies, University of Primorska, 6000 Koper, Slovenia; (A.B.A.); (D.B.)
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Yadav S, Carvalho J, Trujillo I, Prado M. Microsatellite Markers in Olives ( Olea europaea L.): Utility in the Cataloging of Germplasm, Food Authenticity and Traceability Studies. Foods 2021; 10:foods10081907. [PMID: 34441688 PMCID: PMC8394707 DOI: 10.3390/foods10081907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/27/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023] Open
Abstract
The olive fruit, a symbol of Mediterranean diets, is a rich source of antioxidants and oleic acid (55–83%). Olive genetic resources, including cultivated olives (cultivars), wild olives as well as related subspecies, are distributed widely across the Mediterranean region and other countries. Certain cultivars have a high commercial demand and economical value due to the differentiating organoleptic characteristics. This might result in economically motivated fraudulent practices and adulteration. Hence, tools to ensure the authenticity of constituent olive cultivars are crucial, and this can be achieved accurately through DNA-based methods. The present review outlines the applications of microsatellite markers, one of the most extensively used types of molecular markers in olive species, particularly referring to the use of these DNA-based markers in cataloging the vast olive germplasm, leading to identification and authentication of the cultivars. Emphasis has been given on the need to adopt a uniform platform where global molecular information pertaining to the details of available markers, cultivar-specific genotyping profiles (their synonyms or homonyms) and the comparative profiles of oil and reference leaf samples is accessible to researchers. The challenges of working with microsatellite markers and efforts underway, mainly advancements in genotyping methods which can be effectively incorporated in olive oil varietal testing, are also provided. Such efforts will pave the way for the development of more robust microsatellite marker-based olive agri-food authentication platforms.
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Affiliation(s)
- Shambhavi Yadav
- Genetics and Tree Improvement Division, Forest Research Institute, P.O. New Forest, Dehradun 248001, India
- Correspondence: (S.Y.); (I.T.)
| | - Joana Carvalho
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga, Portugal; (J.C.); (M.P.)
- Department of Analytical Chemistry, Nutrition and Food Science, Campus Vida, College of Pharmacy/School of Veterinary Sciences, University of Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Isabel Trujillo
- Excellence Unit of Maria de Maeztu, Department of Agronomy, Rabanales Campus, International Campus of Excellence on Agrofood (ceiA3), University of Córdoba, 14014 Córdoba, Spain
- Correspondence: (S.Y.); (I.T.)
| | - Marta Prado
- Food Quality and Safety Research Group, International Iberian Nanotechnology Laboratory (INL), 4715-330 Braga, Portugal; (J.C.); (M.P.)
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Pavan S, Vergine M, Nicolì F, Sabella E, Aprile A, Negro C, Fanelli V, Savoia MA, Montilon V, Susca L, Delvento C, Lotti C, Nigro F, Montemurro C, Ricciardi L, De Bellis L, Luvisi A. Screening of Olive Biodiversity Defines Genotypes Potentially Resistant to Xylella fastidiosa. FRONTIERS IN PLANT SCIENCE 2021; 12:723879. [PMID: 34484283 PMCID: PMC8415753 DOI: 10.3389/fpls.2021.723879] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/23/2021] [Indexed: 06/12/2023]
Abstract
The recent outbreak of the Olive Quick Decline Syndrome (OQDS), caused by Xylella fastidiosa subsp. pauca (Xf), is dramatically altering ecosystem services in the peninsula of Salento (Apulia Region, southeastern Italy). Here we report the accomplishment of several exploratory missions in the Salento area, resulting in the identification of thirty paucisymptomatic or asymptomatic plants in olive orchards severely affected by the OQDS. The genetic profiles of such putatively resistant plants (PRPs), assessed by a selection of ten simple sequence repeat (SSR) markers, were compared with those of 141 Mediterranean cultivars. Most (23) PRPs formed a genetic cluster (K1) with 22 Italian cultivars, including 'Leccino' and 'FS17', previously reported as resistant to Xf. The remaining PRPs displayed relatedness with genetically differentiated germplasm, including a cluster of Tunisian cultivars. Markedly lower colonization levels were observed in PRPs of the cluster K1 with respect to control plants. Field evaluation of four cultivars related to PRPs allowed the definition of partial resistance in the genotypes 'Frantoio' and 'Nocellara Messinese'. Some of the PRPs identified in this study might be exploited in cultivation, or as parental clones of breeding programs. In addition, our results indicate the possibility to characterize resistance to Xf in cultivars genetically related to PRPs.
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Affiliation(s)
- Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Bari, Italy
| | - Marzia Vergine
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Francesca Nicolì
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Erika Sabella
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Alessio Aprile
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Carmine Negro
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Bari, Italy
| | | | - Vito Montilon
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Bari, Italy
| | - Leonardo Susca
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Bari, Italy
| | - Chiara Delvento
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Bari, Italy
| | - Concetta Lotti
- Department of Agriculture, Food, Natural Resources and Engineering, University of Foggia, Foggia, Italy
| | - Franco Nigro
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Bari, Italy
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, University of Bari “Aldo Moro”, Bari, Italy
| | - Luigi De Bellis
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | - Andrea Luvisi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
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Duran ST, Aghayeva S, Akparov Z, Mammadov A, Asgarova R, Uslu OY, Kirikoglu O, Duran UT, Ipek M, Barut E, Ercisli S, Ilhan G, Ipek A. Genetic variation and relationships between Azerbaijani and Turkish olive genetic resources. Mol Biol Rep 2021; 49:5209-5217. [PMID: 34291396 DOI: 10.1007/s11033-021-06564-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 07/13/2021] [Indexed: 11/25/2022]
Abstract
Olive (Olea europaea L.) is one of the most economically important crop from east to the west around the world. The aim of this research was to investigate the genetic relationship among 41 olive genotypes, including 11 well-known Turkish cultivars and 30 Azerbaijani olive genotypes using simple sequence repeat (SSR) markers. In this study, 19 SSR markers were amplified 115 polymorphic SSR alleles. The number of polymorphic alleles ranged from 3 to 10 with an average of 6.05. The observed heterozygosity (Ho) varied from 0.05 to 0.93 with an average of 0.63 and expected heterozygosity (He) differed from 0.26 to 0.86 with an average of 0.72. The polymorphism information content (PIC) ranged from 0.23 to 0.85 with a mean of 0.68. A UPGMA cluster analysis grouped olive genotypes into two distinct clusters and both clusters were divided into two subgroups. Similarly, STRUCTURE analysis assigned olive genotypes into two different gene pools (K = 2) and four gene pools were identified representing the two subgroups by STRUCTURE analysis for K = 4. The genetic similarity of olive genotypes ranged from 0.36 to 0.95. These results revealed that there was a high genetic variation among 30 Azerbaijani olive genotypes. 'Ayvalık 1'and 'Ayvalık 2' from Azerbaijani olive genotypes were different from Turkish local olive cultivar, "Ayvalık" indicating homonymy. This research also highlighted that Azerbaijani olive genotypes were totally distinct from Turkish olive cultivars demonstrating that these olive genotypes might have been imported to Azerbaijan from different countries other than Turkey. The outcomes of this study indicated that these diverse olive genotypes could be useful for development of new olive varieties in Azerbaijan and future breeding programs between two countries could be enhanced by means of these results.
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Affiliation(s)
- Sevin Teoman Duran
- Department of Crop and Animal Production, Organic Agriculture Programme, Karacabey Vocational School, Bursa Uludağ University, Bursa, Turkey
| | - Saltanat Aghayeva
- Genetic Resources Institute of Azerbaijan, National Academy of Sciences, Baku, Azerbaijan
| | - Zeynal Akparov
- Genetic Resources Institute of Azerbaijan, National Academy of Sciences, Baku, Azerbaijan
| | - Ayaz Mammadov
- Genetic Resources Institute of Azerbaijan, National Academy of Sciences, Baku, Azerbaijan
| | - Rana Asgarova
- Genetic Resources Institute of Azerbaijan, National Academy of Sciences, Baku, Azerbaijan
| | - Osman Yasar Uslu
- Department of Horticulture, Faculty of Agriculture, Bursa Uludağ University, Bursa, Turkey
| | - Osman Kirikoglu
- Department of Horticulture, Faculty of Agriculture, Bursa Uludağ University, Bursa, Turkey
| | - Ufuk Tan Duran
- Department of Horticulture, Faculty of Agriculture, Bursa Uludağ University, Bursa, Turkey
| | - Meryem Ipek
- Department of Horticulture, Faculty of Agriculture, Bursa Uludağ University, Bursa, Turkey
| | - Erdogan Barut
- Department of Horticulture, Faculty of Agriculture, Bursa Uludağ University, Bursa, Turkey
| | - Sezai Ercisli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240, Erzurum, Turkey.
| | - Gulce Ilhan
- Department of Horticulture, Faculty of Agriculture, Ataturk University, 25240, Erzurum, Turkey
| | - Ahmet Ipek
- Department of Crop and Animal Production, Organic Agriculture Programme, Karacabey Vocational School, Bursa Uludağ University, Bursa, Turkey.,Department of Horticulture, Faculty of Agriculture, Bursa Uludağ University, Bursa, Turkey
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8
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Atrouz K, Bousba R, Marra FP, Marchese A, Conforti FL, Perrone B, Harkat H, Salimonti A, Zelasco S. Algerian Olive Germplasm and Its Relationships with the Central-Western Mediterranean Varieties Contributes to Clarify Cultivated Olive Diversification. PLANTS (BASEL, SWITZERLAND) 2021; 10:678. [PMID: 33916098 PMCID: PMC8066573 DOI: 10.3390/plants10040678] [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: 03/06/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 12/03/2022]
Abstract
Olive tree with its main final product, olive oil, is an important element of Mediterranean history, considered the emblematic fruit of a civilization. Despite its wide diffusion and economic and cultural importance, its evolutionary and phylogenetic history is still difficult to clarify. As part of the Mediterranean basin, Algeria was indicated as a secondary diversification center. However, genetic characterization studies from Maghreb area, are currently underrepresented. In this context, we characterized 119 endemic Algerian accessions by using 12 microsatellite markers with the main goal to evaluate the genetic diversity and population structure. In order to provide new insights about the history of olive diversification events in the Central-Western Mediterranean basin, we included and analyzed a sample of 103 Italian accessions from Sicily and, a set of molecular profiles of cultivars from the Central-Western Mediterranean area. The phylogenetic investigation let us to evaluate genetic relationships among Central-Mediterranean basin olive germplasm, highlight new synonymy cases to support the importance of vegetative propagation in the cultivated olive diffusion and consolidate the hypothesis of more recent admixture events occurrence. This work provided new information about Algerian germplasm biodiversity and contributed to clarify olive diversification process.
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Affiliation(s)
- Kamel Atrouz
- Council for Agricultural Research and Economics-Research Centre for Olive, Fruit and Citrus Crops, 87036 Rende, Italy; (K.A.); (A.S.)
- Department of Biology and Plant Ecology, Faculty of Natural Sciences and Life, Frères, Mentouri University, Constantine 25000, Algeria; (R.B.); (H.H.)
| | - Ratiba Bousba
- Department of Biology and Plant Ecology, Faculty of Natural Sciences and Life, Frères, Mentouri University, Constantine 25000, Algeria; (R.B.); (H.H.)
| | | | - Annalisa Marchese
- Department of Agricultural, Food and Forest Sciences, University of Palermo, 90128 Palermo, Italy;
| | - Francesca Luisa Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.L.C.); (B.P.)
| | - Benedetta Perrone
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy; (F.L.C.); (B.P.)
| | - Hamza Harkat
- Department of Biology and Plant Ecology, Faculty of Natural Sciences and Life, Frères, Mentouri University, Constantine 25000, Algeria; (R.B.); (H.H.)
| | - Amelia Salimonti
- Council for Agricultural Research and Economics-Research Centre for Olive, Fruit and Citrus Crops, 87036 Rende, Italy; (K.A.); (A.S.)
| | - Samanta Zelasco
- Council for Agricultural Research and Economics-Research Centre for Olive, Fruit and Citrus Crops, 87036 Rende, Italy; (K.A.); (A.S.)
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Genetic Structure and Core Collection of Olive Germplasm from Albania Revealed by Microsatellite Markers. Genes (Basel) 2021; 12:genes12020256. [PMID: 33578843 PMCID: PMC7916616 DOI: 10.3390/genes12020256] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 11/16/2022] Open
Abstract
Olive is considered one of the oldest and the most important cultivated fruit trees in Albania. In the present study, the genetic diversity and structure of Albanian olive germplasm is represented by a set of 194 olive genotypes collected in-situ in their natural ecosystems and in the ex-situ collection. The study was conducted using 26 microsatellite markers (14 genomic SSR and 12 Expressed Sequence Tag microsatellites). The identity analysis revealed 183 unique genotypes. Genetic distance-based and model-based Bayesian analyses were used to investigate the genetic diversity, relatedness, and the partitioning of the genetic variability among the Albanian olive germplasm. The genetic distance-based analysis grouped olives into 12 clusters, with an average similarity of 50.9%. Albanian native olives clustered in one main group separated from introduced foreign cultivars, which was also supported by Principal Coordinate Analysis (PCoA) and model-based methods. A core collection of 57 genotypes representing all allelic richness found in Albanian germplasm was developed for the first time. Herein, we report the first extended genetic characterization and structure of olive germplasm in Albania. The findings suggest that Albanian olive germplasm is a unique gene pool and provides an interesting genetic basis for breeding programs.
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NMR-based metabolomic study of Apulian Coratina extra virgin olive oil extracted with a combined ultrasound and thermal conditioning process in an industrial setting. Food Chem 2020; 345:128778. [PMID: 33310250 DOI: 10.1016/j.foodchem.2020.128778] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 11/23/2022]
Abstract
The innovative combination of ultrasound (Us) with a thermal exchanger to produce high quality extra virgin olive oil (EVOO) was studied using Nuclear Magnetic Resonance (NMR) spectroscopy and multivariate analysis (MVA). Major and minor metabolomic components of Apulian Coratina EVOO obtained using the two methods were compared. Early and late olive ripening stages were also considered. An increased amount of polyphenols was found for EVOOs obtained using the Us with respect to the conventional method for both early and late ripening stages (900.8 ± 10.3 and 571.9 ± 9.9 mg/kg versus 645.1 ± 9.3 and 440.8 ± 10.4 mg/kg). NMR spectroscopy showed a significant increase (P < 0.05) in polyunsaturated fatty acids (PUFA) as well as in the tyrosol and hydroxytyrosol derivatives, such as oleocanthal, oleacein, and elenolic acid, for both ripening stages. In conclusion, NMR spectroscopy provides information about the metabolomic components of EVOOs to producers, while the Us process increases the levels of healthy bioactive components.
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11
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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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Abstract
Tunisia is one of the world’s largest producers of olive oil, and it preserves pools of olive genetic diversity that are still unexplored. A recent prospection and collection program of the National Gene Bank of Tunisia (NGBT) focused on the vast oasis of Degache, in the south west part of Tunisia, where 47 samples were collected and genetically characterized through simple sequence repeat (SSR) markers. Identification and authentication of genotypes were obtained through comparison with reference cultivars belonging to the Olive National Collection of Tunisia (IOC) and with cultivars from Algeria, Italia, Syria and Lebanon. Degache olive genotypes showed large genetic variability, a significant diversity from the reference germplasm, and a clear differentiation from modern varieties. The population structure analysis identified four gene pools characterizing genotypes from different area of origin. Two gene pools appear to be more represented in germplasm from southern Tunisia, where environmental conditions at critical plant development phases, are harsher. This suggests that this germplasm might present traits of adaptation useful for breeding to improve resilience to abiotic stresses. Our results will support ex situ and in situ conservation activities of Tunisian olive germplasm pursued by the National Gene Bank of Tunisia.
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Martínez MC, Santiago JL, Boso S, Gago P, Álvarez-Acero I, De Vega ME, Martínez-Bartolomé M, Álvarez-Nogal R, Molíst P, Caser M, Scariot V, Gómez-García D. Narcea-an unknown, ancient cultivated rose variety from northern Spain. HORTICULTURE RESEARCH 2020; 7:44. [PMID: 32257230 PMCID: PMC7109042 DOI: 10.1038/s41438-020-0266-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 02/06/2020] [Accepted: 02/12/2020] [Indexed: 05/18/2023]
Abstract
The present work reports the discovery and the complete characterisation of an ancient cultivated rose variety found growing in a private garden in the southwest of the Principality of Asturias (northern Spain). The variety is here given the name Narcea. The majority of roses currently cultivated belong to the so-called group of 'Modern Roses', all of which were obtained after 1867 via artificial crosses and improvement programmes. All are destined for ornamental use. Until the 19th century, the great majority of the many ancient cultivated roses in Europe were used in perfumery and cosmetics, or had medicinal uses. Rosa damascena and Rosa centifollia are still grown and used by the French and Bulgarian perfume industries. The Asturian Massif of the Cantabrian Mountain Range provides a natural habitat for some 75% of the wild members of the genus Rosa, but until now there was no evidence that this area was home to ancient cultivated roses. A complete botanical description is here provided for a discovered ancient rose. It is also characterised according to a series of sequence tagged microsatellite sites, and its agronomic features are reported. In addition, a histological description (optical and scanning electronic microscope studies) of the petals is offered, along with an analysis of the volatile compounds present in these organs as determined by solid phase microextraction and gas chromatography-mass spectroscopy. The results reveal the uniqueness of this ancient type of rose and suggest it may be of interest to the perfume industry.
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Affiliation(s)
| | - José-Luis Santiago
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra Spain
| | - Susana Boso
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra Spain
| | - Pilar Gago
- Misión Biológica de Galicia (CSIC), Carballeira 8, Salcedo, 36143 Pontevedra Spain
| | - Inmaculada Álvarez-Acero
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (CSIC) (Spain), C/José Antonio Novais 10, 28040 Madrid, Spain
| | - María-Estela De Vega
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (CSIC) (Spain), C/José Antonio Novais 10, 28040 Madrid, Spain
| | - Miguel Martínez-Bartolomé
- Instituto de Ciencia y Tecnología de Alimentos y Nutrición (CSIC) (Spain), C/José Antonio Novais 10, 28040 Madrid, Spain
| | - Rafael Álvarez-Nogal
- Departamento de Biología Molecular-Área de Biología Celular, Universidad de León, Campus de Vegazana s/n, 24071 León, Spain
| | - Pilar Molíst
- Grupo Neurolamb, Biología funcional y Ciencias de la Salud, Universidad de Vigo (Spain), 36310 As Lagoas-Marcosende, Spain
| | - Matteo Caser
- Department of Agricultural, Forest and Food Sciences, University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Turin Italy
| | - Valentina Scariot
- Department of Agricultural, Forest and Food Sciences, University of Torino, Largo Paolo Braccini 2, 10095 Grugliasco, Turin Italy
| | - Daniel Gómez-García
- Instituto Pirenaico de Ecología (CSIC), Dpto. Conservación de Ecosistemas Naturales, Avda. Montaña S/N, Zaragoza, 50016 Zaragoza, Spain
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14
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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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15
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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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16
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Crawford LM, Carrasquilla-Garcia N, Cook D, Wang SC. Analysis of Microsatellites (SSRs) in Processed Olives as a Means of Cultivar Traceability and Authentication. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:1110-1117. [PMID: 31891498 DOI: 10.1021/acs.jafc.9b06890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Select cultivars of table olives have more desirable traits and a higher economic value. There are suspected issues with cultivar mislabeling and traceability in the supply chain. Here, we describe a method to identify cultivars by genotyping of processed olives. DNA was extracted from leaves and California-style olives of seven commonly packed cultivars. Processed olive fruits yielded relatively low DNA concentrations (0.04-0.86 μg/g), and extracts had more impurities compared with leaves. From 15 candidate SSRs, five markers showing the highest number of unique allele combinations and discriminatory power were selected. These SSRs were successfully amplified and analyzed in all cultivars of olives except one. When directly comparing any two cultivars, different allele combinations were typically present for at least four of the five SSRs. Microsatellite analysis shows potential as a simple yet robust diagnostic tool. The method can be expanded to include other cultivars, styles of table olives, and potentially other processed plant-based foods.
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Affiliation(s)
- Lauren M Crawford
- Department of Food Science and Technology , University of California, Davis , Davis , California 95616 , United States
| | - Noelia Carrasquilla-Garcia
- Department of Plant Pathology , University of California, Davis , Davis , California 95616 , United States
| | - Doug Cook
- Department of Plant Pathology , University of California, Davis , Davis , California 95616 , United States
| | - Selina C Wang
- Department of Food Science and Technology , University of California, Davis , Davis , California 95616 , United States
- Olive Center, Robert Mondavi Institute for Wine and Food Science , University of California, Davis , Davis , California 95616 , United States
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17
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Salimonti A, Carbone F, Romano E, Pellegrino M, Benincasa C, Micali S, Tondelli A, Conforti FL, Perri E, Ienco A, Zelasco S. Association Study of the 5'UTR Intron of the FAD2-2 Gene With Oleic and Linoleic Acid Content in Olea europaea L. FRONTIERS IN PLANT SCIENCE 2020; 11:66. [PMID: 32117401 PMCID: PMC7031445 DOI: 10.3389/fpls.2020.00066] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 01/16/2020] [Indexed: 05/21/2023]
Abstract
Cultivated olive (Olea europaea L. subsp. europaea var. europaea) is the most ancient and spread tree crop in the Mediterranean basin. An important quality trait for the extra virgin olive oil is the fatty acid composition. In particular, a high content of oleic acid and low of linoleic, linolenic, and palmitic acid is considered very relevant in the health properties of the olive oil. The oleate desaturase enzyme encoding-gene (FAD2-2) is the main responsible for the linoleic acid content in the olive fruit mesocarp and, therefore, in the olive oil revealing to be the most important candidate gene for the linoleic acid biosynthesis. In this study, an in silico and structural analysis of the 5'UTR intron of the FAD2-2 gene was conducted with the aim to explore the natural sequence variability and its role in the gene expression regulation. In order to identify functional allele variants, the 5'UTR intron was isolated and partially sequenced in 97 olive cultivars. The sequence analysis allowed to find a 117-bp insertion including two long duplications never found before in FAD2-2 genes in olive and the existence of many intron-mediated enhancement (IME) elements. The sequence polymorphism analysis led to detect 39 SNPs. The candidate gene association study conducted for oleic and linoleic acids content revealed seven SNPs and one indel significantly associated able to explain a phenotypic variation ranging from 7% to 16% among the years. Our study highlighted new structural variants within the FAD2-2 gene in olive, putatively involved in the regulation mechanisms of gene expression associated with the variation of the content of oleic and linoleic acid.
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Affiliation(s)
- Amelia Salimonti
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | - Fabrizio Carbone
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | - Elvira Romano
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | | | - Cinzia Benincasa
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | - Sabrina Micali
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Roma, Italy
| | - Alessandro Tondelli
- Research Centre for Genomics and Bioinformatics, CREA, Fiorenzuola D’Arda, Italy
| | - Francesca L. Conforti
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, Rende, Italy
| | - Enzo Perri
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
| | | | - Samanta Zelasco
- Research Centre for Olive, Citrus and Tree Fruit, CREA, Rende, Italy
- *Correspondence: Samanta Zelasco,
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18
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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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19
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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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20
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A Robust DNA Isolation Protocol from Filtered Commercial Olive Oil for PCR-Based Fingerprinting. Foods 2019; 8:foods8100462. [PMID: 31601039 PMCID: PMC6836273 DOI: 10.3390/foods8100462] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 09/27/2019] [Accepted: 10/06/2019] [Indexed: 12/12/2022] Open
Abstract
Extra virgin olive oil (EVOO) has elevated commercial value due to its health appeal, desirable characteristics and quantitatively limited production, and thus it has become an object of intentional adulteration. As EVOOs on the market might consist of a blend of olive varieties or sometimes even of a mixture of oils from different botanical species, an array of DNA-fingerprinting methods have been developed to check the varietal composition of the blend. Starting from a comparison between publicly available DNA extraction protocols, we set up a timely, low-cost, reproducible and effective DNA isolation protocol, which allows an adequate amount of DNA to be recovered even from commercial filtered EVOOs. Then, in order to verify the effectiveness of the DNA extraction protocol herein proposed, we applied PCR-based fingerprinting methods starting from the DNA extracted from three EVOO samples of unknown composition. In particular, genomic regions harboring nine simple sequence repeats (SSRs) and eight genotyping-by-sequencing-derived single nucleotide polymorphism (SNP) markers were amplified for authentication and traceability of the three EVOO samples. The whole investigation strategy herein described might favor producers in terms of higher revenues and consumers in terms of price transparency and food safety.
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21
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Lombardo L, Fila G, Lombardo N, Epifani C, Duffy DH, Godino G, Salimonti A, Zelasco S. Uncovering Olive Biodiversity through Analysis of Floral and Fruiting Biology and Assessment of Genetic Diversity of 120 Italian Cultivars with Minor or Marginal Diffusion. BIOLOGY 2019; 8:biology8030062. [PMID: 31466369 PMCID: PMC6783865 DOI: 10.3390/biology8030062] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/18/2019] [Accepted: 08/26/2019] [Indexed: 11/16/2022]
Abstract
The primary impetus behind this research was to provide a boost to the characterization of the Italian olive biodiversity by acquiring reliable and homogeneous data over the course of an eight-year trial on the floral and fruiting biology of 120 molecularly analyzed cultivars, most of which have either low or very low diffusion. The obtained data highlighted a considerable variability to almost all of the analyzed parameters, which given the uniformity of environment and crop management was indicative of a large genetic variability in the accessions under observation, as confirmed through the molecular analysis. Several cases of synonymy were reported for the first time, even among plants cultivated in different regions, whilst all of the varieties examined, with only one exception, showed very low percentages of self-fruit-set, indicating a need for the employment of suitable pollinator plants. Eventually, a fitted model allowed us to evaluate the clear effects of the thermal values on blossoming, particularly in the months of March and April, whereas the climatic conditions during the flowering time had only a modest effect on its duration.
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Affiliation(s)
- Luca Lombardo
- Center Agriculture Food Environment (C3A), University of Trento, 38122 Trento, Italy
- Research and Innovation Centre, Fondazione Edmund Mach, 38010 San Michele all’Adige, Italy
- Correspondence:
| | - Gianni Fila
- CREA Research Centre for Agriculture and Environment, 40128 Bologna, Italy;
| | - Nicola Lombardo
- CREA Research Centre for Olive, Citrus and Tree Fruit, 87036 Rende, Italy; (N.L.); (G.G.); (A.S.); (S.Z.)
| | - Chiara Epifani
- CREA Research Centre for Agriculture and Environment, 00184 Roma, Italy;
| | - Donald H. Duffy
- Department of Computer Science and Automation Control, University of Salamanca, 37007 Salamanca, Spain;
- Ketensis, New York, NY 10036, USA
| | - Gianluca Godino
- CREA Research Centre for Olive, Citrus and Tree Fruit, 87036 Rende, Italy; (N.L.); (G.G.); (A.S.); (S.Z.)
| | - Amelia Salimonti
- CREA Research Centre for Olive, Citrus and Tree Fruit, 87036 Rende, Italy; (N.L.); (G.G.); (A.S.); (S.Z.)
| | - Samanta Zelasco
- CREA Research Centre for Olive, Citrus and Tree Fruit, 87036 Rende, Italy; (N.L.); (G.G.); (A.S.); (S.Z.)
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Safari H, Zebarjadi A, Kahrizi D, Jafari AA. The study of inter-specific relationships of Bromus genus based on SCoT and ISSR molecular markers. Mol Biol Rep 2019; 46:5209-5223. [PMID: 31313131 DOI: 10.1007/s11033-019-04978-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Accepted: 07/11/2019] [Indexed: 10/26/2022]
Abstract
The genus of Bromus is one of the most important collection of rangeland plants, which are distributed in a wide range of natural areas of Iran. Interspecific relationships were evaluated in 90 accessions of 18 Bromus species based on 15 ISSR and 15 SCoT primers. SCoT markers separated the accessions better than ISSR marker. In addition, there was a high interspecific diversity between surveying germplasm. The sections of Bromus genus completely separated based on DNA molecular markers. SCoT markers could separate the accessions in each species. The primers of SC5 and SC35 from SCoT marker and UBC861, UBC857 and UBC844 primers from ISSR marker were identified as the best primers in revealing of genetic diversity between accessions. The sections of Ceratochloa, Genea, Pnigma and Bromus were monophyletic and were placed in one cluster. The section Bromus had a direct relationship with section Genea. In other words, section Ceratochloa has a direct relationship with Pnigma. B. tectorum and B. sericeus. B. sterilis had the most distance with other species in section Genea. B. squarrosus and B. japonicus had the most similarity and B. briziformis with B. danthoniae and B. scoparius with B. rechingeri had a moderate relationship in section Bromus. B. tomentosus and B. persicus had the highest similarity and B. riparius with B. biebersteinii and B. tomentellus with B. inermis had a moderate similarity in section Pnigma.
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Affiliation(s)
- Hooshmand Safari
- Department of Agronomy and Plant Breeding, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah, Iran.,Faculty Member of Research Department of Forests and Rangelands, Kermanshah Agricultural and Natural Resources Research and Education Center, AREEO, Kermanshah, Iran
| | - Alireza Zebarjadi
- Department of Agronomy and Plant Breeding, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah, Iran.
| | - Danial Kahrizi
- Department of Agronomy and Plant Breeding, Faculty of Science and Agricultural Engineering, Razi University, Kermanshah, Iran
| | - Ali Ashraf Jafari
- Research Institute of Forests and Rangelands, Agricultural Research, Education and Extension Organization (AREEO), Tehran, Iran
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23
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Xu Y, Hu Z, Li W, Zeng T, Zhang X, Li J, Zhang W, Yue B. Isolation and strategies of novel tetranucleotide microsatellites with polymorphisms from different chromosomes of the rhesus monkey (Macaca mulatta). Mol Biol Rep 2019; 46:3955-3966. [PMID: 31119442 DOI: 10.1007/s11033-019-04842-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 04/26/2019] [Indexed: 11/26/2022]
Abstract
A total of 45 tetranucleotide chromosome-specific microsatellite markers with polymorphism were developed successfully based on three reference rhesus monkey genomes and on In-silico PCR prescreening. The polymorphic information content (PIC) values of 45 polymorphic microsatellite loci ranged from 0.487 to 0.879, with an average of 0.715, which were proven to be moderate to highly polymorphic. We detected 315 alleles on 45 microsatellite loci in 24 Rhesus monkeys. The number of alleles ranged from 3 to 15 and the mean number of alleles was 7 for each locus. Accordingly, the observed and expected heterozygosities obtained were between 0.417 and 1.0 and between 0.550 and 0.908, with an average value of 0.736 and 0.767, respectively. Genetic information demonstrated that 10 loci significantly deviated from Hardy-Weinberg equilibrium (P < 0.05). All 45 primers were not significant with regard to linkage disequilibrium (P > 0.001). Pearson correlation indicated that the PIC value exhibited a significant negative correlation with the loci number (r = - 0.741, P = 0.022), whereas the positive correlation with the number of the samples (r = 0.847, P = 0.070) was not significant. This may be attributed to the presence of random particularities within the loci. The T test of the sample groups indicated that the PIC difference was not significant when the number of samples was set at 10 and/or ≥ 15 (P = 0.7472 ~ 0.8564). These polymorphic and valuable microsatellite loci will facilitate further conservation genetics studies for rhesus monkeys and can be further applied to develop novel genetic markers for other species.
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Affiliation(s)
- Yongtao Xu
- Research Center for Wildlife Resources Conservation, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Zongxiu Hu
- Yibin HengShu Animal Models Resourse Industry Technology Academy, Yibin, 644609, People's Republic of China
| | - Wujiao Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Tao Zeng
- Yibin HengShu Animal Models Resourse Industry Technology Academy, Yibin, 644609, People's Republic of China
| | - Xiuyue Zhang
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Jing Li
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China
| | - Weiwei Zhang
- Research Center for Wildlife Resources Conservation, College of Forestry, Jiangxi Agricultural University, Nanchang, 330045, People's Republic of China
| | - Bisong Yue
- Key Laboratory of Bio-resources and Eco-environment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, People's Republic of China.
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Montemurro C, Dambruoso G, Bottalico G, Sabetta W. Self-Incompatibility Assessment of Some Italian Olive Genotypes ( Olea europaea L.) and Cross-Derived Seedling Selection by SSR Markers on Seed Endosperms. FRONTIERS IN PLANT SCIENCE 2019; 10:451. [PMID: 31031787 PMCID: PMC6473062 DOI: 10.3389/fpls.2019.00451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/26/2019] [Indexed: 05/29/2023]
Abstract
The morphology of olive flowers allows either self- or cross-pollination that could partially explain the existence of both reproductive features in this species. However, a high degree of self-incompatibility is reported for many olive genotypes, that could be an important reproductive barrier influencing olive yield. Due to the strong environmental influence, results of compatibility tests are often contradictory, making cultivar classification quite imprecise. In this study, the self-incompatibility value has been determined for four olive genotypes (Bella di Spagna, Coratina, Leccino, and Ogliarola barese) widespread in the Mediterranean basin. Moreover, the incompatibility relationships of cultivar Coratina with some suitable pollinizers (Leccino, Oliastro, and Picholine) have been studied in controlled crosses: the in vitro germination potential of progenies has been evaluated and the selection of cross-derived embryos has been indirectly performed by the molecular characterization of the corresponding endosperm. The results increase knowledge on factors affecting self-compatibility in olive. Moreover, they provide useful information to farmers about the most effective cultivars for the set-up of new olive grove or for graft planning. Finally, they provide a new strategy and procedure based on endosperm analysis by SSRs for an accurate, fast, and relatively cheap screening of embryos/seedlings.
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Affiliation(s)
- Cinzia Montemurro
- Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro,”, Bari, Italy
- SINAGRI S.r.l. – Spin off University of Bari, Bari, Italy
| | - Giovanni Dambruoso
- Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro,”, Bari, Italy
| | - Giovanna Bottalico
- Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro,”, Bari, Italy
- SINAGRI S.r.l. – Spin off University of Bari, Bari, Italy
| | - Wilma Sabetta
- Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro,”, Bari, Italy
- SINAGRI S.r.l. – Spin off University of Bari, Bari, Italy
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Agrimonti C, Marmiroli N. Food Genomics for the Characterization of PDO and PGI Virgin Olive Oils. EUR J LIPID SCI TECH 2018. [DOI: 10.1002/ejlt.201800132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Caterina Agrimonti
- Department of Chemistry, Life Sciences and Environmental Sustainability. University of Parmav.le Parco Area delle Scienze 11/A43124 ParmaItaly
| | - Nelson Marmiroli
- Department of Chemistry, Life Sciences and Environmental Sustainability. University of Parmav.le Parco Area delle Scienze 11/A43124 ParmaItaly
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26
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Girelli CR, Coco LD, Zelasco S, Salimonti A, Conforti FL, Biagianti A, Barbini D, Fanizzi FP. Traceability of "Tuscan PGI" Extra Virgin Olive Oils by ¹H NMR Metabolic Profiles Collection and Analysis. Metabolites 2018; 8:metabo8040060. [PMID: 30274398 PMCID: PMC6316653 DOI: 10.3390/metabo8040060] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 09/26/2018] [Accepted: 09/28/2018] [Indexed: 12/20/2022] Open
Abstract
According to Coldiretti, Italy still continues to hold the European Quality record in extra virgin olive oils with origin designation and protected geographical indication (PDO and PGI). To date, 46 Italian brands are recognized by the European Union: 42 PDO and 4 PGI (Tuscan PGI, Calabria PGI; Tuscia PGI and PGI Sicily). Specific regulations, introduced for these quality marks, include the designation of both the geographical areas and the plant varieties contributing to the composition of the olive oil. However, the PDO and PGI assessment procedures are currently based essentially on farmer declarations. Tuscan PGI extra virgin olive oil is one of the best known Italian trademarks around the world. Tuscan PGI varietal platform is rather wide including 31 specific olive cultivars which should account for at least 95% of the product. On the other hand, while the characteristics of other popular Italian extra virgin olive oils (EVOOs) cultivars from specific geographical areas have been extensively studied (such as those of Coratina based blends from Apulia), little is still known about Tuscan PGI EVOO constituents. In this work, we performed, for the first time, a large-scale analysis of Tuscan PGI monocultivar olive oils by 1H NMR spectroscopy and multivariate statistical analyses (MVA). After genetic characterization of 217 leaf samples from 24 selected geographical areas, distributed all over the Tuscany, a number of 202 micro-milled oil samples including 10 PGI cultivars, was studied. The results of the present work confirmed the need of monocultivar genetically certified EVOO samples for the construction of 1H-NMR-metabolic profiles databases suitable for cultivar and/or geographical origin assessment. Such specific PGI EVOOs databases could be profitably used to justify the high added value of the product and the sustainability of the related supply chain.
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Affiliation(s)
- Chiara Roberta Girelli
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Prov.le Lecce-Monteroni, 73100 Lecce, Italy.
| | - Laura Del Coco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Prov.le Lecce-Monteroni, 73100 Lecce, Italy.
| | - Samanta Zelasco
- Council for Agricultural Research and Economics⁻Research Centre for Olive, Citrus and Tree Fruit C. da Rocchi, 87036 Rende (CS), Italy.
| | - Amelia Salimonti
- Council for Agricultural Research and Economics⁻Research Centre for Olive, Citrus and Tree Fruit C. da Rocchi, 87036 Rende (CS), Italy.
| | | | - Andrea Biagianti
- Certified Origins Italia srl, Località il Madonnino, 58100 Grosseto, Italy.
| | - Daniele Barbini
- Certified Origins Italia srl, Località il Madonnino, 58100 Grosseto, Italy.
| | - Francesco Paolo Fanizzi
- Department of Biological and Environmental Sciences and Technologies, University of Salento, Prov.le Lecce-Monteroni, 73100 Lecce, Italy.
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27
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Olive Tree (Olea europaea L.) Diversity in Traditional Small Farms of Ficalho, Portugal. DIVERSITY 2018. [DOI: 10.3390/d10010005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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28
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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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Molecular characterization of Dalmatian cultivars and the influence of the olive fruit harvest period on chemical profile, sensory characteristics and oil oxidative stability. Eur Food Res Technol 2017. [DOI: 10.1007/s00217-017-2954-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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30
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Kassa A, Konrad H, Geburek T. Landscape genetic structure of Olea europaea subsp. cuspidata in Ethiopian highland forest fragments. CONSERV GENET 2017. [DOI: 10.1007/s10592-017-0993-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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31
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Poortavakoli S, Sheidai M, Alishah O, Noormohammadi Z. Genetic diversity analysis in drought stress tolerant cottons. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0197-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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32
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İpek A, İpek M, Ercişli S, Tangu NA. Transcriptome-based SNP discovery by GBS and the construction of a genetic map for olive. Funct Integr Genomics 2017; 17:493-501. [PMID: 28213629 DOI: 10.1007/s10142-017-0552-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Revised: 02/04/2017] [Accepted: 02/07/2017] [Indexed: 10/20/2022]
Abstract
Molecular markers located in the genic regions of plants are valuable tools for the identification of candidate genes of economically important traits and consequent use in marker-assisted selection (MAS). In the past, simple sequence repeat markers (SSRs) and single-nucleotide polymorphisms (SNPs) located in expressed sequence tags (ESTs) were developed by sequencing RNA derived from different plant tissues, which involves laborious RNA extraction, mRNA isolation, and cDNA synthesis. In order to develop SNP markers located in olive transcriptomes, we used the recently developed genotyping-by-sequencing (GBS) technique. An analysis was done for 125 olive DNA samples (123 DNA samples from a cross-pollinated F1 mapping population, and two samples from parents). From 45 to 66% of Illumina reads from GBS analysis were aligned to the olive transcriptome. A total of 22,033 transcriptome-based SNP markers were identified, and 3384 of these were mapped in the olive genome. The genetic linkage map constructed in this study consists of 1 cleaved amplified polymorphic sequence (CAPS), 19 SSR, and 3384 transcriptome-based SNP markers. The map covers 3340.8 cM of the olive genome in 23 linkage groups, with the length of the linkage groups ranging from 55.6 to 248.7 cM. Average map distance between flanking markers was 0.98 cM. This genetic linkage map is a saturated genetic map and will be a useful tool for the localization of quantitative trait loci (QTLs) and gene(s) of interest and for the identification of candidate genes for economically important traits.
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Affiliation(s)
- Ahmet İpek
- Faculty of Agriculture, Horticulture Department, Uludag University, Bursa, Turkey.
| | - Meryem İpek
- Faculty of Agriculture, Horticulture Department, Uludag University, Bursa, Turkey
| | - Sezai Ercişli
- Faculty of Agriculture, Horticulture Department, Atatürk University, Erzurum, Turkey
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Barazani O, Keren-Keiserman A, Westberg E, Hanin N, Dag A, Ben-Ari G, Fragman-Sapir O, Tugendhaft Y, Kerem Z, Kadereit JW. Genetic variation of naturally growing olive trees in Israel: from abandoned groves to feral and wild? BMC PLANT BIOLOGY 2016; 16:261. [PMID: 27964727 PMCID: PMC5154132 DOI: 10.1186/s12870-016-0947-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 12/05/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND Naturally growing populations of olive trees are found in the Mediterranean garrigue and maquis in Israel. Here, we used the Simple Sequence Repeat (SSR) genetic marker technique to investigate whether these represent wild var. sylvestris. Leaf samples were collected from a total of 205 trees at six sites of naturally growing olive populations in Israel. The genetic analysis included a multi-locus lineage (MLL) analysis, Rousset's genetic distances, Fst values, private alleles, other diversity values and a Structure analysis. The analyses also included scions and suckers of old cultivated olive trees, for which the dominance of one clone in scions (MLL1) and a second in suckers (MLL7) had been shown earlier. RESULTS The majority of trees from a Judean Mts. population and from one population from the Galilee showed close genetic similarity to scions of old cultivated trees. Different from that, site-specific and a high number of single occurrence MLLs were found in four olive populations from the Galilee and Carmel which also were genetically more distant from old cultivated trees, had relatively high genetic diversity values and higher numbers of private alleles. Whereas in two of these populations MLL7 (and partly MLL1) were found in low frequency, the two other populations did not contain these MLLs and were very similar in their genetic structure to suckers of old cultivated olive trees that originated from sexual reproduction. CONCLUSIONS The genetic distinctness from old cultivated olive trees, particularly of one population from Galilee and one from Carmel, suggests that trees at these sites might represent wild var. sylvestris. The similarity in genetic structure of these two populations with the suckers of old cultivated trees implies that wild trees were used as rootstocks. Alternatively, trees at these two sites may be remnants of old cultivated trees in which the scion-derived trunk died and was replaced by suckers. However, considering landscape and topographic environment at the two sites this second interpretation is less likely.
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Affiliation(s)
- Oz Barazani
- Institute of Plant Sciences, the Israel Plant Gene Bank, Agricultural Research Organization, Rishon LeZion, 75359 Israel
| | - Alexandra Keren-Keiserman
- Institute of Plant Sciences, the Israel Plant Gene Bank, Agricultural Research Organization, Rishon LeZion, 75359 Israel
- Herbarium, the National Natural History Collections, the Hebrew University of Jerusalem, Jerusalem, 91904 Israel
| | - Erik Westberg
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Nir Hanin
- Institute of Plant Sciences, the Israel Plant Gene Bank, Agricultural Research Organization, Rishon LeZion, 75359 Israel
| | - Arnon Dag
- Institute of Plant Sciences, Department of Fruit Tree Sciences, Agricultural Research Organization, Gilat Research Center, Gilat, 85280 Israel
| | - Giora Ben-Ari
- Institute of Plant Sciences, Department of Fruit Trees Sciences, Agricultural Research Organization, Rishon LeZion, 75359 Israel
| | - Ori Fragman-Sapir
- Jerusalem Botanical Gardens, the Hebrew University, Giv’at Ram, Jerusalem, 9021904 Israel
| | - Yizhar Tugendhaft
- Institute of Plant Sciences, Department of Fruit Tree Sciences, Agricultural Research Organization, Gilat Research Center, Gilat, 85280 Israel
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Zohar Kerem
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, the Hebrew University of Jerusalem, Rehovot, 76100 Israel
| | - Joachim W. Kadereit
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
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Pasqualone A, Montemurro C, di Rienzo V, Summo C, Paradiso VM, Caponio F. Evolution and perspectives of cultivar identification and traceability from tree to oil and table olives by means of DNA markers. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2016; 96:3642-3657. [PMID: 26991131 DOI: 10.1002/jsfa.7711] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 02/21/2016] [Accepted: 03/08/2016] [Indexed: 06/05/2023]
Abstract
In recent years, an increasing number of typicality marks has been awarded to high-quality olive oils produced from local cultivars. In this case, quality control requires effective varietal checks of the starting materials. Moreover, accurate cultivar identification is essential in vegetative-propagated plants distributed by nurseries and is a pre-requisite to register new cultivars. Food genomics provides many tools for cultivar identification and traceability from tree to oil and table olives. The results of the application of different classes of DNA markers to olive with the purpose of checking cultivar identity and variability of plant material are extensively discussed in this review, with special regard to repeatability issues and polymorphism degree. The characterization of olive germplasm from all countries of the Mediterranean basin and from less studied geographical areas is described and innovative high-throughput molecular tools to manage reference collections are reviewed. Then the transferability of DNA markers to processed products - virgin olive oils and table olives - is overviewed to point out strengths and weaknesses, with special regard to (i) the influence of processing steps and storage time on the quantity and quality of residual DNA, (ii) recent advances to overcome the bottleneck of DNA extraction from processed products, (iii) factors affecting whole comparability of DNA profiles between fresh plant materials and end-products, (iv) drawbacks in the analysis of multi-cultivar versus single-cultivar end-products and (v) the potential of quantitative polymerase chain reaction (PCR)-based techniques. © 2016 Society of Chemical Industry.
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Affiliation(s)
- Antonella Pasqualone
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Valentina di Rienzo
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Carmine Summo
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Vito Michele Paradiso
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
| | - Francesco Caponio
- Department of Soil, Plant, and Food Sciences, University of Bari 'Aldo Moro', Via Amendola 165/A, I-70126, Bari, Italy
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35
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Ben Ayed R, Ben Hassen H, Ennouri K, Ben Marzoug R, Rebai A. OGDD (Olive Genetic Diversity Database): a microsatellite markers' genotypes database of worldwide olive trees for cultivar identification and virgin olive oil traceability. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:bav090. [PMID: 26827236 PMCID: PMC4733328 DOI: 10.1093/database/bav090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2015] [Accepted: 08/24/2015] [Indexed: 01/18/2023]
Abstract
Olive (Olea europaea), whose importance is mainly due to nutritional and health features, is one of the most economically significant oil-producing trees in the Mediterranean region. Unfortunately, the increasing market demand towards virgin olive oil could often result in its adulteration with less expensive oils, which is a serious problem for the public and quality control evaluators of virgin olive oil. Therefore, to avoid frauds, olive cultivar identification and virgin olive oil authentication have become a major issue for the producers and consumers of quality control in the olive chain. Presently, genetic traceability using SSR is the cost effective and powerful marker technique that can be employed to resolve such problems. However, to identify an unknown monovarietal virgin olive oil cultivar, a reference system has become necessary. Thus, an Olive Genetic Diversity Database (OGDD) (http://www.bioinfo-cbs.org/ogdd/) is presented in this work. It is a genetic, morphologic and chemical database of worldwide olive tree and oil having a double function. In fact, besides being a reference system generated for the identification of unkown olive or virgin olive oil cultivars based on their microsatellite allele size(s), it provides users additional morphological and chemical information for each identified cultivar. Currently, OGDD is designed to enable users to easily retrieve and visualize biologically important information (SSR markers, and olive tree and oil characteristics of about 200 cultivars worldwide) using a set of efficient query interfaces and analysis tools. It can be accessed through a web service from any modern programming language using a simple hypertext transfer protocol call. The web site is implemented in java, JavaScript, PHP, HTML and Apache with all major browsers supported. Database URL: http://www.bioinfo-cbs.org/ogdd/
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Affiliation(s)
- Rayda Ben Ayed
- Centre of Biotechnology of Sfax, PB '1177', 3018 Sfax, Tunisia and
| | - Hanen Ben Hassen
- Laboratory of Physics Mathematics and Applications, Faculty of Sciences of Sfax, Sfax, Tunisia
| | - Karim Ennouri
- Centre of Biotechnology of Sfax, PB '1177', 3018 Sfax, Tunisia and
| | | | - Ahmed Rebai
- Centre of Biotechnology of Sfax, PB '1177', 3018 Sfax, Tunisia and
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Ramos-Gómez S, Busto MD, Albillos SM, Ortega N. Novel qPCR systems for olive (Olea europaea L.) authentication in oils and food. Food Chem 2015; 194:447-54. [PMID: 26471578 DOI: 10.1016/j.foodchem.2015.08.036] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2015] [Revised: 07/20/2015] [Accepted: 08/11/2015] [Indexed: 11/24/2022]
Abstract
The traceability of olive oil is an unresolved issue that remains a challenge. In this field, DNA-based techniques are very powerful tools for discrimination that are less negatively influenced by environmental conditions than other techniques. More specifically, quantitative real time PCR (qPCR) achieves a high degree of sensitivity, although the DNA that it can directly isolate from these oils presents drawbacks. Our study reports the analysis of eight systems, in order to determine their suitability for olive detection in oil and oil-derived foodstuffs. The eight systems were analyzed on the basis of their sensitivity and specificity in the qPCR assay, their relative sensitivity to olive DNA detection and DNA mixtures, their sensitivity and specificity to olive in vegetable oils and the detection of olive in commercial products. The results show that the PetN-PsbM system, designed in this study, is a suitable and reliable technique in relation to olive oil and olive ingredients in both food authentication and food safety processes.
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Affiliation(s)
- Sonia Ramos-Gómez
- Department of Biotechnology and Food Science, University of Burgos, Plaza Misael Bañuelos, s/n, 09001 Burgos, Spain
| | - María D Busto
- Department of Biotechnology and Food Science, University of Burgos, Plaza Misael Bañuelos, s/n, 09001 Burgos, Spain
| | - Silvia M Albillos
- Department of Biotechnology and Food Science, University of Burgos, Plaza Misael Bañuelos, s/n, 09001 Burgos, Spain
| | - Natividad Ortega
- Department of Biotechnology and Food Science, University of Burgos, Plaza Misael Bañuelos, s/n, 09001 Burgos, Spain.
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Abstract
The aim of the research was to verify the applicability of microsatellite (SSR) markers in High Resolution Melting (HRM) analysis for the identification of the olive cultivars used in the “Terra di Bari” PDO extra virgin olive oil. A panel of nine cultivars, widespread in Apulia region, was tested with seventeen SSR primer pairs and the PCR products were at first analysed with a Genetic Analyzer automatic sequencer. An identification key was obtained for the nine cultivars, which showed an unambiguous discrimination among the varieties constituting the “Terra di Bari” PDO extra virgin olive oil: Cima di Bitonto, Coratina, and Ogliarola. Subsequently, an SSR based method was set up with the DCA18 marker, coupled with HRM analysis for the distinction of the Terra di Bari olive oil from non-Terra di Bari olive oil using different mixtures. Thus, this analysis enabled the distinction and identification of the PDO mixtures. Hence, this assay provided a flexible, cost-effective, and closed-tube microsatellite genotyping method, well suited to varietal identification and authentication analysis in olive oil.
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Evaluation of genetic diversity in cultivated (O. europaea subsp. europaea L. ssp. europea var. europaea) and wild olives (Olea cuspidata Wall) using genome size and RAPD markers. THE NUCLEUS 2014. [DOI: 10.1007/s13237-014-0125-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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Paternity analysis of the olive variety "Istrska belica" and identification of pollen donors by microsatellite markers. ScientificWorldJournal 2014; 2014:208590. [PMID: 25097869 PMCID: PMC4109215 DOI: 10.1155/2014/208590] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Accepted: 06/20/2014] [Indexed: 11/18/2022] Open
Abstract
The leading olive variety in Slovenia is “Istrska belica” (Olea europaea L.), which currently represents 70% of all olive trees in productive orchards. Paternity analysis based on microsatellite markers was used for genotyping and identification of the potential pollen donors of “Istrska belica” and for assessing the proportion of self-fertilization in monovarietal olive orchards in the Slovene Istria. Seven microsatellite loci were used for genotyping thirty-one olive embryos from “Istrska belica” trees and for all potential pollen donor varieties, which are grown in the region and could participate as pollinators. Genotyping results and allele identification were performed using the FaMoz software. The most probable pollen donor was assigned to 39% of all analyzed embryos. Among all analyzed embryos no single case of self-fertilization was confirmed. According to the present results, the variety “Istrska belica” was in all cases fertilized by foreign pollen. The results will contribute to defining the new guidelines for farmers regarding the proper management and growing practice in monovarietal olive groves.
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Barazani O, Westberg E, Hanin N, Dag A, Kerem Z, Tugendhaft Y, Hmidat M, Hijawi T, Kadereit JW. A comparative analysis of genetic variation in rootstocks and scions of old olive trees - a window into the history of olive cultivation practices and past genetic variation. BMC PLANT BIOLOGY 2014; 14:146. [PMID: 24886387 PMCID: PMC4049413 DOI: 10.1186/1471-2229-14-146] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 05/13/2014] [Indexed: 05/23/2023]
Abstract
BACKGROUND Past clonal propagation of olive trees is intimately linked to grafting. However, evidence on grafting in ancient trees is scarce, and not much is known about the source of plant material used for rootstocks. Here, the Simple Sequence Repeat (SSR) marker technique was used to study genetic diversity of rootstocks and scions in ancient olive trees from the Levant and its implications for past cultivation of olives. Leaf samples were collected from tree canopies (scions) and shoots growing from the trunk base (suckers). A total of 310 trees were sampled in 32 groves and analyzed with 14 SSR markers. RESULTS In 82.7% of the trees in which both scion and suckers could be genotyped, these were genetically different, and thus suckers were interpreted to represent the rootstock of grafted trees. Genetic diversity values were much higher among suckers than among scions, and 194 and 87 multi-locus genotypes (MLGs) were found in the two sample groups, respectively. Only five private alleles were found among scions, but 125 among suckers. A frequency analysis revealed a bimodal distribution of genetic distance among MLGs, indicating the presence of somatic mutations within clones. When assuming that MLGs differing by one mutation are identical, scion and sucker MLGs were grouped in 20 and 147 multi-locus lineages (MLLs). The majority of scions (90.0%) belonged to a single common MLL, whereas 50.5% of the suckers were single-sample MLLs. However, one MLL was specific to suckers and found in 63 (22.6%) of the samples. CONCLUSIONS Our results provide strong evidence that the majority of olive trees in the study are grafted, that the large majority of scions belong to a single ancient cultivar containing somatic mutations, and that the widespread occurrence of one sucker genotype may imply rootstock selection. For the majority of grafted trees it seems likely that saplings were used as rootstocks; their genetic diversity probably is best explained as the result of a long history of sexual reproduction involving cultivated, feral and wild genotypes.
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Affiliation(s)
- Oz Barazani
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Erik Westberg
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
| | - Nir Hanin
- Institute of Plant Sciences, Israel Plant Gene Bank, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Arnon Dag
- Institute of Plant Sciences, Department of Fruit Tree Sciences, Agricultural Research Organization, Gilat Research Center, Gilat, Israel
| | - Zohar Kerem
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Yizhar Tugendhaft
- Institute of Plant Sciences, Department of Fruit Tree Sciences, Agricultural Research Organization, Gilat Research Center, Gilat, Israel
- Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Mohammed Hmidat
- Association for Integrated Rural Development (AIRD), Ramallah, Jerusalem Street, Al Nabali Building, P.O.Box 6, Ramallah, The Palestinian Authority
| | - Thameen Hijawi
- Association for Integrated Rural Development (AIRD), Ramallah, Jerusalem Street, Al Nabali Building, P.O.Box 6, Ramallah, The Palestinian Authority
| | - Joachim W Kadereit
- Institut für Spezielle Botanik und Botanischer Garten, Johannes Gutenberg-Universität Mainz, D-55099 Mainz, Germany
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Genetic biodiversity of Italian olives (Olea europaea) germplasm analyzed by SSR markers. ScientificWorldJournal 2014; 2014:296590. [PMID: 24723801 PMCID: PMC3958686 DOI: 10.1155/2014/296590] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/22/2014] [Indexed: 11/18/2022] Open
Abstract
The olive is an important fruit species cultivated for oil and table olives in Italy and the Mediterranean basin. The conservation of cultivated plants in ex situ collections is essential for the optimal management and use of their genetic resources. The largest ex situ olive germplasm collection consists of approximately 500 Italian olive varieties and corresponding to 85% of the total Italian olive germplasm is maintained at the Consiglio per la Ricerca e sperimentazione per l'Agricoltura, Centro di Ricerca per l'Olivicoltura e l'Industria Olearia (CRA-OLI), in Italy. In this work, eleven preselected nuclear microsatellite markers were used to assess genetic diversity, population structure, and gene flows with the aim of assembling a core collection. The dendrogram obtained utilizing the unweighted pair group method highlights the presence of homonymy and synonymy in olive tree datasets analyzed in this study. 439 different unique genotype profiles were obtained with this combination of 11 loci nSSR, representing 89.8% of the varieties analyzed. The remaining 10.2% comprises different variety pairs in which both accessions are genetically indistinguishable. Clustering analysis performed using BAPS software detected seven groups in Italian olive germplasm and gene flows were determined among identified clusters. We proposed an Italian core collection of 23 olive varieties capturing all detected alleles at microsatellites. The information collected in this study regarding the CRA-OLI ex situ collection can be used for breeding programs, for germplasm conservation, and for optimizing a strategy for the management of olive gene pools.
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Atienza SG, de la Rosa R, Domínguez-García MC, Martín A, Kilian A, Belaj A. Use of DArT markers as a means of better management of the diversity of olive cultivars. Food Res Int 2013. [DOI: 10.1016/j.foodres.2013.08.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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Besnard G, Dupuy J, Larter M, Cuneo P, Cooke D, Chikhi L. History of the invasive African olive tree in Australia and Hawaii: evidence for sequential bottlenecks and hybridization with the Mediterranean olive. Evol Appl 2013; 7:195-211. [PMID: 24567742 PMCID: PMC3927883 DOI: 10.1111/eva.12110] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2013] [Accepted: 09/04/2013] [Indexed: 11/30/2022] Open
Abstract
Humans have introduced plants and animals into new continents and islands with negative effects on local species. This has been the case of the olive that was introduced in Australia, New Zealand and Pacific islands where it became invasive. Two subspecies were introduced in Australia, and each successfully invaded a specific area: the African olive in New South Wales (NSW) and the Mediterranean olive in South Australia. Here, we examine their origins and spread and analyse a large sample of native and invasive accessions with chloroplast and nuclear microsatellites. African olive populations from the invaded range exhibit two South African chlorotypes hence supporting an introduction from South Africa, while populations from South Australia exhibit chlorotypes of Mediterranean cultivars. Congruently, nuclear markers support the occurrence of two lineages in Australia but demonstrate that admixture took place, attesting that they hybridized early after introduction. Furthermore, using an approximate Bayesian computation framework, we found strong support for the serial introduction of the African olive from South Africa to NSW and then from NSW to Hawaii. The taxon experienced successive bottlenecks that did not preclude invasion, meaning that rapid decisions need to be taken to avoid naturalization where it has not established a large population yet.
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Affiliation(s)
- Guillaume Besnard
- Laboratoire Evolution & Diversité Biologique, CNRS, UPS, ENFA, UMR 5174 Toulouse, France
| | - Jérémy Dupuy
- Laboratoire Evolution & Diversité Biologique, CNRS, UPS, ENFA, UMR 5174 Toulouse, France
| | | | - Peter Cuneo
- The Australian Botanic Garden, Mount Annan, Royal Botanic Gardens and Domain Trust Mount Annan, NSW, Australia
| | - David Cooke
- Department of Primary Industries and Resources PIRSA, Biosecurity SA Adelaide, SA, Australia
| | - Lounes Chikhi
- Laboratoire Evolution & Diversité Biologique, CNRS, UPS, ENFA, UMR 5174 Toulouse, France ; Instituto Gulbenkian de Ciência Oreiras, Portugal
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Besnard G, El Bakkali A, Haouane H, Baali-Cherif D, Moukhli A, Khadari B. Population genetics of Mediterranean and Saharan olives: geographic patterns of differentiation and evidence for early generations of admixture. ANNALS OF BOTANY 2013; 112:1293-302. [PMID: 24013386 PMCID: PMC3806528 DOI: 10.1093/aob/mct196] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS The olive (Olea europaea subsp. europaea) was domesticated in the Mediterranean area but its wild relatives are distributed over three continents, from the Mediterranean basin to South Africa and south-western Asia. Recent studies suggested that this crop originated in the Levant while a secondary diversification occurred in most westward areas. A possible contribution of the Saharan subspecies (subsp. laperrinei) has been highlighted, but the data available were too limited to draw definite conclusions. Here, patterns of genetic differentiation in the Mediterranean and Saharan olives are analysed to test for recent admixture between these taxa. METHODS Nuclear microsatellite and plastid DNA (ptDNA) data were compiled from previous studies and completed for a sample of 470 cultivars, 390 wild Mediterranean trees and 270 Saharan olives. A network was reconstructed for the ptDNA haplotypes, while a Bayesian clustering method was applied to identify the main gene pools in the data set and then simulate and test for early generations of admixture between Mediterranean and Saharan olives. KEY RESULTS Four lineages of ptDNA haplotypes are recognized: three from the Mediterranean basin and one from the Sahara. Only one haplotype, primarily distributed in the Sahara, is shared between laperrinei and europaea. This haplotype is detected once in 'Dhokar', a cultivar from the Maghreb. Nuclear microsatellites show geographic patterns of genetic differentiation in the Mediterranean olive that reflect the primary origins of cultivars in the Levant, and indicate a high genetic differentiation between europaea and laperrinei. No first-generation hybrid between europaea and laperrinei is detected, but recent, reciprocal admixture between Mediterranean and Saharan subspecies is found in a few accessions, including 'Dhokar'. CONCLUSIONS This study reports for the first time admixture between Mediterranean and Saharan olives. Although its contribution remains limited, Laperrine's olive has been involved in the diversification of cultivated olives.
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Affiliation(s)
- G. Besnard
- CNRS-UPS-ENFA, EDB, UMR 5174, Bât. 4R1, 31062 Toulouse cedex 9, France
- For correspondance. E-mail
| | - A. El Bakkali
- INRA/CBNMed, UMR 1334, AGAP, 34060 Montpellier, France
- INRA, UR APCRPG, BP 578, Meknès, Morocco
| | - H. Haouane
- INRA/CBNMed, UMR 1334, AGAP, 34060 Montpellier, France
| | - D. Baali-Cherif
- BP44, Laboratoire de Recherche sur les Zones Arides, USTHB/INA, Alger, Algeria
| | - A. Moukhli
- INRA Marrakech, UR Amélioration des Plantes, Marrakech, Morocco
| | - B. Khadari
- INRA/CBNMed, UMR 1334, AGAP, 34060 Montpellier, France
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Kaya HB, Cetin O, Kaya H, Sahin M, Sefer F, Kahraman A, Tanyolac B. SNP discovery by illumina-based transcriptome sequencing of the olive and the genetic characterization of Turkish olive genotypes revealed by AFLP, SSR and SNP markers. PLoS One 2013; 8:e73674. [PMID: 24058483 PMCID: PMC3772808 DOI: 10.1371/journal.pone.0073674] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/19/2013] [Indexed: 11/18/2022] Open
Abstract
Background The olive tree (Olea europaea L.) is a diploid (2n = 2x = 46) outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP) discovery in olive. The objectives of this study were (1) to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2) to characterize 96 olive genotypes originating from different regions of Turkey. Methodology/Principal Findings Next-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR) markers. Conclusions/Significance This study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL) analysis, association mapping and map-based gene cloning in the olive. High levels of genetic variation among Turkish olive genotypes revealed by SNPs, AFLPs and SSRs allowed us to characterize the Turkish olive genotype.
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Affiliation(s)
| | | | | | | | | | | | - Bahattin Tanyolac
- Department of Bioengineering, Ege University, Izmir, Turkey
- * E-mail:
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Pasqualone A, Di Rienzo V, Nasti R, Blanco A, Gomes T, Montemurro C. Traceability of Italian Protected Designation of Origin (PDO) table olives by means of microsatellite molecular markers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2013; 61:3068-3073. [PMID: 23461435 DOI: 10.1021/jf400014g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The aim of this work was to develop a DNA microsatellite-based method of analysis to allow traceability of the three Italian Protected Designation of Origin (PDO) table olives in comparison with fruits of another seven highly diffused table olive cultivars. The analyses were carried out by using 16 primer pairs, with a mean of five different alleles detected per primer set, and power of discrimination from 0.56 to 0.90. Allelic error rates in the range of 0-3.8% were observed. By combining data from the most reliable and highly informative microsatellites (DCA3, DCA16, DCA17, DCA18, UDO-043, and GAPU101), it was possible to identify the PDO fruits over the panel of 10 cultivars, with the probability of a chance match between different cultivars as low as 10(-9) and with 0.5% error rate. The amplification profile is independent of environmental and processing conditions and is helpful to verify the authenticity of PDO samples.
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Affiliation(s)
- Antonella Pasqualone
- Food Science and Technology Unit, University of Bari, Via Amendola 165/A, I 70126 Bari, Italy.
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Pasqualone A, Di Rienzo V, Blanco A, Summo C, Caponio F, Montemurro C. Characterization of virgin olive oil from Leucocarpa cultivar by chemical and DNA analysis. Food Res Int 2012. [DOI: 10.1016/j.foodres.2011.05.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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49
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Olive oil traceability by means of chemical and sensory analyses: A comparison with SSR biomolecular profiles. Food Chem 2011. [DOI: 10.1016/j.foodchem.2011.05.122] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Díez CM, Trujillo I, Barrio E, Belaj A, Barranco D, Rallo L. Centennial olive trees as a reservoir of genetic diversity. ANNALS OF BOTANY 2011; 108:797-807. [PMID: 21852276 PMCID: PMC3177672 DOI: 10.1093/aob/mcr194] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
BACKGROUND AND AIMS Genetic characterization and phylogenetic analysis of the oldest trees could be a powerful tool both for germplasm collection and for understanding the earliest origins of clonally propagated fruit crops. The olive tree (Olea europaea L.) is a suitable model to study the origin of cultivars due to its long lifespan, resulting in the existence of both centennial and millennial trees across the Mediterranean Basin. METHODS The genetic identity and diversity as well as the phylogenetic relationships among the oldest wild and cultivated olives of southern Spain were evaluated by analysing simple sequence repeat markers. Samples from both the canopy and the roots of each tree were analysed to distinguish which trees were self-rooted and which were grafted. The ancient olives were also put into chronological order to infer the antiquity of traditional olive cultivars. KEY RESULTS Only 9·6 % out of 104 a priori cultivated ancient genotypes matched current olive cultivars. The percentage of unidentified genotypes was higher among the oldest olives, which could be because they belong to ancient unknown cultivars or because of possible intra-cultivar variability. Comparing the observed patterns of genetic variation made it possible to distinguish which trees were grafted onto putative wild olives. CONCLUSIONS This study of ancient olives has been fruitful both for germplasm collection and for enlarging our knowledge about olive domestication. The findings suggest that grafting pre-existing wild olives with olive cultivars was linked to the beginnings of olive growing. Additionally, the low number of genotypes identified in current cultivars points out that the ancient olives from southern Spain constitute a priceless reservoir of genetic diversity.
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Affiliation(s)
- Concepción M Díez
- Departamento de Agronomía, Campus Universitario de Rabanales, Ctra. Madrid-Cádiz Km. 396, Córdoba, Spain.
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