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Oleaceae Genetics
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Oleaceae Genetics

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (15 October 2020) | Viewed by 27619

Special Issue Editor

Dr. Cinzia Montemurro

E-Mail Website
Guest Editor
Department of Soil, Plants and Food Sciences, Faculty of Agricultural Science, University of Bari “Aldo Moro”, 70126 Bari, Italy
Interests: genotyping by sequencing; olive germplasm; grapevine; genetic diversity; functional genomics; molecular polymorphism
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The Oleaceae are a family of angiosperms containing 25 genera and 620 species, including the olive tree, taking its botanical name from the Latin word “Olea”. The family includes ornamental and crop plants. All of them are diploids with a chromosome number ranging from 22 to 48. Different members of the family are economically important: the olive (Olea europaea) is important both for fruits and for the extracted olive oil. The ashes (Fraxinus) are valued for their tough wood. Forsythias, lilacs, jasmines, osmanthuses, privets, and fringe trees are valued as ornamental plants in gardens and landscaping.

Despite its importance, there is a lack of molecular phylogenetic studies on the family, limited to only a few species for noncoding chloroplast loci. Recently, many studies have tried to focalize the attention on important traits and related coding genes for the members of the family that are more relevant. However, a deeper knowledge of genetics of the Oleaceae family, not limited to few major species, could increase the available information about genetic diversity, molecular markers, phylogenetic studies, gene functions, molecular pathway characterization, and molecular mechanisms involved in plant adaptation to biotic and abiotic stress.

The forthcoming Special Issue aims to provide a comprehensive understanding of Oleaceae genetics, both for the most important like olive and Fraxinus, as well as ornamental ones like jasmines, lilacs, and others.

Prof. Dr. Cinzia Montemurro
Guest Editor

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Oleaceae
  • genetic diversity
  • gene function
  • molecular analysis for plant adaptation
  • molecular phylogenies

Published Papers (8 papers)

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Research

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18 pages, 2240 KiB  
Article
Genetic Structure and Core Collection of Olive Germplasm from Albania Revealed by Microsatellite Markers
by Aida Dervishi, Jernej Jakše, Hairi Ismaili, Branka Javornik and Nataša Štajner
Genes 2021, 12(2), 256; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12020256 - 10 Feb 2021
Cited by 15 | Viewed by 3011
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Oleaceae Genetics)
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18 pages, 471 KiB  
Article
Resolving the Phylogeny of the Olive Family (Oleaceae): Confronting Information from Organellar and Nuclear Genomes
by Julia Dupin, Pauline Raimondeau, Cynthia Hong-Wa, Sophie Manzi, Myriam Gaudeul and Guillaume Besnard
Genes 2020, 11(12), 1508; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11121508 - 16 Dec 2020
Cited by 19 | Viewed by 4546
Abstract
The olive family, Oleaceae, is a group of woody plants comprising 28 genera and ca. 700 species, distributed on all continents (except Antarctica) in both temperate and tropical environments. It includes several genera of major economic and ecological importance such as olives, ash [...] Read more.
The olive family, Oleaceae, is a group of woody plants comprising 28 genera and ca. 700 species, distributed on all continents (except Antarctica) in both temperate and tropical environments. It includes several genera of major economic and ecological importance such as olives, ash trees, jasmines, forsythias, osmanthuses, privets and lilacs. The natural history of the group is not completely understood yet, but its diversification seems to be associated with polyploidisation events and the evolution of various reproductive and dispersal strategies. In addition, some taxonomical issues still need to be resolved, particularly in the paleopolyploid tribe Oleeae. Reconstructing a robust phylogenetic hypothesis is thus an important step toward a better comprehension of Oleaceae’s diversity. Here, we reconstructed phylogenies of the olive family using 80 plastid coding sequences, 37 mitochondrial genes, the complete nuclear ribosomal cluster and a small multigene family encoding phytochromes (phyB and phyE) of 61 representative species. Tribes and subtribes were strongly supported by all phylogenetic reconstructions, while a few Oleeae genera are still polyphyletic (Chionanthus, Olea, Osmanthus, Nestegis) or paraphyletic (Schrebera, Syringa). Some phylogenetic relationships among tribes remain poorly resolved with conflicts between topologies reconstructed from different genomic regions. The use of nuclear data remains an important challenge especially in a group with ploidy changes (both paleo- and neo-polyploids). This work provides new genomic datasets that will assist the study of the biogeography and taxonomy of the whole Oleaceae. Full article
(This article belongs to the Special Issue Oleaceae Genetics)
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28 pages, 9036 KiB  
Article
Genetic Resources of Olea europaea L. in the Garda Trentino Olive Groves Revealed by Ancient Trees Genotyping and Parentage Analysis of Drupe Embryos
by Paula Moreno-Sanz, Luca Lombardo, Silvia Lorenzi, Franco Michelotti and Maria Stella Grando
Genes 2020, 11(10), 1171; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11101171 - 06 Oct 2020
Cited by 7 | Viewed by 3187
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 [...] Read more.
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. Full article
(This article belongs to the Special Issue Oleaceae Genetics)
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19 pages, 1309 KiB  
Article
EST–SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives
by Roberto Mariotti, Angjelina Belaj, Raul De La Rosa, Lorenzo Leòn, Federico Brizioli, Luciana Baldoni and Soraya Mousavi
Genes 2020, 11(8), 916; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11080916 - 10 Aug 2020
Cited by 15 | Viewed by 2577
Abstract
Background: The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are [...] Read more.
Background: The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are not yet identified, beyond a few plastidial markers. Methods: In the present work, more than 1000 transcript-specific SNP markers obtained by the genotyping of 260 individuals were studied. These genotypes included cultivated, oleasters, and samples of subspecies guanchica, and were analyzed in silico, in order to identify polymorphisms on key genes distinguishing different Olea europaea forms. Results: Phylogeny inference and principal coordinate analysis allowed to detect two distinct clusters, clearly separating wilds and guanchica samples from cultivated olives, meanwhile the structure analysis made possible to differentiate these three groups. Sequences carrying the polymorphisms that distinguished wild and cultivated olives were analyzed and annotated, allowing to identify 124 candidate genes that have a functional role in flower development, stress response, or involvement in important metabolic pathways. Signatures of selection that occurred during olive domestication, were detected and reported. Conclusion: This deep EST–SNP analysis provided important information on the genetic and genomic diversity of the olive complex, opening new opportunities to detect gene polymorphisms with potential functional and evolutionary roles, and to apply them in genomics-assisted breeding, highlighting the importance of olive germplasm conservation. Full article
(This article belongs to the Special Issue Oleaceae Genetics)
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12 pages, 3023 KiB  
Article
Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L.
by Erli Niu, Chengying Jiang, Wei Wang, Yu Zhang and Shenlong Zhu
Genes 2020, 11(8), 879; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11080879 - 03 Aug 2020
Cited by 13 | Viewed by 3202
Abstract
Olive (Olea europaea L.) is a very important woody tree and favored by consumers because of the fruit’s high-quality olive oil. Chloroplast genome analysis will provide insights into the chloroplast variation and genetic evolution of olives. The complete chloroplast genomes of three [...] Read more.
Olive (Olea europaea L.) is a very important woody tree and favored by consumers because of the fruit’s high-quality olive oil. Chloroplast genome analysis will provide insights into the chloroplast variation and genetic evolution of olives. The complete chloroplast genomes of three accessions (O. europaea subsp. cuspidata isolate Yunnan, O. europaea subsp. europaea var. sylvestris, and O. europaea subsp. europaea var. frantoio) were obtained by next-generation sequencing technology. A total of 133 coding regions were identified in the three chloroplast genomes without rearrangement. O. europaea subsp. europaea var. sylvestris and O. europaea subsp. europaea var. frantoio had the same sequences (155,886 bp), while O. europaea subsp. cuspidata isolate Yunnan (155,531 bp) presented a large gap between rps16 and trnQ-UUG genes with six small gaps and fewer microsatellites. The whole chloroplast genomes of 11 O. europaea were divided into two main groups by a phylogenetic tree and O. europaea subsp. cuspidata formed a separate group (Cuspidata group) with the other subspecies (Mediterranean/North African group). Identification of consistency and diversity among O. europaea subspecies will benefit the exploration of domestication events and facilitate molecular-assisted breeding for O. europaea. Full article
(This article belongs to the Special Issue Oleaceae Genetics)
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20 pages, 12769 KiB  
Article
Gene Expression Pattern in Olive Tree Organs (Olea europaea L.)
by Jorge A. Ramírez-Tejero, Jaime Jiménez-Ruiz, María de la O Leyva-Pérez, Juan Bautista Barroso and Francisco Luque
Genes 2020, 11(5), 544; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11050544 - 12 May 2020
Cited by 16 | Viewed by 3962
Abstract
The olive tree (Olea europaea L.) was one of the first plant species in history to be domesticated. Throughout olive domestication, gene expression has undergone drastic changes that may affect tissue/organ-specific genes. This is an RNA-seq study of the transcriptomic activity of [...] Read more.
The olive tree (Olea europaea L.) was one of the first plant species in history to be domesticated. Throughout olive domestication, gene expression has undergone drastic changes that may affect tissue/organ-specific genes. This is an RNA-seq study of the transcriptomic activity of different tissues/organs from adult olive tree cv. “Picual” under field conditions. This analysis unveiled 53,456 genes with expression in at least one tissue, 32,030 of which were expressed in all organs and 19,575 were found to be potential housekeeping genes. In addition, the specific expression pattern in each plant part was studied. The flower was clearly the organ with the most exclusively expressed genes, 3529, many of which were involved in reproduction. Many of these organ-specific genes are generally involved in regulatory activities and have a nuclear protein localization, except for leaves, where there are also many genes with a plastid localization. This was also observed in stems to a lesser extent. Moreover, pathogen defense and immunity pathways were highly represented in roots. These data show a complex pattern of gene expression in different organs, and provide relevant data about housekeeping and organ-specific genes in cultivated olive. Full article
(This article belongs to the Special Issue Oleaceae Genetics)
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Review

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20 pages, 593 KiB  
Review
How to Choose a Good Marker to Analyze the Olive Germplasm (Olea europaea L.) and Derived Products
by Sara Sion, Michele Antonio Savoia, Susanna Gadaleta, Luciana Piarulli, Isa Mascio, Valentina Fanelli, Cinzia Montemurro and Monica Marilena Miazzi
Genes 2021, 12(10), 1474; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12101474 - 23 Sep 2021
Cited by 11 | Viewed by 2882
Abstract
The olive tree (Olea europaea L.) is one of the most cultivated crops in the Mediterranean basin. Its economic importance is mainly due to the intense production of table olives and oil. Cultivated varieties are characterized by high morphological and genetic variability [...] Read more.
The olive tree (Olea europaea L.) is one of the most cultivated crops in the Mediterranean basin. Its economic importance is mainly due to the intense production of table olives and oil. Cultivated varieties are characterized by high morphological and genetic variability and present a large number of synonyms and homonyms. This necessitates the introduction of a rapid and accurate system for varietal identification. In the past, the recognition of olive cultivars was based solely on analysis of the morphological traits, however, these are highly influenced by environmental conditions. Therefore, over the years, several methods based on DNA analysis were developed, allowing a more accurate and reliable varietal identification. This review aims to investigate the evolving history of olive tree characterization approaches, starting from the earlier morphological methods to the latest technologies based on molecular markers, focusing on the main applications of each approach. Furthermore, we discuss the impact of the advent of next generation sequencing and the recent sequencing of the olive genome on the strategies used for the development of new molecular markers. Full article
(This article belongs to the Special Issue Oleaceae Genetics)
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16 pages, 1838 KiB  
Review
Olive (Olea europaea L.) Genetic Transformation: Current Status and Future Prospects
by Elena Palomo-Ríos, Isabel Narváez, Fernando Pliego-Alfaro and José A. Mercado
Genes 2021, 12(3), 386; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12030386 - 09 Mar 2021
Cited by 6 | Viewed by 3439
Abstract
Olive (Olea europaea L.) is the most characteristic and important oil crop of the Mediterranean region. Traditional olive cultivation is based on few tens cultivars of ancient origin. To improve this crop, novel selections with higher tolerance to biotic and abiotic stress, [...] Read more.
Olive (Olea europaea L.) is the most characteristic and important oil crop of the Mediterranean region. Traditional olive cultivation is based on few tens cultivars of ancient origin. To improve this crop, novel selections with higher tolerance to biotic and abiotic stress, adaptable to high-density planting systems and resilient to climate change are needed; however, breeding programs are hindered by the long juvenile period of this species and few improved genotypes have been released so far. Genetic transformation could be of great value, in the near future, to develop new varieties or rootstocks in a shorter time; in addition, it has currently become an essential tool for functional genomic studies. The recalcitrance of olive tissues to their in vitro manipulation has been the main bottleneck in the development of genetic transformation procedures in this species; however, some important traits such as fungal resistance, flowering or lipid composition have successfully been manipulated through the genetic transformation of somatic embryos of juvenile or adult origin, providing a proof of the potential role that this technology could have in olive improvement. However, the optimization of these protocols for explants of adult origin is a prerequisite to obtain useful materials for the olive industry. In this review, initially, factors affecting plant regeneration via somatic embryogenesis are discussed. Subsequently, the different transformation approaches explored in olive are reviewed. Finally, transgenic experiments with genes of interest undertaken to manipulate selected traits are discussed. Full article
(This article belongs to the Special Issue Oleaceae Genetics)
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