Olive Domestication Research Articles

Evaluation of genetic diversity among olive trees (Olea europaea L.) from Jordan.

This study aimed to identify and evaluate the genetic diversity of olive trees in Jordan, a country located in the eastern Mediterranean, where olive domestication originated. For this purpose, a total of 386 olive trees were analyzed, including 338 collected from two surveys (JOCC-1 and JOCC-2) across seven regions, and 48 selected accessions from the Olive Germplasm Bank of Jordan (JGBOC). These trees underwent comprehensive phenotypic and molecular characterization using different tools. Significant differences in morphological traits were detected among tested regions using the Chi-square test. Principal components analysis revealed that fruit color change and growth habit as the most discriminating traits, segregating the trees into two groups, with the first group including the Kanabisi cultivar and the second group including the Kfari Baladi cultivar. Utilizing Kompetitive Allele Specific PCR assay, two sets of informative SNPs were used for the genetic diversity analysis. Cladograms were constructed using the maximum likelihood method, revealing a consistent pattern where two clades containing identical genotypes were observed to cluster with the Kfari Baladi or Kanabisi. In addition, the SNP data was used to perform a comparative analysis with the Worldwide Olive Germplasm Bank of Córdoba, which revealed 73 unreported olive genotypes from Jordan. Genetic structure analyses using Discriminant Analysis of Principal Components (DAPC) identified four clusters with distinctive patterns of relatedness among 149 unique accessions, including 52 olive accessions from various Mediterranean countries (IOCC-3). ADMIXTURE analysis revealed four genetic clusters, consistent with the clustering observed in DAPC and cladogram analysis, indicating a high level of genetic admixture among Jordanian olive germplasm. In conclusion, the results show that olive trees in Jordan are highly diverse, providing valuable information for future conservation and management plans.

EST-SNP Study of Olea europaea L. Uncovers Functional Polymorphisms between Cultivated and Wild Olives.

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.

Gene Expression Pattern in Olive Tree Organs (Olea europaea L.).

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.

Transposon activation is a major driver in the genome evolution of cultivated olive trees (Olea europaea L.).

The primary domestication of olive (Olea europaea L.) in the Levant dates back to the Neolithic period, around 6,000-5,500 BC, as some archeological remains attest. Cultivated olive trees are reproduced clonally, with sexual crosses being the sporadic events that drive the development of new varieties. In order to determine the genomic changes which have occurred in a modern olive cultivar, the genome of the Picual cultivar, one of the most popular olive varieties, was sequenced. Additional 40 cultivated and 10 wild accessions were re-sequenced to elucidate the evolution of the olive genome during the domestication process. It was found that the genome of the 'Picual' cultivar contains 79,667 gene models, of which 78,079 were protein-coding genes and 1,588 were tRNA. Population analyses support two independent events in olive domestication, including an early possible genetic bottleneck. Despite genetic bottlenecks, cultivated accessions showed a high genetic diversity driven by the activation of transposable elements (TE). A high TE gene expression was observed in presently cultivated olives, which suggests a current activity of TEs in domesticated olives. Several TEs families were expanded in the last 5,000 or 6,000 years and produced insertions near genes that may have been involved in selected traits during domestication as reproduction, photosynthesis, seed development, and oil production. Therefore, a great genetic variability has been found in cultivated olive as a result of a significant activation of TEs during the domestication process.

Paternity tests support a diallelic self-incompatibility system in a wild olive (Olea europaea subsp. laperrinei, Oleaceae).

Self‐incompatibility (SI) is the main mechanism that favors outcrossing in plants. By limiting compatible matings, SI interferes in fruit production and breeding of new cultivars. In the Oleeae tribe (Oleaceae), an unusual diallelic SI system (DSI) has been proposed for three distantly related species including the olive (Olea europaea), but empirical evidence has remained controversial for this latter. The olive domestication is a complex process with multiple origins. As a consequence, the mixing of S‐alleles from two distinct taxa, the possible artificial selection of self‐compatible mutants and the large phenological variation of blooming may constitute obstacles for deciphering SI in olive. Here, we investigate cross‐genotype compatibilities in the Saharan wild olive (O. e. subsp. laperrinei). As this taxon was geographically isolated for thousands of years, SI should not be affected by human selection. A population of 37 mature individuals maintained in a collection was investigated. Several embryos per mother were genotyped with microsatellites in order to identify compatible fathers that contributed to fertilization. While the pollination was limited by distance inside the collection, our results strongly support the DSI hypothesis, and all individuals were assigned to two incompatibility groups (G1 and G2). No self‐fertilization was observed in our conditions. In contrast, crosses between full or half siblings were frequent (ca. 45%), which is likely due to a nonrandom assortment of related trees in the collection. Finally, implications of our results for orchard management and the conservation of olive genetic resources are discussed.

Phylogenetic and evolutionary applications of analyzing endocarp morphological characters by classification binary tree and leaves by SSR markers for the characterization of olive germplasm

Seed (endocarp) morphology is useful for genotype discrimination and cultivar classification. Over a 20-year period, 504 olive trees (Olea europaea subsp. europaea) previously assigned to different cultivars originating from Greece (n = 37), Spain (n = 2), and Italy (n = 2) as well as one accession of Olea europaea subsp. cuspidata were evaluated employing 11 endocarp morphological markers and 9 SSR markers. A matrix of 42 morphotypes in total was subjected to classification binary tree (CBT) analysis. In addition, cultivars were fingerprinted employing 9 microsatellite (SSR) markers and placed on a similarity dendrogram. All 41 olive cultivars and one accession of Olea europaea subsp. cuspidata employed in the present study yielded different morphological profiles produced by the 11 endocarp traits. In the resulting CBT, the total reduction in error, that is, the total information in the set of all 42 morphotypes, was 100%. This meant that the set of 11 morphological characters—having 28 different states in all—was sufficient to remove all data noise and to correctly classify all examined olive cultivars. In addition, all olive cultivars were successfully discriminated by the 9 SSR markers employed. It is suggested that cultivars with large seeds—and concomitantly large fruits—are more distant from the wild forms and probably more evolved compared to cultivars with small seeds. In corroboration to the above, based on seed shape, some of the olive cultivars showed high resemblance to wild olives leading thus to the hypothesis that they were produced or selected during the early ages of olive domestication.

Primary Selection and Secondary Diversification: Two Key Processes in the History of Olive Domestication

Knowledge on the crop domestication process is important from a cultural and agricultural standpoint since it can shed light on the origin and history of human civilizations as well as the management of genetic resources, while offering guidance for modern breeding. The olive tree (Olea europaeassp.europaea) is the most iconic of the old crop species of the Mediterranean Basin (MB). Primary domestication from wild olive probably occurred around 6000 BP in the Middle East. However, the question remains as to whether cultivated olive derived from a single domestication event in the Levant, followed by secondary diversification, or whether it was the result of independent domestication events. Here, we analyzed a comprehensive sample collected from 35 wild populations (722 individuals) and 410 cultivars from across the MB using nuclear and plastid DNA markers. Our genetic investigations argue in favor of a single primary domestication event in the eastern MB, followed by diffusion of the first domesticated olive and diversification in the central and western MB as key processes in the olive tree history.

New insights on olive domestication in Turkey

New insights on olive domestication in Turkey

Quality of olives: A focus on agricultural preharvest factors

Abstract More than 11 million ha of olives (Olea europaea L.) are currently grown worldwide, 98% of which are localized in the Mediterranean Basin, with olives being one of the most important fruit trees in the area. The olive fruit is a very particular drupe since it not may be directly consumed but must instead be processed. Table olives and virgin olive oil are the two main processed products derived from olive fruits. Both are considered staple foods of the Mediterranean Diet and have been produced in the area for centuries, presumably since olive domestication occurred approximately 6.000 years ago. Despite their long history and economic importance, the focus on quality is quite recent. The presence of various and copious amounts of bioactive compounds, some of which are exclusive to olives, is drawing attention to the nutraceutical value of these products. This review aims to integrate the available information regarding the quality of table olives and olive oil with a focus on how preharvest factors may affect quality. The first part of the review describes the main quality attributes considered for each product from different perspectives, including the legal, organoleptic and nutritional points of view, among others. The physiological mechanisms involved in fruit development and ripening, which significantly affect the quality of the fruits, i.e., the raw material for obtaining both products, are also discussed. The review also addresses the potential of both the considerable number of traditional olive cultivars and recent olive breeding programs to obtain products with distinct quality attributes (in terms of sensorial profile and bioactive compounds). Finally, the most recent literature concerning the effect of environmental (soil and climate) and agronomical factors (irrigation, fertilization, canopy management and harvesting) is extensively reviewed.

On the origins and domestication of the olive: a review and perspectives.

Background Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. Scope The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. Conclusion The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.

Ongoing domestication and diversification in grafted olive–oleaster agroecosystems in Northern Morocco

This paper analyzes sociohistorical and biological factors that shape olive–oleaster agroecosystems (hereafter OOAs), in northern Morocco and their continuing roles in olive domestication, diversification and food security. Forests are cleared and oleasters (wild olive trees) are preserved by farmers for their valuable oil and for use as rootstocks to graft olive. This practice is among those that have shaped olive domestication in the Mediterranean region. It contributes to the creation of forest-based olive agroecosystems and favors olive intraspecific diversity that is highly adapted to heterogeneous mountain environments. Productions contribute to food security, short trade circuits, land tenure and cultural identity. Ethnobiological studies show a continuity of classification, naming and uses between selected oleaster types and olive varieties suggesting an ongoing domestication process. This is supported by genetic analyses which show a higher concentration of genotypes selected from seedlings that propagate through sexual propagation in OOAs as compared to areas where management of oleasters for oil and as rootstocks is absent. Photointerpretation of aerial images corroborated with field-based observations, show the impacts of exogenous projects since the French and Spanish Protectorate periods to contemporary projects of the state policy “Plan Maroc Vert.” We discuss the importance of OOAs for the preservation of on-farm genetic resources, food security and as models for future agroecosystems within the context of climate change.

On the origins and domestication of the olive: a review and perspectives.

Unravelling domestication processes is crucial for understanding how species respond to anthropogenic pressures, forecasting crop responses to future global changes and improving breeding programmes. Domestication processes for clonally propagated perennials differ markedly from those for seed-propagated annual crops, mostly due to long generation times, clonal propagation and recurrent admixture with local forms, leading to a limited number of generations of selection from wild ancestors. However, additional case studies are required to document this process more fully. The olive is an iconic species in Mediterranean cultural history. Its multiple uses and omnipresence in traditional agrosystems have made this species an economic pillar and cornerstone of Mediterranean agriculture. However, major questions about the domestication history of the olive remain unanswered. New paleobotanical, archeological, historical and molecular data have recently accumulated for olive, making it timely to carry out a critical re-evaluation of the biogeography of wild olives and the history of their cultivation. We review here the chronological history of wild olives and discuss the questions that remain unanswered, or even unasked, about their domestication history in the Mediterranean Basin. We argue that more detailed ecological genomics studies of wild and cultivated olives are crucial to improve our understanding of olive domestication. Multidisciplinary research integrating genomics, metagenomics and community ecology will make it possible to decipher the evolutionary ecology of one of the most iconic domesticated fruit trees worldwide. The olive is a relevant model for improving our knowledge of domestication processes in clonally propagated perennial crops, particularly those of the Mediterranean Basin. Future studies on the ecological and genomic shifts linked to domestication in olive and its associated community will provide insight into the phenotypic and molecular bases of crop adaptation to human uses.

Bronze Age olive domestication in the north Jordan valley: new morphological evidence for regional complexity in early arboricultural practice from Pella in Jordan

Recent research from the site of Pella in Jordan examines the process and timing of olive cultivation. The frequent presence of olive remains from the Pottery Neolithic, beginning in the Yarmoukian, suggests that exploitation of the olive dates from as early as c. 6200 cal bce, with evidence of oil pressing from at least c. 5200 cal bce. Morphometric data, spanning the Late Neolithic to the Middle Iron Age II, using the measurement of olive endocarp length and width, demonstrates a reduction in the size variation of olive endocarps through time, in addition to an increase in their length, likely the result of selection pressure on trees. At Pella, this change occurs sometime after the Chalcolithic and before the Late Bronze Age, probably post-dating the earliest phases of the Early Bronze Age. Domestication is thus later than Teleilat Ghassul (Jordan), which has the earliest morphological evidence for olive domestication, and suggests that olive domestication was a regionally and temporally diverse process.

Erratum to: Plant remains from Roman period town of Obulco (today Porcuna) in Andalusia (Spain)—distribution and domestication of olive in the west Mediterranean region

Erratum to: Plant remains from Roman period town of Obulco (today Porcuna) in Andalusia (Spain)—distribution and domestication of olive in the west Mediterranean region

Plant remains from Roman period town of Obulco (today Porcuna) in Andalusia (Spain)—distribution and domestication of olive in the west Mediterranean region

The aim of this work is (1) to identify the key characteristics of agriculture and the role of olive in Porcuna (Andalusia) of Roman period and (2) to derive a conclusion about the origin of cultivated olive. The study of the literature showed that the olive is one of the most esteemed fruit species in the Classical Mediterranean world and is considered to have been domesticated first in Levant region. The signs of cultivation appear since the Neolithic. The authors analysed 18 samples from archaeological sites. Sorting and identification were carried out using a binocular microscope with the help of comparative collection of seeds/fruits and identification atlases (Digital Seed Atlas of the Netherlands: Cappers et al. 2006). A total number of 19,616 remains was studied. The remains belong to groups of fruit trees, cereals, pulses and synanthropic plants. The cultivated species were used for domestic purposes. The cereals, pulses and mesocarps of the fruits served as food. Important characteristic trait was the overrepresentation of olives. The authors give a summary of the development that led to the cultivation and domestication of the olive tree and to reconstruct its early diffusion using different sources of information, such as archaeobotanical analysis, archaeological data and genetical studies. As a result, a better understanding of the domestication and use of olive on a Mediterranean scale is given. This study also discusses cultivated and synanthropic species in Roman settlements on the Iberian Peninsula.

Evidence of a short-lived episode of olive (Olea europaea L.) cultivation during the Early Bronze Age in western Mediterranean (southern Italy)

Anthracological analysis was carried out in the archaeological site of Punta di Zambrone on the Tyrrhenian coast of Calabria in southern Italy. Archaeological excavation documented at the site settlement deposits dated mainly to Early Bronze Age (EBA, 21st–18th century BC) and the Recent Bronze Age (RBA, 13th to early 12th century BC). In the phase of the EBA village, the high frequency of Olea europaea in the charcoal data suggests the tree may well have been cultivated by favouring the spread of the scant olive trees growing wild. Comparison with existing archaeobotanical data indicates that olive cultivation spread over a large portion of southern Italy from the EBA and the early Middle Bronze Age (MBA, 17th–15th century BC), thus calling into question the hypothesis of its first cultivation related to the interaction between Mycenaean Greece and local cultures in southern Italy. The early domestication event at Punta di Zambrone supports the idea of multiple independent primary events of olive domestication throughout the Mediterranean basin. In the following phase of the fortified settlement dated to the RBA, the frequency of olive charcoal diminished and the expansion of a more or less dense forest dominated by Quercus was judged to be a consequence of human depopulation that characterises the end of MBA and also a different land use of RBA. This forest increase, also recorded by other archaeobotanical proxies in the central and southern Italian peninsula, is found to be related to the diffusion in southern Calabria of the Subapennine culture, spreading from more northerly areas of Italy and bringing different economic systems and agronomic knowledge. These far-reaching changes appear to have brought to a halt the first event of olive cultivation recorded at Punta di Zambrone.

Olive domestication and diversification in the Mediterranean Basin.

Olive (Olea europaea ssp.europaea) is the most important oil fruit crop in temperate areas, but the origin of the cultivated olive remains unclear. The existence of one or several domestication events in the Mediterranean Basin (MB) is still debated. We analyzed a dataset of 387 cultivated and wild accessions that were genotyped at 25 simple-sequence repeat (SSR) loci. The sample represented genetic diversity at the geographic extremes of the MB. We inferred relationships among samples and also applied approximate Bayesian computation to estimate the most probable demographic model of our samples. Cultivated olives clustered into three different gene pools (Q1, Q2 and Q3), corresponding loosely to the west, central and eastern MB, respectively. Q1 consisted primarily of accessions from southern Spain, retained the fingerprint of a genetic bottleneck, and was closely related to accessions from the eastern MB. Q2 showed signs of recent admixture with wild olives and may derive from a local domestication event in the central MB. Overall our results suggest that admixture shaped olive germplasm and perhaps also local domestication events.

Genetic diversity and relationships of wild and cultivated olives in Turkey

In the present study, we proposed to determine the genetic diversity and relationships between local cultivars and wild olive trees from three important olive-growing regions, i.e., Marmara, Aegean, and Mediterranean, of Turkey. This is the first known large-scale molecular study to investigate the relationships between local cultivars and wild olives from the eastern Mediterranean basin. Two hundred and four oleaster trees and 27 cultivars were sampled to represent molecular diversity. We used 11 simple sequence repeat and 13 sequence-related amplified polymorphism markers to assess genetic variations and inter-relationships among the samples. The results of the analysis showed differences in the levels of allelic composition and heterozygosity between cultivated and wild olive trees. The observation of a high proportion of a certain wild-type genetic background in the cultivars may indicate the former use of local wild trees in olive domestication in Turkey, a possible autochthonal origin of cultivars. “Gemlik” was found to be the most common olive cultivar in the Marmara region and most of the wild olive samples from this region may be feral forms derived from cultivar seed spreading. The information obtained from this study can help to assist the management of an olive collection and sheds some light on the origin of Turkish olive cultivars.

Primary domestication and early uses of the emblematic olive tree: palaeobotanical, historical and molecular evidence from the Middle East

Our knowledge of the origins of olive tree domestication in the Middle East and on the processes governing its extension and persistence in different vegetation types from prehistory through antiquity to modern times derives from diverse sources, spanning the biological sciences to the humanities. Nonetheless, it lacks a robust overview that may lead to floating interpretations. This is especially true in the Middle East, considered as the cradle of agriculture, and where the evolutionary history of this emblematic tree is intertwined with that of civilizations. Olive fruit, oil and wood have been, since Prehistoric times, characteristic products of the lands bordering the Mediterranean Sea. In the domestic economy of these countries, the olive tree gradually became a traditional tree crop since the first oil extraction, through the emergence of regional commerce that accompanied the rise and fall of early Near-Middle Eastern urbanism, until the development of modern trade, with an oil production estimated at circa 3000000 tons per year. The rising importance of the olive tree in human life has turned the tree into an endless source of fascination in the Aegean and Eastern Mediterranean, a symbol and a sacred tree, widely cited in the Bibles, the Koran, and in ancient literature. Here we argue that advances in radiocarbon chronology, palaeobotany, genetics, and archaeology-history have profoundly refined the history of olive trees in the Middle East. This review shows that the heartland of primary olive domestication must be enlarged to the Levant and not only focus on the Jordan Valley. The domestication of the olive tree is a long and ongoing process, linked to the early production of oil and the development of the olive trade. We also suggest that the olive tree became a particular icon, a sacred tree, during the Biblical period in the Levant.

Centennial olive trees as a reservoir of genetic diversity

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. 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. 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. 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.