Olive domestication and diversification in the Mediterranean Basin

Early production of table olives at a mid-7th millennium BP submerged site off the Carmel coast (Israel)

We present here the earliest evidence for large-scale table olive production from the mid-7^th millennium BP inundated site of Hishuley Carmel on the northern Mediterranean coast of Israel. Olive pit size and fragmentation patterns, pollen as well as the architecture of installations associated with pits from this site, were compared to finds from the nearby and slightly earlier submerged Kfar Samir site. Results indicate that at Kfar Samir olive oil was extracted, while at Hishuley Carmel the data showed that large quantities of table olives, the oldest reported to date, were prepared. This process was most probably facilitated by the site’s proximity to the Mediterranean Sea, which served as a source of both sea water and salt required for debittering/pickling/salting the fruit, as experimentally demonstrated in this study. Comparison of pit morphometry from modern cultivars, wild-growing trees and the archaeological sites, intimates that in pit morphology the ancient pits resemble wild olives, but we cannot totally exclude the possibility that they derive from early cultivated trees. Our findings demonstrate that in this region, olive oil production may have predated table olive preparation, with each development serving as a milestone in the early exploitation of the olive.

Accessing Ancestral Origin and Diversity Evolution by Net Divergence of an Ongoing Domestication Mediterranean Olive Tree Variety

Olea europaea 'Galega vulgar' variety is a blend of West and Central Mediterranean germplasm with cultivated-wild admixture characteristics. 'Galega vulgar' is known for its high rusticity and superior-quality olive oil, being the main Portuguese variety with high impact for bioeconomy. Nevertheless, it has been replaced by higher-yielding and more adapted to intensive production foreign varieties. To clarify the potential ancestral origin, genetic diversity evolution, and existing genetic relationships within the national heritage of 'Galega vulgar', 595 trees, belonging to ancient and centenary age groups and prospected among ten traditional production regions, were characterized using 14 SSR markers after variety validation by endocarp measurements. Ninety-five distinguishable genets were identified, revealing the presence of a reasonable amount of intra-genetic and morphological variability. A minimum spanning tree, depicting the complete genealogy of all identified genets, represented the 'Galega vulgar' intra-varietal diversity, with 94% of the trees showing only a two-allele difference from the most frequent genet (C001). Strong correlations between the number of differentiating alleles from C001, the clonal size, and their net divergence suggested an ancestral monoclonal origin of the 'Galega vulgar', with the most frequent genet identified as the most likely origin of all the genets and phenotypic diversification occurring through somatic mutations. Genetic erosion was detected through the loss of some allele combinations across time. This work highlights the need to recover the lost diversity in this traditional olive variety by including ancient private genets (associated with potential adaptation traits) in future breeding programs and investing in the protection of these valuable resources in situ by safeguarding the defined region of origin and dispersion of 'Galega vulgar'. Furthermore, this approach proved useful on a highly diverse olive variety and thus applicable to other diverse varieties due either to their intermediate nature between different gene pools or to the presence of a mixture of cultivated and wild traits (as is the case of 'Galega vulgar').

Interspecific introgression and natural selection in the evolution of Japanese apricot (Prunus mume)

Domestication and population differentiation in crops involve considerable phenotypic changes. The logs of these evolutionary paths, including natural/artificial selection, can be found in the genomes of the current populations. However, these profiles have been little studied in tree crops, which have specific characters, such as long generation time and clonal propagation, maintaining high levels of heterozygosity. We conducted exon-targeted resequencing of 129 genomes in the genus Prunus, mainly Japanese apricot (Prunus mume), and apricot (Prunus armeniaca), plum (Prunus salicina), and peach (Prunus persica). Based on their genome-wide single-nucleotide polymorphisms merged with published resequencing data of 79 Chinese P. mume cultivars, we inferred complete and ongoing population differentiation in P. mume. Sliding window characterization of the indexes for genetic differentiation identified interspecific fragment introgressions between P. mume and related species (plum and apricot). These regions often exhibited strong selective sweeps formed in the paths of establishment or formation of substructures of P. mume, suggesting that P. mume has frequently imported advantageous genes from other species in the subgenus Prunus as adaptive evolution. These findings shed light on the complicated nature of adaptive evolution in a tree crop that has undergone interspecific exchange of genome fragments with natural/artificial selections.

Genome-wide genotyping elucidates the geographical diversification and dispersal of the polyploid and clonally propagated yam (Dioscorea alata)

BACKGROUND AND AIMS

Inferring the diffusion history of many human-dispersed species is still not straightforward due to unresolved past human migrations. The centre of diversification and routes of migration of the autopolyploid and clonally propagated greater yam, Dioscorea alata, one of the oldest edible tubers, remain unclear. Here, we address yam demographic and dispersal history using a worldwide sample.

METHODS

We characterized genome-wide patterns of genetic variation using genotyping by sequencing 643 greater yam accessions spanning four continents. First, we disentangled the polyploid and clonal components of yam diversity using allele frequency distribution and identity by descent approaches. We then addressed yam geographical origin and diffusion history with a model-based coalescent inferential approach.

KEY RESULTS

Diploid genotypes were more frequent than triploids and tetraploids worldwide. Genetic diversity was generally low and clonality appeared to be a main factor of diversification. The most likely evolutionary scenario supported an early divergence of mainland Southeast Asian and Pacific gene pools with continuous migration between them. The genetic make-up of triploids and tetraploids suggests that they have originated from these two regions before westward yam migration. The Indian Peninsula gene pool gave origin to the African gene pool, which was later introduced to the Caribbean region.

CONCLUSIONS

Our results are congruent with the hypothesis of independent domestication origins of the two main Asian and Pacific gene pools. The low genetic diversity and high clonality observed suggest a strong domestication bottleneck followed by thousands of years of widespread vegetative propagation and polyploidization. Both processes reduced the extent of diversity available for breeding, and this is likely to threaten future adaptation.

Genomic evidence for recurrent genetic admixture during the domestication of Mediterranean olive trees (Olea europaea L.)

BACKGROUND

Olive tree (Olea europaea L. subsp. europaea, Oleaceae) has been the most emblematic perennial crop for Mediterranean countries since its domestication around 6000 years ago in the Levant. Two taxonomic varieties are currently recognized: cultivated (var. europaea) and wild (var. sylvestris) trees. However, it remains unclear whether olive cultivars derive from a single initial domestication event followed by secondary diversification, or whether cultivated lineages are the result of more than a single, independent primary domestication event. To shed light into the recent evolution and domestication of the olive tree, here we analyze a group of newly sequenced and available genomes using a phylogenomics and population genomics framework.

RESULTS

We improved the assembly and annotation of the reference genome, newly sequenced the genomes of twelve individuals: ten var. europaea, one var. sylvestris, and one outgroup taxon (subsp. cuspidata)-and assembled a dataset comprising whole genome data from 46 var. europaea and 10 var. sylvestris. Phylogenomic and population structure analyses support a continuous process of olive tree domestication, involving a major domestication event, followed by recurrent independent genetic admixture events with wild populations across the Mediterranean Basin. Cultivated olives exhibit only slightly lower levels of genetic diversity than wild forms, which can be partially explained by the occurrence of a mild population bottleneck 3000-14,000 years ago during the primary domestication period, followed by recurrent introgression from wild populations. Genes associated with stress response and developmental processes were positively selected in cultivars, but we did not find evidence that genes involved in fruit size or oil content were under positive selection. This suggests that complex selective processes other than directional selection of a few genes are in place.

CONCLUSIONS

Altogether, our results suggest that a primary domestication area in the eastern Mediterranean basin was followed by numerous secondary events across most countries of southern Europe and northern Africa, often involving genetic admixture with genetically rich wild populations, particularly from the western Mediterranean Basin.

Influence of genetic and interannual factors on the phenolic profiles of virgin olive oils

Phenolic compounds in virgin olive oil (VOO) contribute to its health properties, organoleptic features and oxidative stability. In this study, a total of 44 olive tree cultivars categorized by the International Olive Council to be among the most internationally widespread varieties were exhaustively and homogenously evaluated by analysis of the VOO phenolic profile during three consecutive crop seasons. Differences among cultivars resulted in up to 15-fold variations in the total phenol concentration. The 'cultivar' factor contributed the most to the variance (66.8% for total phenolic concentration) for almost all the phenols. However, the 'interannual variability' factor and the interaction 'cultivar x interannual variability' exhibited significant influences on specific phenols. According to the phenolic profile of the VOOs, we determined the presence of three groups of cultivars marked by the predominance of secoiridoid derivatives, which supports the phenolic profile as a criterion to be considered in olive breeding programs.

Genetic Resources of Olea europaea L. in the Garda Trentino Olive Groves Revealed by Ancient Trees Genotyping and Parentage Analysis of Drupe Embryos

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.

Adaptive response to olive cultivation in a generalist parasitic nematode (Meloidogyne javanica)

Cultivated plants usually differ from their wild progenitors in several morphological and/or physiological traits. Their microbe communities might also differ because of adaptation to new conditions related to cultivation. To test this hypothesis, we investigated morphological traits in a parthenogenetic root-knot nematode (Meloidogyne javanica) from natural and agricultural environments. Seventeen populations of M. javanica were sampled on cultivated and wild olives in Morocco, then maintained in controlled conditions for a ‘common garden’ experiment. We estimated the genetic variation based on three traits (stylet size, neck width and body width) by a quantitative genetic design (ten families per population and nine individuals per family were measured), and molecular variation was investigated with a mitochondrial marker to identify the genetic lineages of nematode isolates sampled from wild and cultivated olives. Significant morphological differences were detected between individuals from wild vs. cultivated hosts for the three traits, whereas no phylogenetic clustering was observed among isolates collected on those two hosts. Our results thus suggest an adaptive response of the asexual parasite, possibly related to the deep modification of soil nematode communities between natural olive stands and orchards.

A Hot Spot of Olive Biodiversity in the Tunisian Oasis of Degache

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.

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.

Chloroplast Genome Variation and Evolutionary Analysis of Olea europaea L

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.

An Updated Checklist of the Sicilian Native Edible Plants: Preserving the Traditional Ecological Knowledge of Century-Old Agro-Pastoral Landscapes

The traditional use of native wild food plants (NWFP) may represent a valuable supplementary food source for the present and future generations. In Sicily, the use of wild plants in the human diet dates back to very ancient times and still plays an important role in some rural communities. Moreover, in this regard, the natural and cultural inheritance of this island is wealthy and diversified for several reasons. First, Sicily hosts a rich vascular flora, with 3,000 native and 350 endemic plants. Second, due to its central position in the Mediterranean, the island has acted as a veritable melting pot for the ethnobotanical knowledge of the rural communities of the entire basin. We reviewed all the available literature and, starting from such omnicomprehensive checklist, partially improved thanks to the data issuing from recent field investigations, we critically revised the whole species list, basing our review on field data issuing from interviews and on our expert knowledge. As a result, we provide a substantially updated list of 292 NWFP growing on the island. Further 34 species, reported as NWFP on previous papers were discarded because they are not native to Sicily, while 45 species were listed separately because their identity, occurrence and local use as food is doubtful and needs to be further investigated. Moreover, we tried to shed light on the ecology (growth form and preferential habitat) of the Sicilian NWFP, with special focus on crop wild relatives (CWR). Our preliminary ecological analyses point out that a high percentage of these plants are linked with the so-called 'cultural' landscapes, patchy semi-natural environments rich in ecotones, leading to the conclusion that the maintenance of century-old agro-pastoral practices may represent an effective way to preserve the local heritage of edible plants. Our study allowed to identify as much as 102 taxa of agronomic interest which could be tested as novel crops in order to face ongoing global changes and to comply with sustainable agriculture policies. Among them, 39 taxa show promising traits in terms of tolerance to one or more environmental stress factors, while 55 more are considered CWR and/or can be easily cultivated and/or show high productivity/yield potential.

Genotypic variability in radial resistance to water flow in olive roots and its response to temperature variations

As radial root resistance (Rp) represents one of the key components of the soil-plant-atmosphere continuum resistance catena modulating water transport, understanding its control is essential for physiologists, modelers and breeders. Reports of Rp, however, are still scarce and scattered in the scientific literature. In this study, we assessed genetic variability in Rp and its dependence on temperature in five widely used olive cultivars. In a first experiment, cultivar differences in Rp at 25 °C were evaluated from flow-pressure measurements in excised roots and subsequent analysis of root traits. In a second experiment, similar determinations were performed continually over a 5-h period in which temperature was gradually increased from 12 to 32 °C, enabling the assessment of Rp response to changing temperature. Despite some variability, our results did not show statistical differences in Rp among cultivars in the first experiment. In the second, cultivar differences in Rp were not significant at 12 °C, but they became so as temperature increased. Furthermore, the changes in Rp between 12 and 32 °C were higher than those expected by the temperature-driven decrease in water viscosity, with the degree of that change differing among cultivars. Also, Rp at 25 °C reached momentarily in the second experiment was consistently higher than in the first at that same, but fixed, temperature. Overall, our results suggest that there is limited variability in Rp among the studied cultivars when plants have been exposed to a given temperature for sufficient time. Temperature-induced variation in Rp might thus be partly explained by changes in membrane permeability that occur slowly, which explains why our values at 25 °C differed between experiments. The observed cultivar differences in Rp with warming also indicate faster acclimation of Rp to temperature changes in some cultivars than others.

Projected climate changes are expected to decrease the suitability and production of olive varieties in southern Spain

World olive production is based on the cultivation of different varieties that respond differently to abiotic factors. Climate change may affect the area of land suitable for olive cultivation and change production levels, thus causing serious damage to this economically-relevant and highly-productive olive grove agroecosystem. In Mediterranean regions such as Andalusia, one of the main areas of olive production, the effect of climate change seems threatening. Thus, our main aims are: (1) to examine the abiotic factors that characterise the current cultivated locations and predict the current and potential distribution of these locations; (2) to evaluate the effect of climate change (based on regional scenarios) on the future environmental suitability of each olive variety; and (3) to analyse the expected alteration in the annual olive production. We used the seven most-productive olive varieties in Andalusia and the wild olive species to develop Species Distribution Models (SDMs), coupled with soil properties, geomorphology, water balance and (bio-)climatic predictors at a fine scale. We also derived future climate projections to assess the effect of climate change on the environmental suitability and productivity of each olive variety. We found that soil pH was the most-important factor for most distribution models, while (bio-)climatic predictors - such as continentality index, summer and autumn precipitation and winter temperature - provided important contributions. In general, projections based on regional climate change scenarios point to a decrease in the area suitable for olive crops in Andalusia, due to an increase in evapotranspiration and a decrease in precipitation. These changes in suitable area are also projected to decrease olive production for almost all the olive-growing provinces investigated. Our findings may anticipate the effects of climate change on olive crops and provide early estimates of fruit production, at local and regional scales, as well as forming the basis of adaptation strategies.

Molecular Analysis of the Official Algerian Olive Collection Highlighted a Hotspot of Biodiversity in the Central Mediterranean Basin

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.

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.

The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions

Background

Olive (Olea europaea L.) is an important oil and fruit crop worldwide, owning a rich germplasm with a large number of cultivars. Simple sequence repeats (SSRs) are excellent markers and have been used for the identification of olive cultivars. However, the limited number of SSR markers and the occurrence of confusion on the names of cultivars, as well as the possible appearance of clonal variation make it difficult to identify cultivars and interpret relationships among olive cultivars.

Method

SSR markers were designed based on trinucleotide repeat sequences by screening the whole genome of olive, and the polymorphic SSR markers were developed that were applied to the identification of 53 olive accessions. The genetic characteristics and relationships of these olive accessions were evaluated based on the developed SSR markers.

Results

Twenty-one highly polymorphic genomic-SSR markers were developed, covering most chromosomes of olive. These SSR markers could well distinguish all 53 olive accessions, confirming their effectiveness. DNA fingerprints of the 53 olive accessions were constructed based on the 21 SSR markers. The dendrogram clearly divided the tested accessions into two main groups, which was also supported by the results of principal coordinate analysis. A total of 31 private alleles were detected in 15 olive accessions, which reflected the genetic diversity within 53 olive accessions to some extent. Six homonymy cases were also clarified by genetic analysis. These results suggest that the newly developed olive SSR markers are informative for the exploitation, preservation and breeding of olive.

Cultivated Olive Diversification at Local and Regional Scales: Evidence From the Genetic Characterization of French Genetic Resources

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.

Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)

Olive (Olea europaea L.) is one of the most economically and historically important fruit crops worldwide. Genetic progress for valuable agronomic traits has been slow in olive despite its importance and benefits. Advances in next generation sequencing technologies provide inexpensive and highly reproducible genotyping approaches such as Genotyping by Sequencing, enabling genome wide association study (GWAS). Here we present the first comprehensive GWAS study on olive using GBS. A total of 183 accessions (FULL panel) were genotyped using GBS, 94 from the Turkish Olive GenBank Resource (TOGR panel) and 89 from the USDA-ARS National Clonal Germplasm Repository (NCGR panel) in the USA. After filtering low quality and redundant markers, GWAS was conducted using 24,977 SNPs in FULL, TOGR and NCGR panels. In total, 52 significant associations were detected for leaf length, fruit weight, stone weight and fruit flesh to pit ratio using the MLM_K. Significant GWAS hits were mapped to their positions and 19 candidate genes were identified within a 10-kb distance of the most significant SNP. Our findings provide a framework for the development of markers and identification of candidate genes that could be used in olive breeding programs.

Effects of reclaimed wastewater irrigation and fertigation level on olive oil composition and quality

BACKGROUND

Irrigation of olives increases fruit and oil yields. Due to scarcity of freshwater, low-quality water including recycled wastewater (RWW) is utilized in orchards. Here, effects of irrigation with RWW and of fertilization on the composition and quality of olive oil were studied.

RESULTS

Long-term RWW irrigation of 'Barnea' and 'Leccino' olive had no significant negative effects on either oil composition or quality parameters, including free fatty acids (FFAs), peroxide value (PV), total phenolics content (TPC), fatty acid profiles and organoleptic characteristics. The average FFA contents for both cultivars were less than 0.8% during most of the experimental period, except the seasons 2009 and 2012-2013 for Barnea where the values were raised up to 1.4%. The measured PV levels were less than 9 and 5 mmol O₂ kg^-1 oil for Barnea and Leccino, respectively. In the last season of the experiment for each cultivar, higher TPC were observed in oils obtained from RWW irrigation with reduced fertilization (Re-) as compared to the treatments with the recommended fertilization [freshwater irrigation (Fr) and RWW irrigation (Re+) with standard dose of fertilizers], where the TPC increment exceeded 70% in Barnea and 25% in Leccino. The treatments had only minor effects on the fatty acid profile, reflected in slightly altered levels of C18:2 and C18:3 fatty acids.

CONCLUSION

The use of RWW, combined with the consideration of nutrients arriving with such water to provide appropriate fertilization, was found suitable for olive irrigation to ensure optimal yields while preserving oil quality. © 2019 Society of Chemical Industry.

Characterization of Worldwide Olive Germplasm Banks of Marrakech (Morocco) and Córdoba (Spain): Towards management and use of olive germplasm in breeding programs

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.

Evolutionary transcriptomics reveals the origins of olives and the genomic changes associated with their domestication

The olive (Olea europaea L. subsp. europaea) is one of the oldest and most socio-economically important cultivated perennial crop in the Mediterranean region. Yet, its origins are still under debate and the genetic bases of the phenotypic changes associated with its domestication are unknown. We generated RNA-sequencing data for 68 wild and cultivated olive trees to study the genetic diversity and structure both at the transcription and sequence levels. To localize putative genes or expression pathways targeted by artificial selection during domestication, we employed a two-step approach in which we identified differentially expressed genes and screened the transcriptome for signatures of selection. Our analyses support a major domestication event in the eastern part of the Mediterranean basin followed by dispersion towards the West and subsequent admixture with western wild olives. While we found large changes in gene expression when comparing cultivated and wild olives, we found no major signature of selection on coding variants and weak signals primarily affected transcription factors. Our results indicated that the domestication of olives resulted in only moderate genomic consequences and that the domestication syndrome is mainly related to changes in gene expression, consistent with its evolutionary history and life history traits.

Phoenix phylogeny, and analysis of genetic variation in a diverse collection of date palm (Phoenix dactylifera) and related species

Date palm (Phoenix dactylifera), one of the most ancient crops, is grown commercially in >30 countries. Using whole plastome assemblies, phylogenetic analyses revealed that cultivated date palm accessions share the same clade with P hoenix sylvestris, P hoenix pusilla and P hoenix acaulis, which are native to the Indian subcontinent, and Phoenix caespitosa that is native to the Arabian Peninsula and the deserts of Somalia. Analysis of genetic diversity and genetic relationships among date palm accessions from 13 producing countries involved 195 date palm accessions that were genotyped at 19 microsatellite loci. Extensive genetic diversity was observed, with many accessions heterozygous for most markers in this clonally propagated crop. The average number of alleles per locus (42.1), expected heterozygosity (0.8), observed heterozygosity (0.47) and fixation indices (FST = 0.42) demonstrated substantial genetic diversity and population structure. Iraqi accessions were found to have the richest allelic diversity, and the most private alleles. The model-based Bayesian method indicated that these accessions could be broadly divided into two structure groups, one group with predominantly African accessions and another predominantly Asian. Some germplasm, especially from Tunisia and Iraq, deviated from this generalization. Many accessions in the STRUCTURE-derived groups were found to be genetic admixtures, with gene flow between Asian and African groups. Indian and Pakistani date palms were found to be most closely related to North African germplasm.

DNA analysis of Castanea sativa (sweet chestnut) in Britain and Ireland: Elucidating European origins and genepool diversity

Castanea sativa is classified as non-indigenous in Britain and Ireland. It was long held that it was first introduced into Britain by the Romans, until a recent study found no corroborative evidence of its growing here before c. AD 650. This paper presents new data on the genetic diversity of C. sativa in Britain and Ireland and potential ancestral sources in continental Europe. Microsatellite markers and analytical methods tested in previous European studies were used to genotype over 600 C. sativa trees and coppice stools, sampled from ancient semi-natural woodlands, secondary woodlands and historic cultural sites across Britain and Ireland. A single overall genepool with a diverse admixture of genotypes was found, containing two sub groups differentiating Wales from Ireland, with discrete geographical and typological clusters. C. sativa genotypes in Britain and Ireland were found to relate predominantly to some sites in Portugal, Spain, France, Italy and Romania, but not to Greece, Turkey or eastern parts of Europe. C. sativa has come to Britain and Ireland from these western European areas, which had acted as refugia in the Last Glacial Maximum; we compare its introduction with the colonization/translocation of oak, ash, beech and hazel into Britain and Ireland. Clones of C. sativa were identified in Britain, defining for the first time the antiquity of some ancient trees and coppice stools, evincing both natural regeneration and anthropogenic propagation over many centuries and informing the chronology of the species’ arrival in Britain. This new evidence on the origins and antiquity of British and Irish C. sativa trees enhances their conservation and economic significance, important in the context of increasing threats from environmental change, pests and pathogens.

Genetic Diversity Analysis of Olive Germplasm (Olea europaea L.) With Genotyping-by-Sequencing Technology

Olive (Olea europaea L.) is a very important edible oil crop and has been cultivated for about 4,000 years in the Mediterranean area. Due to its nutritional and economic importance, researches on germplasm characterization received extensive attention. In this study, using the genotyping-by-sequencing (GBS) technology, we carried out genetic diversity analysis on 57 olive cultivars with different geographical origins. In total, 73,482 high-quality single-nucleotide polymorphisms (SNPs) with minor allele frequency (MAF) > 5%, call rate > 50%, and heterozygosity rate < 10% were obtained at the whole genome level. Genetic structure and phylogenetic analysis showed that the 57 olive cultivars could be classified into two groups (Group I and Group II). No clear geographical distributions of cultivars were observed generally between the two groups. The average nucleotide diversities (π) specific for Group I and Group II were 0.317 and 0.305. The fixation index (F ST) between Group I and Group II was 0.033. In Group II, cultivars could be further divided into two subgroups (Group IIa and Group IIb), which seem to be associated with their fruit sizes. The five Chinese-bred cultivars were all clustered in Group II, showing a closer genetic relationship with those from the central Mediterranean region and limited genetic background. It is therefore necessary for Chinese olive breeding programs to incorporate other genetic basis by utilizing germplasm from the other regions particularly from the east Mediterranean region as breeding parents. The results showed that GBS is an effective marker choice for cultivar characterization and genetic diversity analysis in olive and will help us better understand the genetic backgrounds of the crop.

Genetic Characterization of Apulian Olive Germplasm as Potential Source in New Breeding Programs

The olive is a fruit tree species with a century-old history of cultivation in theMediterranean basin. In Apulia (Southern Italy), the olive is of main social, cultural and economicimportance, and represents a hallmark of the rural landscape. However, olive cultivation in thisregion is threatened by the recent spread of the olive quick decline syndrome (OQDS) disease, thusthere is an urgent need to explore biodiversity and search for genetic sources of resistance. Herein,a genetic variation in Apulian olive germplasm was explored, as a first step to identify genotypeswith enhanced bio-agronomic traits, including resistance to OQDS. A preselected set of nuclearmicrosatellite markers allowed the acquisition of genotypic profiles, and to define geneticrelationships between Apulian germplasm and widespread cultivars. The analysis highlighted thebroad genetic variation in Apulian accessions and the presence of different unique genetic profiles.The results of this study lay a foundation for the organization of new breeding programs for olivegenetic improvement.

Trait-based plant ecology a flawed tool in climate studies? The leaf traits of wild olive that pattern with climate are not those routinely measured

Climate-related studies have generally focussed upon physiologically well-defined 'mechanistic' traits rather than 'functional' ones relating indirectly to resource capture. Nevertheless, field responses to climate are likely to typically include both 'mechanistic' specialization to climatic extremes and 'functional' strategies that optimize resource acquisition during less climatically-severe periods. Here, this hypothesis was tested. Seventeen traits (six 'functional', six 'mechanistic' and five 'intermediate') were measured from 19 populations of oleaster (wild olive) along a climatic gradient in Morocco. Principal components analysis of the trait dataset identified size and the 'worldwide leaf economics spectrum' as PCA axes 1 and 2. However, contrary to our prediction, these axes, and commonly-measured 'functional' traits, were little correlated with climate. Instead, PCA 3, perhaps relating to water-use and succulence, together stomatal density, specific leaf water content and leaf shape, patterned with altitude, aridity, rainfall and temperature. We concluded that, at least for slow-growing species, such as oleaster, 'mechanistic' traits are key to identifying mechanisms of climatic restriction. Meaningful collaboration between 'mechanistic' and 'functional' disciplines provides the best way of improving our understanding of the global impacts of climate change on species distribution and performance.

Genotype-dependent regulation of vitamin E biosynthesis in olive fruits as revealed through metabolic and transcriptional profiles

Vitamin E is a general term used to describe a group of eight lipophilic compounds known as tocochromanols. These vitamin E variants are chemically categorised into two classes formed by α-, β-, γ- and δ- tocopherols and tocotrienols isoforms, respectively. The present study describes the concurrent regulation of genes and metabolites orchestrating vitamin E biosynthesis in olive drupes of five distinctive Greek olive cultivars. A combination of analytical, biochemical and molecular approaches was employed in order to carry out comparative analyses, including real-time RT-qPCR for gene expression levels and HPLC analysis of metabolite content. Findings indicated that tocochromanol levels and composition, oil content, gene expression levels as well as total antioxidant activity were highly dependent on cultivar and, to a lesser extent, on fruit developmental stage. Specifically, cultivars 'Kalokairida' and 'Lianolia Kerkyras' demonstrated the highest vitamin E content. The latter possessed high tocochromanol content combined with highest overall antioxidant activity in all developmental stages, concomitant with the up-regulation expression profile of HPPD. The genotypic imprint versus the temporal contribution to vitamin E levels, as well as the potential link to lipid peroxidation amelioration, are discussed.

Delineation of the Olive Pollen Proteome and Its Allergenome Unmasks Cyclophilin as a Relevant Cross-Reactive Allergen

Olive pollen is a major allergenic source worldwide due to its extensive cultivation. We have combined available genomics data with a comprehensive proteomics approach to get the annotated olive tree (Olea europaea L.) pollen proteome and define its complex allergenome. A total of 1907 proteins were identified by LC-MS/MS using predicted protein sequences from its genome. Most proteins (60%) were predicted to possess catalytic activity and be involved in metabolic processes. In total, 203 proteins belonging to 47 allergen families were found in olive pollen. A peptidyl-prolyl cis-trans isomerase, cyclophilin, produced in Escherichia coli, was found as a new olive pollen allergen (Ole e 15). Most Ole e 15-sensitized patients were children (63%) and showed strong IgE recognition to the allergen. Ole e 15 shared high sequence identity with other plant, animal, and fungal cyclophilins and presented high IgE cross-reactivity with pollen, plant food, and animal extracts.

Genetic insights into the modification of the pre-fertilization mechanisms during plant domestication

Plant domestication is the process of adapting plants to human use by selecting specific traits. The selection process often involves the modification of some components of the plant reproductive mechanisms. Allelic variants of genes associated with flowering time, vernalization, and the circadian clock are responsible for the adaptation of crops, such as rice, maize, barley, wheat, and tomato, to non-native latitudes. Modifications in the plant architecture and branching have been selected for higher yields and easier harvests. These phenotypes are often produced by alterations in the regulation of the transition of shoot apical meristems to inflorescences, and then to floral meristems. Floral homeotic mutants are responsible for popular double-flower phenotypes in Japanese cherries, roses, camellias, and lilies. The rise of peloric flowers in ornamentals such as snapdragon and florists' gloxinia is associated with non-functional alleles that control the relative expansion of lateral and ventral petals. Mechanisms to force outcrossing such as self-incompatibility have been removed in some tree crops cultivars such as almonds and peaches. In this review, we revisit some of these important concepts from the plant domestication perspective, focusing on four topics related to the pre-fertilization mechanisms: flowering time, inflorescence architecture, flower development, and pre-fertilization self-incompatibility mechanisms.

Phylogenomics using low-depth whole genome sequencing: A case study with the olive tribe

Species trees have traditionally been inferred from a few selected markers, and genome-wide investigations remain largely restricted to model organisms or small groups of species for which sampling of fresh material is available, leaving out most of the existing and historical species diversity. The genomes of an increasing number of species, including specimens extracted from natural history collections, are being sequenced at low depth. While these data sets are widely used to analyse organelle genomes, the nuclear fraction is generally ignored. Here we evaluate different reference-based methods to infer phylogenies of large taxonomic groups from such data sets. Using the example of the Oleeae tribe, a worldwide-distributed group, we build phylogenies based on single nucleotide polymorphisms (SNPs) obtained using two reference genomes (the olive and ash trees). The inferred phylogenies are overall congruent, yet present differences that might reflect the effect of distance to the reference on the amount of missing data. To limit this issue, genome complexity was reduced by using pairs of orthologous coding sequences as the reference, thus allowing us to combine SNPs obtained using two distinct references. Concatenated and coalescence trees based on these combined SNPs suggest events of incomplete lineage sorting and/or hybridization during the diversification of this large phylogenetic group. Our results show that genome-wide phylogenetic trees can be inferred from low-depth sequence data sets for eukaryote groups with complex genomes, and histories of reticulate evolution. This opens new avenues for large-scale phylogenomics and biogeographical analyses covering both the extant and the historical diversity stored in museum collections.

Facing Climate Change: Biotechnology of Iconic Mediterranean Woody Crops

The Mediterranean basin is especially sensitive to the adverse outcomes of climate change and especially to variations in rainfall patterns and the incidence of extremely high temperatures. These two concurring adverse environmental conditions will surely have a detrimental effect on crop performance and productivity that will be particularly severe on woody crops such as citrus, olive and grapevine that define the backbone of traditional Mediterranean agriculture. These woody species have been traditionally selected for traits such as improved fruit yield and quality or alteration in harvesting periods, leaving out traits related to plant field performance. This is currently a crucial aspect due to the progressive and imminent effects of global climate change. Although complete genome sequence exists for sweet orange (Citrus sinensis) and clementine (Citrus clementina), olive tree (Olea europaea) and grapevine (Vitis vinifera), the development of biotechnological tools to improve stress tolerance still relies on the study of the available genetic resources including interspecific hybrids, naturally occurring (or induced) polyploids and wild relatives under field conditions. To this respect, post-genomic era studies including transcriptomics, metabolomics and proteomics provide a wide and unbiased view of plant physiology and biochemistry under adverse environmental conditions that, along with high-throughput phenotyping, could contribute to the characterization of plant genotypes exhibiting physiological and/or genetic traits that are correlated to abiotic stress tolerance. The ultimate goal of precision agriculture is to improve crop productivity, in terms of yield and quality, making a sustainable use of land and water resources under adverse environmental conditions using all available biotechnological tools and high-throughput phenotyping. This review focuses on the current state-of-the-art of biotechnological tools such as high throughput -omics and phenotyping on grapevine, citrus and olive and their contribution to plant breeding programs.

The extent of adaptive wild introgression in crops

The study of crop evolution has focused primarily on the process of initial domestication. Post-domestication adaptation during the expansion of crops from their centers of origin has received considerably less attention. Recent research has revealed that, in at least some instances, crops have received introgression from their wild relatives that has facilitated adaptation to novel conditions encountered during expansion. Such adaptive introgression could have an important impact on the basic study of domestication, affecting estimates of several evolutionary processes of interest (e.g. the strength of the domestication bottleneck, the timing of domestication, the targets of selection during domestication). Identification of haplotypes introgressed from the wild may also help in the identification of alleles that are beneficial under particular environmental conditions. Here we review mounting evidence for substantial adaptive wild introgression in several crops and consider the implications of such gene flow to our understanding of crop histories.

High Levels of Variation Within Gene Sequences of Olea europaea L

Gene sequence variation in cultivated olive (Olea europaea L. subsp. europaea var. europaea), the most important oil tree crop of the Mediterranean basin, has been poorly evaluated up to now. A deep sequence analysis of fragments of four genes, OeACP1, OeACP2, OeLUS and OeSUT1, in 90 cultivars, revealed a wide range of polymorphisms along all recognized allele forms and unexpected allele frequencies and genotype combinations. High linkage values among most polymorphisms were recorded within each gene fragment. The great sequence variability corresponded to a low number of alleles and, surprisingly, to a small fraction of genotype combinations. The distribution, frequency, and combination of the different alleles at each locus is possibly due to natural and human pressures, such as selection, ancestrality, or fitness. Phylogenetic analyses of allele sequences showed distant and complex patterns of relationships among cultivated olives, intermixed with other related forms, highlighting an evolutionary connection between olive cultivars and the O. europaea subspecies cuspidata and cerasiformis. This study demonstrates how a detailed and complete sequence analysis of a few gene portions and a thorough genotyping on a representative set of cultivars can clarify important issues related to sequence polymorphisms, reconstructing the phylogeny of alleles, as well as the genotype combinations. The identification of regions representing blocks of recombination could reveal polymorphisms that represent putatively functional markers. Indeed, specific mutations found on the analyzed OeACP1 and OeACP2 fragments seem to be correlated to the fruit weight.

Adaptive Introgression: An Untapped Evolutionary Mechanism for Crop Adaptation

Global environmental changes strongly impact wild and domesticated species biology and their associated ecosystem services. For crops, global warming has led to significant changes in terms of phenology and/or yield. To respond to the agricultural challenges of this century, there is a strong need for harnessing the genetic variability of crops and adapting them to new conditions. Gene flow, from either the same species or a different species, may be an immediate primary source to widen genetic diversity and adaptions to various environments. When the incorporation of a foreign variant leads to an increase of the fitness of the recipient pool, it is referred to as "adaptive introgression". Crop species are excellent case studies of this phenomenon since their genetic variability has been considerably reduced over space and time but most of them continue exchanging genetic material with their wild relatives. In this paper, we review studies of adaptive introgression, presenting methodological approaches and challenges to detecting it. We pay particular attention to the potential of this evolutionary mechanism for the adaptation of crops. Furthermore, we discuss the importance of farmers' knowledge and practices in shaping wild-to-crop gene flow. Finally, we argue that screening the wild introgression already existing in the cultivated gene pool may be an effective strategy for uncovering wild diversity relevant for crop adaptation to current environmental changes and for informing new breeding directions.

Inferring the Origin of Cultivated Zizania latifolia, an Aquatic Vegetable of a Plant-Fungus Complex in the Yangtze River Basin

Crop domestication is one of the essential topics in evolutionary biology. Cultivated Zizania latifolia, domesticated as the special form of a plant-fungus (the host Zizania latifolia and the endophyte Ustilago esculenta) complex, is a popular aquatic vegetable endemic in East Asia. The rapid domestication of cultivated Z. latifolia can be traced in the historical literature but still need more evidence. This study focused on deciphering the genetic relationship between wild and cultivated Z. latifolia, as well as the corresponding parasitic U. esculenta. Twelve microsatellites markers were used to study the genetic variations of 32 wild populations and 135 landraces of Z. latifolia. Model simulations based on approximate Bayesian computation (ABC) were then performed to hierarchically infer the population history. We also analyzed the ITS sequences of the smut fungus U. esculenta to reveal its genetic structure. Our results indicated a significant genetic divergence between cultivated Z. latifolia and its wild ancestors. The wild Z. latifolia populations showed significant hierarchical genetic subdivisions, which may be attributed to the joint effect of isolation by distance and hydrological unconnectedness between watersheds. Cultivated Z. latifolia was supposedly domesticated once in the low reaches of the Yangtze River. The genetic structure of U. esculenta also indicated a single domestication event, and the genetic variations in this fungus might be associated with the diversification of cultivars. These findings provided molecular evidence in accordance with the historical literature that addressed the domestication of cultivated Z. latifolia involved adaptive evolution driven by artificial selection in both the plant and fungus.

Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for Ceratonia siliqua (Leguminosae)

PREMISE OF THE STUDY

Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected.

METHODS

In this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, Ceratonia siliqua. Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results.

RESULTS

The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates.

DISCUSSION

Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.

GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars

Information on the distribution of genetic variation is essential to preserve olive germplasm from erosion and to recover alleles lost through selective breeding. In addition, knowledge on population structure and genotype-phenotype associations is crucial to support modern olive breeding programs that must respond to new environmental conditions imposed by climate change and novel biotic/abiotic stressors. To further our understanding of genetic variation in the olive, we performed genotype-by-sequencing on a panel of 94 Italian olive cultivars. A reference-based and a reference-independent SNP calling pipeline generated 22,088 and 8,088 high-quality SNPs, respectively. Both datasets were used to model population structure via parametric and non parametric clustering. Although the two pipelines yielded a 3-fold difference in the number of SNPs, both described wide genetic variability among our study panel and allowed individuals to be grouped based on fruit weight and the geographical area of cultivation. Multidimensional scaling analysis on identity-by-state allele-sharing values as well as inference of population mixtures from genome-wide allele frequency data corroborated the clustering pattern we observed. These findings allowed us to formulate hypotheses about geographical relationships of Italian olive cultivars and to confirm known and uncover novel cases of synonymy.

Demography and its effects on genomic variation in crop domestication

Over two thousand plant species have been modified morphologically through cultivation and human use. Here, we review three aspects of crop domestication that are currently undergoing marked revisions, due to analytical advancements and their application to whole genome resequencing (WGS) data. We begin by discussing the duration and demographic history of domestication. There has been debate as to whether domestication occurred quickly or slowly. The latter is tentatively supported both by fossil data and application of WGS data to sequentially Markovian coalescent methods that infer the history of effective population size. This history suggests the possibility of extended human impacts on domesticated lineages prior to their purposeful cultivation. We also make the point that demographic history matters, because it shapes patterns and levels of extant genetic diversity. We illustrate this point by discussing the evolutionary processes that contribute to the empirical observation that most crops examined to date have more putatively deleterious alleles than their wild relatives. These deleterious alleles may contribute to genetic load within crops and may be fitting targets for crop improvement. Finally, the same demographic factors are likely to shape the spectrum of structural variants (SVs) within crops. SVs are known to underlie many of the phenotypic changes associated with domestication and crop improvement, but we currently lack sufficient knowledge about the mechanisms that create SVs, their rates of origin, their population frequencies and their phenotypic effects.

Genetic flow among olive populations within the Mediterranean basin

Background

The olive tree is a typical crop of the Mediterranean basin where it shows a wide diversity, accounting for more than 2,600 cultivars. The ability to discriminate olive cultivars and determine their genetic variability is pivotal for an optimal exploitation of olive genetic resources.

Methods

We investigated the genetic diversity within 128 olive accessions belonging to four countries in the Mediterranean Basin (Italy, Algeria, Syria, and Malta), with the purpose of better understanding the origin and spread of the olive genotypes across Mediterranean Basin countries. Eleven highly polymorphic simple sequence repeat (SSR) markers were used and proved to be very informative, producing a total of 179 alleles.

Results

Cluster analysis distinguished three main groups according to their geographical origin, with the current sample of Maltese accessions included in the Italian group. Phylogenetic analysis further differentiated Italian and Maltese olive accessions, clarifying the intermediate position of Maltese accessions along the x/y-axes of principal coordinate analysis (PCoA). Model-based and neighbor clustering, PCoA, and migration analysis suggested the existence of two different gene pools (Algerian and Syrian) and that the genetic exchange occurred between the Syrian, Italian and Maltese populations.

Discussion

The close relationship between Syrian and Italian and Maltese olives was consistent with the historical domestication and migration of olive tree from the North Levant to eastern Mediterranean basin. This study lays the foundations for a better understanding of olive genetic diversity in the Mediterranean basin and represents a step toward an optimal conservation and exploitation of olive genetic resources.

Cultivar influence on variability in olive oil phenolic profiles determined through an extensive germplasm survey

Despite the evident influence of the cultivar on olive oil composition, few studies have been devoted to exploring the variability of phenols in a representative number of monovarietal olive oils. In this study, oil samples from 80 cultivars selected for their impact on worldwide oil production were analyzed to compare their phenolic composition by using a method based on LC-MS/MS. Secoiridoid derivatives were the most concentrated phenols in virgin olive oil, showing high variability that was significantly due to the cultivar. Multivariate analysis allowed discrimination between four groups of cultivars through their phenolic profiles: (i) richer in aglycon isomers of oleuropein and ligstroside; (ii) richer in oleocanthal and oleacein; (iii) richer in flavonoids; and (iv) oils with balanced but reduced phenolic concentrations. Additionally, correlation analysis showed no linkage among aglycon isomers and oleocanthal/oleacein, which can be explained by the enzymatic pathways involved in the metabolism of both oleuropein and ligstroside.

Origin and diversity of an underutilized fruit tree crop, cempedak (Artocarpus integer, Moraceae)

PREMISE OF THE STUDY

Underutilized crops and their wild relatives are important resources for crop improvement and food security. Cempedak [Artocarpus integer (Thunb). Merr.] is a significant crop in Malaysia but underutilized elsewhere. Here we performed molecular characterization of cempedak and its putative wild relative bangkong (Artocarpus integer (Thunb). Merr. var. silvestris Corner) to address questions regarding the origin and diversity of cempedak.

METHODS

Using data from 12 microsatellite loci, we assessed the genetic diversity and genetic/geographic structure for 353 cempedak and 175 bangkong accessions from Malaysia and neighboring countries and employed clonal analysis to characterize cempedak cultivars. We conducted haplotype network analyses on the trnH-psbA region in a subset of these samples. We also analyzed key vegetative characters that reportedly differentiate cempedak and bangkong.

KEY RESULTS

We show that cempedak and bangkong are sister taxa and distinct genetically and morphologically, but the directionality of domestication origin is unclear. Genetic diversity was generally higher in bangkong than in cempedak. We found a distinct genetic cluster for cempedak from Borneo as compared to cempedak from Peninsular Malaysia. Finally, cempedak cultivars with the same names did not always share the same genetic fingerprint.

CONCLUSIONS

Cempedak origins are complex, with likely admixture and hybridization with bangkong, warranting further investigation. We provide a baseline of genetic diversity of cempedak and bangkong in Malaysia and found that germplasm collections in Malaysia represent diverse coverage of the four cempedak genetic clusters detected.

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.

Genetic Diversity and Domestication Footprints of Chinese Cherry [Cerasus pseudocerasus (Lindl.) G.Don] as Revealed by Nuclear Microsatellites

Chinese cherry [Cerasus pseudocerasus (Lindl.) G.Don] is a commercially important fruit crop in China, but its structure patterns and domestication history remain imprecise. To address these questions, we estimated the genetic structure and domestication history of Chinese cherry using 19 nuclear microsatellite markers and 650 representative accessions (including 118 Cerasus relatives) selected throughout their natural eco-geographical distributions. Our structure analyses detected no genetic contribution from Cerasus relatives to the evolution history of Chinese cherry. A separate genetic structure was detected in wild Chinese cherries and rough geographical structures were observed in cultivated Chinese cherries. One wild (wild Chinese cherry, WC) and two cultivated (cultivated Chinese cherry, CC1 and CC2) genetic clusters were defined. Our approximate Bayesian computation analyses supported an independent domestication history with two domestication events for CC1 and CC2, happening about 3900 and 2200 years ago, respectively. Moderate loss of genetic diversity, over 1000-year domestication bottlenecks and divergent domestication in fruit traits were also detected in cultivated Chinese cherries, which is highly correlated to long-term clonal propagation and different domestication trends and preferences. Our study is the first to comprehensively and systematically investigate the structure patterns and domestication history for Chinese cherry, providing important references for revealing the evolution and domestication history of perennial woody fruit trees.

Domestication Origin and Breeding History of the Tea Plant (Camellia sinensis) in China and India Based on Nuclear Microsatellites and cpDNA Sequence Data

Although China and India are the two largest tea-producing countries, the domestication origin and breeding history of the tea plant in these two countries remain unclear. Our previous study suggested that the tea plant includes three distinct lineages (China type tea, Chinese Assam type tea and Indian Assam type tea), which were independently domesticated in China and India, respectively. To determine the origin and historical timeline of tea domestication in these two countries we used a combination of 23 nSSRs (402 samples) and three cpDNA regions (101 samples) to genotype domesticated tea plants and its wild relative. Based on a combination of demographic modeling, NewHybrids and Neighbour joining tree analyses, three independent domestication centers were found. In addition, two origins of Chinese Assam type tea were detected: Southern and Western Yunnan of China. Results from demographic modeling suggested that China type tea and Assam type tea first diverged 22,000 year ago during the last glacial maximum and subsequently split into the Chinese Assam type tea and Indian Assam type tea lineages 2770 year ago, corresponding well with the early record of tea usage in Yunnan, China. Furthermore, we found that the three tea types underwent different breeding histories where hybridization appears to have been the most important approach for tea cultivar breeding and improvements: a high proportion of the hybrid lineages were found to be F2 and BCs. Collectively, our results underscore the necessity for the conservation of Chinese Assam type tea germplasm and landraces as a valuable resource for future tea breeding.

Long and attenuated: comparative trends in the domestication of tree fruits

This paper asks whether we can identify a recurrent domestication syndrome for tree crops (fruits, nuts) and track archaeologically the evolution of domestication of fruits from woody perennials. While archaeobotany has made major contributions to documenting the domestication process in cereals and other annual grains, long-lived perennials have received less comparative attention. Drawing on examples from across Eurasia, comparisons suggest a tendency for the larger domesticated fruits to contain seeds that are proportionally longer, thinner and with more pointed (acute to attenuated) apices. Therefore, although changes in flavour, such as increased sweetness, are not recoverable, seed metrics and shape provide an archaeological basis for tracking domestication episodes in fruits from woody perennials. Where available, metrical data suggest length increases, as well as size diversification over time, with examples drawn from the Jomon of Japan (Castanea crenata), Neolithic China (Prunus persica) and the later Neolithic of the Near East (Olea europaea, Phoenix dactylifera) to estimate rates of change. More limited data allow us to also compare Mesoamerica avocado (Persea americana) and western Pacific Canarium sp. nuts and Spondias sp. fruits. Data from modern Indian jujube (Ziziphus mauritiana) are also considered in relation to seed length:width trends in relation to fruit contents (flesh proportion, sugar content). Despite the long generation time in tree fruits, rates of change in their seeds are generally comparable to rates of phenotypic evolution in annual grain crops, suggesting that gradual evolution via unconscious selection played a key role in initial processes of tree domestication, and that this had begun in the later Neolithic once annual crops had been domesticated, in both west and east Asia.

Monumental olive trees of Cyprus contributed to the establishment of the contemporary olive germplasm

Even though Cyprus was an important crossing point for the westward spread of olive, and one of the primary regions of domestication, its genetic recourses remain uncharted at a great extent. Throughout the centuries, a number of ancient olive trees remain in the same orchards, contributing to Cypriot oleiculture and society. In an attempt to explore this monumental genetic pool, a survey was conducted to identify centennial olive trees in rural provinces of Cyprus. Microsatellites were employed in order to study their genetic composition (including rootstocks when feasible) and to establish possible associations among genotypes. High numbers of specific alleles, suggestive of the distinctiveness of this germplasm, were detected, and both grafting and rootstock propagation was verified. Moreover, it was determined by Bayesian structural and network reticulate analysis that centennial olives can be divided in two discrete genetic clusters having intermediate admixed accessions. Furthermore, it was determined that all contemporary Cypriot cultivars, that were included in the present study, were highly affiliated exclusively to one genetic group, a strong evidence of selection among elite clones. The information acquired from the current study reveals the genetic rareness of this material and its contribution to the current olive germplasm.

Variability in Susceptibility to Anthracnose in the World Collection of Olive Cultivars of Cordoba (Spain)

Anthracnose of olive (Olea europaea ssp. europaea L.), caused by Colletotrichum species, is a serious disease causing fruit rot and branch dieback, whose epidemics are highly dependent on cultivar susceptibility and environmental conditions. Over a period of 10 years, there have been three severe epidemics in Andalusia (southern Spain) that allowed us to complete the assessment of the World Olive Germplasm Bank of Córdoba, one of the most important cultivar collections worldwide.A total of 308 cultivars from 21 countries were evaluated, mainly Spain (174 cvs.), Syria (29 cvs.), Italy (20 cvs.), Turkey (15 cvs.), and Greece (16 cvs.). Disease assessments were performed using a 0-10 rating scale, specifically developed to estimate the incidence of symptomatic fruit in the tree canopy. Also, the susceptibility of five reference cultivars was confirmed by artificial inoculation. Because of the direct relationship between the maturity of the fruit and their susceptibility to the pathogen, evaluations were performed at the end of fruit ripening, which forced coupling assessments according to the maturity state of the trees. By applying the cluster analysis to the 308 cultivars, these were classified as follows: 66 cvs. highly susceptible (21.4%), 83 cvs. susceptible (26.9%), 66 cvs. moderately susceptible (21.4%), 61 cvs. resistant (19.8%), and 32 cvs. highly resistant (10.4%). Representative cultivars of these five categories are "Ocal," "Lechín de Sevilla," "Arbequina," "Picual," and "Frantoio," respectively. With some exceptions, such as cvs. Arbosana, Empeltre and Picual, most of the Spanish cultivars, such as "Arbequina," "Cornicabra," "Hojiblanca," "Manzanilla de Sevilla," "Morisca," "Picudo," "Farga," and "Verdial de Huévar" are included in the categories of moderately susceptible, susceptible or highly susceptible. The phenotypic evaluation of anthracnose reaction is a limiting factor for the selection of olive cultivars by farmers, technicians, and breeders.