Utility of EST-SNP Markers for Improving Management and Use of Olive Genetic Resources: A Case Study at the Worldwide Olive Germplasm Bank of Córdoba

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.

New insights in the Spanish gene pool of olive (Olea europaea L.) preserved ex situ and in situ based on high-throughput molecular markers

In Spain, several local studies have highlighted the likely presence of unknown olive cultivars distinct from the approximately 260 ones previously described in the literature. Furthermore, recent advancements in identification techniques have significantly enhanced in terms of efficacy and precision. This scenario motivated a new nationwide prospecting effort aimed at recovering and characterizing new cultivated germplasm using high-throughput molecular markers. In the present study, the use of 96 EST-SNP markers allowed the identification of a considerable amount of new material (173 new genotypes) coming from areas with low intensification of production in different regions of Spain. As a result, the number of distinct national genotypes documented in the World Olive Germplasm Bank of IFAPA, Córdoba (WOGBC-ESP046) increased to 427. Likewise, 65 and 24 new synonymy and homonymy cases were identified, respectively. This rise in the number of different national cultivars allowed to deepen the knowledge about the underlying genetic structure. The great genetic variability of Spanish germplasm was confirmed, and a new hot spot of diversity was identified in the northern regions of La Rioja and Aragon. Analysis of the genetic structure showed a clear separation between the germplasm of southern and northern-northeastern Spain and indicated a significantly higher level of admixture in the latter. Given the expansion of modern olive cultivation with only a few cultivars, this cryptic germplasm is in great danger of disappearing. This underlines the fact that maintaining as many cultivars as possible will increase the genetic variability of the olive gene pool to meet the future challenges of olive cultivation.

Characterization of the Metabolic Profile of Olive Tissues (Roots, Stems and Leaves): Relationship with Cultivars' Resistance/Susceptibility to the Soil Fungus Verticillium dahliae

Verticillium wilt of olive (VWO) is one of the most widespread and devastating olive diseases in the world. Harnessing host resistance to the causative agent is considered one of the most important measures within an integrated control strategy of the disease. Aiming to understand the mechanisms underlying olive resistance to VWO, the metabolic profiles of olive leaves, stems and roots from 10 different cultivars with varying levels of susceptibility to this disease were investigated by liquid chromatography coupled to mass spectrometry (LC-MS). The distribution of 56 metabolites among the three olive tissues was quantitatively assessed and the possible relationship between the tissues' metabolic profiles and resistance to VWO was evaluated by applying unsupervised and supervised multivariate analysis. Principal component analysis (PCA) was used to explore the data, and separate clustering of highly resistant and extremely susceptible cultivars was observed. Moreover, partial least squares discriminant analysis (PLS-DA) models were built to differentiate samples of highly resistant, intermediate susceptible/resistant, and extremely susceptible cultivars. Root models showed the lowest classification capability, but metabolites from leaf and stem were able to satisfactorily discriminate samples according to the level of susceptibility. Some typical compositional patterns of highly resistant and extremely susceptible cultivars were described, and some potential resistance/susceptibility metabolic markers were pointed out.

One hundred single-copy nuclear sequence markers for olive variety identification: a case of fingerprinting database construction in China

Olive is an ancient oil-producing tree, widely cultivated in Mediterranean countries, and now spread to other areas of the world, including China. Recently, several molecular databases were constructed in different countries and platforms for olive identification using simple sequence repeats (SSRs) or single-nucleotide polymorphisms (SNPs). However, comparing their results across laboratories was difficult. Herein, hundreds of polymorphic single-copy nuclear sequence markers were developed from the olive genome. Using the advantage of multiplex PCR amplification and high-throughput sequencing, a fingerprint database was constructed for the majority of olives cultivated in China. We used 100 high-quality sequence loci and estimated the genetic diversity and structure among all these varieties. We found that compared with that based on SSRs, the constructed fingerprint database based on these 100 sequences or a few of them, could provide a reliable olive variety identification platform in China, with high discrimination among different varieties using the principle of BLAST algorithm. An example of such identification platform based on this study was displayed on the web for the olive database in China (http://olivedb.cn/jianding). After resolving redundant genotypes, we identified 126 olive varieties with distinct genotypes in China. These varieties could be divided into two clusters, and it was revealed that the grouping of the varieties has a certain relationship with their origin. Herein, it is concluded that these single-copy orthologous nuclear sequences could be used to construct a universal fingerprint database of olives across different laboratories and platforms inexpensively. Based on such a database, variety identification can be performed easily by any laboratory, which would further facilitate olive breeding and variety exchange globally.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01434-9.

Genealogical tracing of Olea europaea species and pedigree relationships of var. europaea using chloroplast and nuclear markers

BACKGROUND

Olive is one of the most cultivated species in the Mediterranean Basin and beyond. Despite being extensively studied for its commercial relevance, the origin of cultivated olive and the history of its domestication remain open questions. Here, we present a genealogical and kinship relationships analysis by mean of chloroplast and nuclear markers of different genera, subgenus, species, subspecies, ecotypes, cultivated, ancient and wild types, which constitutes one of the most inclusive research to date on the diversity within Olea europaea species. A complete survey of the variability across the nuclear and plastid genomes of different genotypes was studied through single nucleotide polymorphisms, indels (insertions and deletions), and length variation.

RESULTS

Fifty-six different chlorotypes were identified among the Oleaceae family including Olea europaea, other species and genera. The chloroplast genome evolution, within Olea europaea subspecies, probably started from subsp. cuspidata, which likely represents the ancestor of all the other subspecies and therefore of wild types and cultivars. Our study allows us to hypothesize that, inside the subspecies europaea containing cultivars and the wild types, the ancestral selection from var. sylvestris occurred both in the eastern side of the Mediterranean and in the central-western part of Basin. Moreover, it was elucidated the origin of several cultivars, which depends on the introduction of eastern cultivars, belonging to the lineage E1, followed by crossing and replacement of the autochthonous olive germplasm of central-western Mediterranean Basin. In fact, our study highlighted that two main 'founders' gave the origin to more than 60% of analyzed olive cultivars. Other secondary founders, which strongly contributed to give origin to the actual olive cultivar diversity, were already detected.

CONCLUSIONS

The application of comparative genomics not only paves the way for a better understanding of the phylogenetic relationships within the Olea europaea species but also provides original insights into other elusive evolutionary processes, such as chloroplast inheritance and parentage inside olive cultivars, opening new scenarios for further research such as the association studies and breeding programs.

Genetic Diversity of Common Olive (Olea europaea L.) Cultivars from Nikita Botanical Gardens Collection Revealed Using RAD-Seq Method

In different countries, interest in the commercial cultivation of the olive has recently greatly increased, which has led to the expansion of its range. The Crimean Peninsula is the northern limit of the common olive (Olea europaea L.) range. A unique collection of common olive's cultivars and hybrids has been collected in the Nikitsky Botanical Gardens (NBG). The aim of this study was to assess the genetic diversity of 151 samples (total of several biological replicates of 46 olive cultivars including 29 introduced and 11 indigenous genotypes) using the ddRAD sequencing method. Structural analysis showed that the studied samples are divided into ten groups, each of which mainly includes cultivars of the same origin. Cultivars introduced to the Crimean Peninsula from different regions formed separate groups, while local cultivars joined different groups depending on their origin. Cultivars of Crimean origin contain admixtures of mainly Italian and Caucasian cultivars' genotypes. Our study showed that the significant number of Crimean cultivars contains an admixture of the Italian cultivar "Coreggiolo". Genetic analysis confirmed the synonymy for the cv. "Otur" and "Nikitskaya 2", but not for the other four putative synonyms. Our results revealed the genetic diversity of the olive collection of NBG and provided references for future research studies, especially in selection studies for breeding programs.

Identification of Genetic Markers and Genes Putatively Involved in Determining Olive Fruit Weight

The fruit size of a cultivated olive tree is consistently larger than its corresponding wild relatives because fruit size is one of the main traits associated with olive tree domestication. Additionally, large fruit size is one of the main objectives of modern olive breeding programs. However, as the long juvenile period is one main hindrance in classic breeding approaches, obtaining genetic markers associated with this trait is a highly desirable tool. For this reason, GWAS analysis of both genetic markers and the genes associated with fruit size determination, measured as fruit weight, was herein carried out in 50 genotypes, of which 40 corresponded to cultivated and 10 to wild olive trees. As a result, 113 genetic markers were identified, which showed a very high statistically significant correlation with fruit weight variability, p < 10−10. These genetic markers corresponded to 39 clusters of genes in linkage disequilibrium. The analysis of a segregating progeny of the cross of “Frantoio” and “Picual” cultivars allowed us to confirm 10 of the 18 analyzed clusters. The annotation of the genes in each cluster and the expression pattern of the samples taken throughout fruit development by RNAseq enabled us to suggest that some studied genes are involved in olive fruit weight determination.

Seedling Selection in Olive Breeding Progenies

The long juvenile period in olive (Olea europaea L.) delays the evaluation of characters of interest and prolongs the selection of new cultivars in the breeding programs. Therefore, it is important to use accurate selection criteria and appropriate selection pressure to make an effective identification of the superior genotypes and to identify which parents transmit lower juvenile periods to their descendants. In this study, the juvenile period, vigor, fruit fresh weight, and oil content of fruit on a dry weight basis were evaluated in 1568 genotypes from two independent open-pollinated populations; G07, that included 520 genotypes from 25 cultivars and 1 breeding selection and G14, with 1048 genotypes from 13 cultivars. This evaluation was used to test different selection criteria and define optimal selection pressure at the initial stage of an olive breeding program. Wide ranges of variation were obtained for all the characters measured, with higher variability within progenies than between progenies. “Askal” and “Barnea” seem to be the cultivars transmitting the shorter juvenile period to the descendants. In the case of fruit fresh weight and oil content, transgression of variability limits of the parents was observed. Significant correlation was found between mean values of fruit fresh weight of progenies and their parents for G07 (0.59) and G14 (0.95). Selection was made using two selection index formulas (SI1 and SI2). A high coincidence was found between the individuals selected by both formulas and the correspondent selection pressures applied; 15% for SI1, and 14% for SI2. A wide variability in the percentage of selected genotypes was found, from no individuals selected from some progenies to more than 20% of genotypes selected in some others. These results underline the need to explore the wide genetic variability currently hosted in germplasm collections for an optimal choice of parents in olive breeding works.