Abstract
Background: The species Olea europaea includes cultivated varieties (subsp. europaea var. europaea), wild plants (subsp. europaea var. sylvestris), and five other subspecies spread over almost all continents. Single nucleotide polymorphisms in the expressed sequence tag able to underline intra-species differentiation are 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.
Highlights
Olive (Olea europaea L.) is a long-living widespread tree species
Based on the evidence of the previous studies, this work aimed to identify potential functional markers for differentiating cultivated from wild olive trees, by addressing the following questions—(a) what genes distinguish cultivars from oleasters and guanchica olives? (b) what are the functions of differently evolved genes? (c) which of these gene polymorphisms could be introgressed into cultivated varieties through genomic-assisted breeding, to improve their performance?
General relationships within populations and amongst populations were described through a principal coordinate analysis (PCoA) performed by GenAlEx 6.5, based on a covariance matrix created from pairwise genetic distances [51], while the three-dimensional visualization was made by the online tool Cubemaker
Summary
Olive (Olea europaea L.) is a long-living widespread tree species. Its genetic patrimony includes thousands of cultivated varieties, wild olives, and related subspecies, such as cuspidata, laperrinei, cerasiformis, maroccana, and guanchica, which grow in natural areas of different continents [1,2,3,4,5].The cultivated and wild ( named oleaster) forms of olive (subsp. europaea, var. europaea and sylvestris, respectively), typical of the Mediterranean area, are diploid, with 23 chromosomes and a genome size of about 1.48 Giga base pairs [6]. The high genetic variability of cultivated olive [8,9,10,11,12] (mainly related to its allogamy), the lack of turnover with modern cultivars, a remarkable tree longevity, and the capacity to survive out of managed cultivation, allowed it to spread over a wide range of environments [13,14,15,16] Inside this diversified scenario, the debate on olive domestication and the contribution of oleasters and related subspecies to this process, is still open and controversial [17,18,19,20,21,22]. 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. 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
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