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

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.

Elucidation of the Origin of the Monumental Olive Tree of Vouves in Crete, Greece

“…sylvestris and another comprising O. europaea subsp. guanchica [40] in contrast to the present work where only one group is detected. This could evidence one of the limitations of the sampling of the present study associated with non-representative number of accessions for some groups, such as guanchica.…”

How to Choose a Good Marker to Analyze the Olive Germplasm (Olea europaea L.) and Derived Products

“…In the olive, the first transcriptomics studies addressed the identification of genes associated with important agronomic traits, such as drupes and reproductive organs development, fruit metabolism and phenolic content during ripening, through strategies such as suppression subtractive hybridization (SSH) and expressed sequence tags (ESTs) analysis [166][167][168][169][170]. SNP variations in EST were used to investigate the functional role of SNPs in specific agronomical performances [152], to uncover functional polymorphism in cultivated and wild olives [171], to infer phylogenies on the Oleae tribe [172] and for genetic identification of wild genotypes [173,174].…”

Olive Oil Sensory Analysis as a Tool to Preserve and Valorize the Heritage of Centenarian Olive Trees

“…This biodiversity analysis can take into account several factors. A survey of the morphological characteristics of olive organs (olive leaves, flowers, fruits, and endocarps) is usually carried out in complement to some aspects of plant behavior, from which genetic markers are usually used for the identification and characterization of olive cultivars [13][14][15]. In other cases, the characterization focuses on different parameters of interest, such as the yield, resistance to pests and diseases or drought conditions, adaptation to mechanical harvest, or chemical quality of the olive oil [16][17][18][19].…”