High Levels of Variation Within Gene Sequences of Olea europaea L.

Nicolò G M Cultrera,Roberto Mariotti,Luciana Baldoni,Livia Lucentini,Vania Sarri,Consolacion Guerrero Ruiz,Marilena Ceccarelli,Soraya Mousavi,Fiammetta Alagna

doi:10.3389/fpls.2018.01932

Abstract

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.

Highlights

Cultivated olive (Olea europaea L. subsp. europaea var. europaea) is the most important oil tree crop of the Mediterranean basin
Combined approaches, including cloning and direct sequencing performed by means of locus- and allele-specific primers, allowed us to distinguish all alleles at the four loci on 90 olive cultivars
Introns carried most of polymorphisms (91.3%), including SNPs, indels, tandem repeats and simple sequence repeats (SSRs)

Summary

Introduction

Cultivated olive (Olea europaea L. subsp. europaea var. europaea) is the most important oil tree crop of the Mediterranean basin. Sylvestris, named as oleaster), followed by empirical local selection, probably associated to episodic varietal substitution, leading to the current varietal framework (Breton et al, 2009; Besnard et al, 2013, 2018; Hosseini-Mazinani et al, 2014; Diez et al, 2015) Since this complex germplasm represents a valuable source of useful traits, a great effort is required to explore, manage, characterize and identify all genotypes. These markers were identified on olive gene sequences and they have been used for cultivar genotyping (Reale et al, 2006; Consolandi et al, 2007; Hakim et al, 2009; Rossi et al, 2012; Kaya et al, 2013; Sabetta et al, 2013; Kalogianni et al, 2015; Uncu et al, 2015; Bazakos et al, 2016), or to reconstruct the phylogenetic relationships within the olive complex (Besnard et al, 2007; Besnard and El Bakkali, 2014; Biton et al, 2015)

Methods

Results

Discussion

Conclusion