Association Study of the 5'UTR Intron of the FAD2-2 Gene With Oleic and Linoleic Acid Content in Olea europaea L.

Amelia Salimonti,Enzo Perri,Elvira Romano,Sabrina Micali,Alessandro Tondelli,Annamaria Ienco,Massimiliano Pellegrino,Francesca L Conforti,Samanta Zelasco,Fabrizio Carbone,Cinzia Benincasa

doi:10.3389/fpls.2020.00066

Abstract

Cultivated olive (Olea europaea L. subsp. europaea var. europaea) is the most ancient and spread tree crop in the Mediterranean basin. An important quality trait for the extra virgin olive oil is the fatty acid composition. In particular, a high content of oleic acid and low of linoleic, linolenic, and palmitic acid is considered very relevant in the health properties of the olive oil. The oleate desaturase enzyme encoding-gene (FAD2-2) is the main responsible for the linoleic acid content in the olive fruit mesocarp and, therefore, in the olive oil revealing to be the most important candidate gene for the linoleic acid biosynthesis. In this study, an in silico and structural analysis of the 5′UTR intron of the FAD2-2 gene was conducted with the aim to explore the natural sequence variability and its role in the gene expression regulation. In order to identify functional allele variants, the 5′UTR intron was isolated and partially sequenced in 97 olive cultivars. The sequence analysis allowed to find a 117-bp insertion including two long duplications never found before in FAD2-2 genes in olive and the existence of many intron-mediated enhancement (IME) elements. The sequence polymorphism analysis led to detect 39 SNPs. The candidate gene association study conducted for oleic and linoleic acids content revealed seven SNPs and one indel significantly associated able to explain a phenotypic variation ranging from 7% to 16% among the years. Our study highlighted new structural variants within the FAD2-2 gene in olive, putatively involved in the regulation mechanisms of gene expression associated with the variation of the content of oleic and linoleic acid.

Highlights

Cultivated olive (Olea europaea L. subsp. europaea var. europaea) is the most ancient and spread tree crop in the Mediterranean basin
Significant correlations were obtained for temperature among the years with a Pearson’s correlation index ranging from 0.95 to 0.99 while no significant correlations were observed for rainfall among the year except for 2003, 2004 versus 2007 year (Table 1), indicating a large rainfall fluctuation over the years
A wide range of variation was observed for the acidic composition covering a large part of the natural variation described for olive (Table S1)

Summary

Introduction

Cultivated olive (Olea europaea L. subsp. europaea var. europaea) is the most ancient and spread tree crop in the Mediterranean basin. The species is characterized by a very big genome size (1C = 1,400–1,500 Mbp) (Loureiro et al, 2007; Unver et al, 2017), a crosspollinating reproductive biology leading to a high heterozygosity (Dìez et al, 2011; Besnard et al, 2014; Kaya et al, 2016) and a long generation time All these aspects, together with the scarce knowledge about the inheritance of most genes controlling agronomical performance and quality traits, have severely restricted breeding strategies to clonal or varietal selection (Rugini et al, 2011). Biparental QTL mapping has many limitations in tree species due to their long generation times and juvenile period, high levels of heterozygosity, time-consuming trait evaluation, slow physiological maturation, and high levels of genetic variation between parents (Tian et al, 2014; Kaya et al, 2016)

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