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

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.

Evolutionary Plant Breeding as a Response to the Complexity of Climate Change

“…However, most of the strategies suggested are based on the identification and incorporation of traits conferring tolerance or resistance to specific biotic or abiotic stresses, failing to recognize the evolving nature of the challenge. This applies also to the attempts to stack tolerance to more than one stress, particularly when this is done in controlled conditions ( Menkir et al., 2020 ). Most of these solutions are “within the capacity for micro-evolutionary change of the parasite” ( Robinson, 2009 ), and several examples of accelerated evolutionary changes in disease organisms, agricultural pests, and weeds have been reported ( Palumbi, 2001 ; McDonald and Stukenbrock, 2016 ; Bøhn and Millstone, 2019 ).…”

CRISPR/Cas9 Based Site-Specific Modification of FAD2 cis-Regulatory Motifs in Peanut (Arachis hypogaea L)

“…FAD2 genes typically have a conserved single large intron in the 5′-untranslated region (UTR), which has been suggested to have enhancer activity in mediating transcriptional regulation. This has been shown in sesame ( Kim et al, 2006 ), and Brassica napus ( Xiao et al, 2014 ) by deletion mapping approaches and Arabidopsis and olives by gene association studies ( Menard et al, 2017 ; Salimonti et al, 2020 ).…”

The chromosome‐scale reference genome of safflower (Carthamus tinctorius) provides insights into linoleic acid and flavonoid biosynthesis

“…These results suggest that ABA signalling induces CarFAD2‐12 expression. A long intron in the 5′ UTR plays a role in the enhancement of FAD2 expression and further regulates LA content in seeds (Salimonti et al., 2020 ). Compared to other safflower CarFAD2 s, only CarFAD2‐12 has a large intron in the 5′ UTR (Figure S48 ).…”