Characterization and validation of olive FAD and SAD gene families: expression analysis in different tissues and during fruit development

Transcriptomic Analysis During Olive Fruit Development and Expression Profiling of Fatty Acid Desaturase Genes

The olive fruit is a drupe whose development and ripening takes several months from flowering to full maturation. During this period, several biochemical and physiological changes occur that affect the skin color, texture, composition, and size of the mesocarp. The final result is a fruit rich in fatty acids, phenolic compounds, tocopherols, pigments, sterols, terpenoids, and other compounds of nutritional interest. In this work, a transcriptomic analysis was performed using flowers (T0) and mesocarp tissue at seven different stages during olive fruit development and ripening (T1-T7) of the 'Picual' cultivar. A total of 1755 genes overexpressed at any time with respect to the flowering stage were further analyzed. These genes were grouped into eight clusters based on their expression profile. The gene enrichment analysis revealed the most relevant biological process of every cluster. Highlighting the important role of hormones at very early stages of fruit development (T1, Cluster 1), whereas genes involved in fatty acid biosynthesis were relevant throughout the fruit developmental process. Hence, genes coding for different fatty acid desaturase (SAD, FAD2, FAD3, FAD4, FAD5, FAD6, and FAD7) enzymes received special attention. In particular, 26 genes coding for different fatty acid desaturase enzymes were identified in the 'Picual' genome, contributing to the improvement of the genome annotation. The expression pattern of these genes during fruit development corroborated their role in determining fatty acid composition.

Systematic characterization of CsbZIP transcription factors in Camelina sativa and functional analysis of CsbZIP-A12 mediating regulation of unsaturated fatty acid-enriched oil biosynthesis

The basic leucine zipper (bZIP) transcription factors (TFs) function importantly in numerous life processes in plants. However, bZIP members and their biological roles remain unknown in Camelina sativa, a worldwide promising oil crop. Here, 220 CsbZIP proteins were identified in camelina and classified into thirteen groups. Two and 347 pairs of tandem and segmental duplication genes were detected to be underwent purification selection, with segmental duplication as the main driven-force of CsbZIP gene family expansion. Most CsbZIP genes displayed a tissue-specific expression pattern. Particularly, CsbZIP-A12 significantly positively correlated with many FA/oil biosynthesis-related genes, indicating CsbZIP-A12 may regulate lipid biosynthesis. Notably, yeast one-hybrid (Y1H), β-Glucuronidase (GUS), dual-luciferase (LUC) and EMSA assays evidenced that CsbZIP-A12 located in nucleus interacted with the promoters of CsSAD2-3 and CsFAD3-3 genes responsible for unsaturated fatty acid (UFA) synthesis, thus activating their transcriptions. Overexpression of CsbZIP-A12 led to an increase of total lipid by 3.275 % compared to the control, followed with oleic and α-linolenic acid levels enhanced by 3.4 % and 5.195 %, and up-regulated the expressions of CsSAD2-3, CsFAD3-3 and CsPDAT2-3 in camelina seeds. Furthermore, heterogeneous expression of CsbZIP-A12 significantly up-regulated the expressions of NtSAD2, NtFAD3 and NtPDAT genes in tobacco plants, thereby improving the levels of total lipids and UFAs in both leaves and seeds without negative effects on other agronomic traits. Together, our findings suggest that CsbZIP-A12 upregulates FA/oil biosynthesis by activating CsSAD2-3 and CsFAD3-3 as well as possible other related genes. These data lay a foundation for further functional analyses of CsbZIPs, providing new insights into the TF-based lipid metabolic engineering to increase vegetable oil yield and health-beneficial quality in oilseeds.

In Silico Identification and Characterization of Fatty Acid Desaturase (FAD) Genes in Argania spinosa L. Skeels: Implications for Oil Quality and Abiotic Stress

Fatty acid desaturase (FAD) is the key enzyme that leads to the formation of unsaturated fatty acids by introducing double bonds into hydrocarbon chains, and it plays a critical role in plant lipid metabolism. However, no data are available on enzyme-associated genes in argan trees. In addition, a candidate gene approach was adopted to identify and characterize the gene sequences of interest that are potentially involved in oil quality and abiotic stress. Based on phylogenetic analyses, 18 putative FAD genes of Argania spinosa L. (AsFAD) were identified and assigned to three subfamilies: stearoyl-ACP desaturase (SAD), Δ-12 desaturase (FAD2/FAD6), and Δ-15 desaturase (FAD3/FAD7). Furthermore, gene structure and motif analyses revealed a conserved exon-intron organization among FAD members belonging to the various oil crops studied, and they exhibited conserved motifs within each subfamily. In addition, the gene structure shows a wide variation in intron numbers, ranging from 0 to 8, with two highly conserved intron phases (0 and 1). The AsFAD and AsSAD subfamilies consist of three (H(X)2-4H, H(X)2-3HH, and H/Q (X)2-3HH) and two (EEN(K)RHG and DEKRHE) conserved histidine boxes, respectively. A set of primer pairs were designed for each FAD gene, and tested on DNA extracted from argan leaves, in which all amplicons of the expected size were produced. These findings of candidate genes in A spinosa L. will provide valuable knowledge that further enhances our understanding of the potential roles of FAD genes in the quality of oil and abiotic stress in the argan tree.

Effect of heterologous expression of FT gene from Medicago truncatula in growth and flowering behavior of olive plants

Olive (Olea europaea L. subsp. europaea) is one of the most important crops of the Mediterranean Basin and temperate areas worldwide. Obtaining new olive varieties adapted to climatic changing conditions and to modern agricultural practices, as well as other traits such as biotic and abiotic stress resistance and increased oil quality, is currently required; however, the long juvenile phase, as in most woody plants, is the bottleneck in olive breeding programs. Overexpression of genes encoding the 'florigen' Flowering Locus T (FT), can cause the loss of the juvenile phase in many perennials including olives. In this investigation, further characterization of three transgenic olive lines containing an FT encoding gene from Medicago truncatula, MtFTa1, under the 35S CaMV promoter, was carried out. While all three lines flowered under in vitro conditions, one of the lines stopped flowering after acclimatisation. In soil, all three lines exhibited a modified plant architecture; e.g., a continuous branching behaviour and a dwarfing growth habit. Gene expression and hormone content in shoot tips, containing the meristems from which this phenotype emerged, were examined. Higher levels of OeTFL1, a gene encoding the flowering repressor TERMINAL FLOWER 1, correlated with lack of flowering. The branching phenotype correlated with higher content of salicylic acid, indole-3-acetic acid and isopentenyl adenosine, and lower content of abscisic acid. The results obtained confirm that heterologous expression of MtFTa1 in olive induced continuous flowering independently of environmental factors, but also modified plant architecture. These phenotypical changes could be related to the altered hormonal content in transgenic plants.

Genome-Wide Identification and Expression Analysis of the Stearoyl-Acyl Carrier Protein Δ9 Desaturase Gene Family under Abiotic Stress in Barley

Stearoyl-acyl carrier protein (ACP) Δ9 desaturase (SAD) is a critical fatty acid dehydrogenase in plants, playing a prominent role in regulating the synthesis of unsaturated fatty acids (UFAs) and having a significant impact on plant growth and development. In this study, we conducted a comprehensive genomic analysis of the SAD family in barley (Hordeum vulgare L.), identifying 14 HvSADs with the FA_desaturase_2 domain, which were divided into four subgroups based on sequence composition and phylogenetic analysis, with members of the same subgroup possessing similar genes and motif structures. Gene replication analysis suggested that tandem and segmental duplication may be the major reasons for the expansion of the SAD family in barley. The promoters of HvSADs contained various cis-regulatory elements (CREs) related to light, abscisic acid (ABA), and methyl jasmonate (MeJA). In addition, expression analysis indicated that HvSADs exhibit multiple tissue expression patterns in barley as well as different response characteristics under three abiotic stresses: salt, drought, and cold. Briefly, this evolutionary and expression analysis of HvSADs provides insight into the biological functions of barley, supporting a comprehensive analysis of the regulatory mechanisms of oil biosynthesis and metabolism in plants under abiotic stress.

Key FAD2, FAD3, and SAD Genes Involved in the Fatty Acid Synthesis in Flax Identified Based on Genomic and Transcriptomic Data

FAD (fatty acid desaturase) and SAD (stearoyl-ACP desaturase) genes play key roles in the synthesis of fatty acids (FA) and determination of oil composition in flax (Linum usitatissimum L.). We searched for FAD and SAD genes in the most widely used flax genome of the variety CDC Bethune and three available long-read assembled flax genomes-YY5, 3896, and Atlant. We identified fifteen FAD2, six FAD3, and four SAD genes. Of all the identified genes, 24 were present in duplicated pairs. In most cases, two genes from a pair differed by a significant number of gene-specific SNPs (single nucleotide polymorphisms) or even InDels (insertions/deletions), except for FAD2a-1 and FAD2a-2, where only seven SNPs distinguished these genes. Errors were detected in the FAD2a-1, FAD2a-2, FAD3c-1, and FAD3d-2 sequences in the CDC Bethune genome assembly but not in the long-read genome assemblies. Expression analysis of the available transcriptomic data for different flax organs/tissues revealed that FAD2a-1, FAD2a-2, FAD3a, FAD3b, SAD3-1, and SAD3-2 were specifically expressed in embryos/seeds/capsules and could play a crucial role in the synthesis of FA in flax seeds. In contrast, FAD2b-1, FAD2b-2, SAD2-1, and SAD2-2 were highly expressed in all analyzed organs/tissues and could be involved in FA synthesis in whole flax plants. FAD2c-2, FAD2d-1, FAD3c-1, FAD3c-2, FAD3d-1, FAD3d-2, SAD3-1, and SAD3-2 showed differential expression under stress conditions-Fusarium oxysporum infection and drought. The obtained results are essential for research on molecular mechanisms of fatty acid synthesis, FAD and SAD editing, and marker-assisted and genomic selection for breeding flax varieties with a determined fatty acid composition of oil.

Meta-analysis of transcriptome reveals key genes relating to oil quality in olive

BACKGROUND

Olive oil contains monounsaturated oleic acid up to 83% and phenolic compounds, making it an excellent source of fat. Due to its economic importance, the quantity and quality of olive oil should be improved in parallel with international standards. In this study, we analyzed the raw RNA-seq data with a meta-analysis approach to identify important genes and their metabolic pathways involved in olive oil quality.

RESULTS

A deep search of RNA-seq published data shed light on thirty-nine experiments associated with the olive transcriptome, four of these proved to be ideal for meta-analysis. Meta-analysis confirmed the genes identified in previous studies and released new genes, which were not identified before. According to the IDR index, the meta-analysis had good power to identify new differentially expressed genes. The key genes were investigated in the metabolic pathways and were grouped into four classes based on the biosynthetic cycle of fatty acids and factors that affect oil quality. Galactose metabolism, glycolysis pathway, pyruvate metabolism, fatty acid biosynthesis, glycerolipid metabolism, and terpenoid backbone biosynthesis were the main pathways in olive oil quality. In galactose metabolism, raffinose is a suitable source of carbon along with other available sources for carbon in fruit development. The results showed that the biosynthesis of acetyl-CoA in glycolysis and pyruvate metabolism is a stable pathway to begin the biosynthesis of fatty acids. Key genes in oleic acid production as an indicator of oil quality and critical genes that played an important role in production of triacylglycerols were identified in different developmental stages. In the minor compound, the terpenoid backbone biosynthesis was investigated and important enzymes were identified as an interconnected network that produces important precursors for the synthesis of a monoterpene, diterpene, triterpene, tetraterpene, and sesquiterpene biosynthesis.

CONCLUSIONS

The results of the current investigation can produce functional data related to the quality of olive oil and would be a useful step in reducing the time of cultivar screening by developing gene specific markers in olive breeding programs, releasing also new genes that could be applied in the genome editing approach.

The Ancient Olive Trees (Olea europaea L.) of the Maltese Islands: A Rich and Unexplored Patrimony to Enhance Oliviculture

A prospecting campaign in the Maltese Islands has ensured the survival of several ancient olive trees (Olea europaea L.), genetically distant from known cultivars. Most of these plants were abandoned or partially cultivated. A two-year evaluation of fruit characteristics and compositions was performed on samples collected from the main representatives of these indigenous genotypes. Analyses were carried out using Gas Chromatography, High-Performance Liquid Chromatography and Near Infrared Spectrometry. Among the fruit samples, a wide range of variations was observed. Some of the genotypes showed fruit traits suitable for table olive production. This is the case of samples with a pulp/pit ratio higher than four, such as 1Wardija, 1Caritas, 1Plattini, 1Bingemma Malta and 3Loretu, whilst 1Bidni, 1Mellieha, 2Qnotta, 3Loretu, 1Bingemma Malta and 1Caritas were suitable for dual purpose. The total phenol content ranged from 6.3 (1Wardija) to 117.9 (2Mtarfa) g/kg of fresh pulp. The average percentage of MUFA was quite low for most of the varieties. These genotypes, which presumably originated in the Maltese Islands and are well adapted to the local pedo-climatic conditions, are being propagated for the following evaluation of their bio-agronomical performance (production, suitability to intensive cultivation, environmental sustainability, product quality, etc.). The purpose is to select, among these local genotypes, the most outstanding varieties, in terms of phenolic and FA profile and agronomical potential, to spread into cultivation, thereby contributing to an increase in the quality of the local table and olive oil production, strongly linked to the territory.

Genetics of Plant Metabolism

This Special Issue is aimed to collect scientific papers that support holistic methodological approaches, both top-down and horizontal, for the correct application of various omics sciences because, when well-integrated, they can contribute to our understanding of the genotypic plasticity of plant species [...].

How Temperatures May Affect the Synthesis of Fatty Acids during Olive Fruit Ripening: Genes at Work in the Field

A major concern for olive cultivation in many extra-Mediterranean regions is the adaptation of recently introduced cultivars to environmental conditions different from those prevailing in the original area, such as the Mediterranean basin. Some of these cultivars can easily adapt their physiological and biochemical parameters in new agro-environments, whereas others show unbalanced values of oleic acid content. The objective of this study was to evaluate the effects of the thermal regime during oil synthesis on the expression of fatty acid desaturase genes and on the unsaturated fatty acid contents at the field level. Two cultivars (Arbequina and Coratina) were included in the analysis over a wide latitudinal gradient in Argentina. The results suggest that the thermal regime exerts a regulatory effect at the transcriptional level on both OeSAD2 and OeFAD2-2 genes and that this regulation is cultivar-dependent. It was also observed that the accumulated thermal time affects gene expression and the contents of oleic and linoleic acids in cv. Arbequina more than in Coratina. The fatty acid composition of cv. Arbequina is more influenced by the temperature regime than Coratina, suggesting its greater plasticity. Overall, findings from this study may drive future strategies for olive spreading towards areas with different or extreme thermal regimes serve as guidance for the evaluation olive varietal patrimony.

Genome-Wide Identification and Functional Differentiation of Fatty Acid Desaturase Genes in Olea europaea L

Olive (Olea europaea L.) is a world-famous woody oil tree and popular for redundant unsaturated fatty acids. Fatty acid desaturase (FAD) genes are responsible for fatty acid desaturation and stress regulation but have not yet been identified in olive at the whole genome level. This study identified 40 and 27 FAD genes in the cultivated olive O. europaea cv. Farga and the wild olive O. europaea var. Sylvestris, respectively. Phylogenetic analysis showed that all the FAD genes could be classified into the soluble FAB2/SAD clade and membrane-bound clade, including ADS/FAD5, DES, FAD4, SLD, ω-6 and ω-3, with the high consistency of subcellular localization, motif composition and exon-intron organization in each group. FAD genes in olive showed the diverse functional differentiation in morphology of different tissues, fruit development and stress responses. Among them, OeFAB2.8 and OeFAD2.3 were up-regulated and OeADS.1, OeFAD4.1 and OeFAD8.2 were down-regulated under the wound, Verticillium dahliae and cold stresses. This study presents a comprehensive analysis of the FAD genes at the whole-genome level in olives and will provide guidance for the improvement of oil quality or stress tolerance of olive trees.

Peach fruit PpNAC1 activates PpFAD3-1 transcription to provide ω-3 fatty acids for the synthesis of short-chain flavor volatiles

Volatile organic compounds (VOCs) derived from fatty acids are major contributors to fruit flavor and affect human preferences. The ω-3 fatty acid linolenic acid 3 (18:3) serves as an important precursor for synthesis of (E)-2-hexenal and (Z)-3-hexenol. These short-chain C6 VOCs provide unique fresh notes in multiple fruit species. Metabolic engineering to improve fruit aroma requires knowledge of the regulation of fatty acid-derived VOCs. Here, we determined that ripe fruit-specific expression of PpFAD3-1 contributes to 18:3 synthesis in peach fruit. However, no significant increases in (E)-2-hexenal and (Z)-3-hexenol were detected after overexpressing PpFAD3-1. Interestingly, overexpressing the PpNAC1 transcription factor increased the content of 18:3 and enhanced the production of its derived volatiles. Moreover, induced expression of genes responsible for downstream VOC synthesis was observed for transgenic tomato fruit overexpressing PpNAC1, but not for transgenic fruit overexpressing PpFAD3-1. Electrophoretic mobility shift and ChIP-Seq assays showed that PpNAC1 activated PpFAD3-1 expression via binding to its promoter. Therefore, PpNAC1 plays an important role in modulating fatty acid flux to produce fruit flavor-related VOCs. In addition to PpNAC1, PpFAD3-1 expression was also associated with epigenetic modifications during peach fruit ripening. Taken together, our results provide new insights into the molecular mechanisms regulating biosynthesis of fatty acid and short-chain VOCs in fruit.

SNP discovery and structural insights into OeFAD2 unravelling high oleic/linoleic ratio in olive oil

Fatty Acid Desaturase 2 (FAD2), a key enzyme in the fatty acid biosynthesis pathway, is involved in the desaturation and conversion of oleic acid to linoleic acid. Therefore, it plays a crucial role in oleic/linoleic acid ratio and the quality of olive oil. DNA sequencing of 19 FAD2 genes from a set of olive oil varieties revealed several single-nucleotide polymorphisms (SNPs) and highlighted associations between some of the SNPs and saturated fatty acids contents. This was further confirmed by SNP-interaction and machine learning approach. Haplotype diversity analysis led to the discovery of three highly polymorphic SNPs and four haplotypes harboring differential oleic/linoleic acid ratios. Moreover, a combination of molecular modeling and docking experiments allowed a deeper and better understanding of the structure-function relationship of the FAD2 enzyme. Sequence patterns and variations involved in the regulation of the FAD2 activity were also identified. Furthermore, S82C and H213N substitutions in OeFAD2 make the Oueslati variety more interesting in terms of fatty acid profile and oleic acid level.

Genome-wide exploration of oil biosynthesis genes in cultivated olive tree varieties (Olea europaea): insights into regulation of oil biosynthesis

Genome-wide oil biosynthesis was explored by de novo sequencing two cultivated olive tree (Olea europaea) varieties (cv. Ayvalik and Picual). This is the first report of the former variety sequencing. As outgroups, raw reads of cv. Leccino and scaffold-level assembly of cv. Farga were also retrieved. Each of these four cultivars was chromosome-scale assembled into 23 pseudochromosomes, with 1.31 Gbp (Farga), 0.93 Gbp (Ayvalik), 0.7 Gbp (Picual), and 0.54 Gbp (Leccino) in size. Ab initio gene finding was performed on these assemblies, using wild olive tree (oleaster)-trained parameters. High numbers of gene models were predicted and anchored to the pseudochromosomes: 69,028 (Ayvalik), 55,073 (Picual), 63,785 (Farga), and 40,449 (Leccino). Using previously reported oil biosynthesis genes from wild olive tree genome project, the following homologous sequences were identified: 1,355 (Ayvalik), 1,269 (Farga), 812 (Leccino), and 774 (Picual). Of these, 358 sequences were commonly shared by all cultivars. Besides, some sequences were cultivar unique: Ayvalik (126), Farga (118), Leccino (46), and Picual (52). These putative sequences were assigned to various GO terms, ranging from lipid metabolism to stress tolerance, from signal transactions to development, and to many others, implicating that oil biosynthesis is synergistically regulated with involvement of various other pathways.

Integrated Analysis of Fatty Acid Metabolism and Transcriptome Involved in Olive Fruit Development to Improve Oil Composition

Olea europaea L. is an important oil crop with excellent nutritional properties. In this study, a full-length transcriptome combined with fatty acid composition was used to investigate the molecular mechanism of fatty acid (FA) metabolism of olive fruits at various stages of development (S1–S5). A total of 34 fatty acids (FAs) were measured using gas chromatography-mass spectrometry (GC-MS). All transcripts of FA metabolism during olive fruit development were studied, including glycolysis, fatty acid synthesis, triacylglycerol synthesis, and FA degradation. A total of 100 transcripts of 11 gene families, 68 transcripts of 12 gene families, 55 transcripts of 7 gene families, and 28 transcripts of 7 gene families were identified as encoding for enzymes involved in FA metabolism. Furthermore, one of the critical reactions in TAG metabolism is the activation of fatty acyl chains to fatty acyl CoA, which is catalyzed by long-chain acyl CoA synthetases (LACS). Phylogenetic analysis showed that 13 putative LACS-encoding genes clustered into five groups, of which two putative transcripts encoding LACS6/7 may participate in FA degradation. The aim of this study was to evaluate the fatty acid from synthesis to degradation pathways during olive fruit development to provide a better understanding of the molecular mechanism of FA metabolism during olive fruit maturation and provide information to improve the synthesis of oil components that are beneficial to human health.

The Oleic/Linoleic Acid Ratio in Olive (Olea europaea L.) Fruit Mesocarp Is Mainly Controlled by OeFAD2-2 and OeFAD2-5 Genes Together With the Different Specificity of Extraplastidial Acyltransferase Enzymes

Fatty acid composition of olive oil has an important effect on the oil quality to such an extent that oils with a high oleic and low linoleic acid contents are preferable from a nutritional and technological point of view. In the present work, we have first studied the diversity of the fatty acid composition in a set of eighty-nine olive cultivars from the Worldwide Olive Germplasm Bank of IFAPA Cordoba (WOGBC-IFAPA), and in a core collection (Core-36), which includes 28 olive cultivars from the previously mentioned set. Our results indicate that oleic and linoleic acid contents displayed the highest degree of variability of the different fatty acids present in the olive oil of the 89 cultivars under study. In addition, the independent study of the Core-36 revealed two olive cultivars, Klon-14 and Abou Kanani, with extremely low and high linoleic acid contents, respectively. Subsequently, these two cultivars were used to investigate the specific contribution of different fatty acid desaturases to the linoleic acid content of mesocarp tissue during olive fruit development and ripening. Fatty acid desaturase gene expression levels, together with lipid analysis, suggest that not only OeFAD2-2 and OeFAD2-5 but also the different specificities of extraplastidial acyltransferase enzymes are responsible for the variability of the oleic/linoleic acid ratio in olive cultivars. All this information allows for an advancement in the knowledge of the linoleic acid biosynthesis in different olive cultivars, which can impact olive breeding programs to improve olive oil quality.

Transcriptome analyses reveals the dynamic nature of oil accumulation during seed development of Plukenetia volubilis L

Sacha inchi (Plukenetia volubilis L.) is a shrub native to Amazon rainforests that’s of commercial interest as its seeds contain 35–60% edible oil (dry weight). This oil is one of the healthiest vegetable oils due to its high polyunsaturated fatty acid content and favourable ratio of omega-6 to omega-3 fatty acids. De novo transcriptome assembly and comparative analyses were performed on sacha inchi seeds from five stages of seed development in order to identifying genes associated with oil accumulation and fatty acid production. Of 30,189 unigenes that could be annotated in public databases, 20,446 were differentially expressed unigenes. A total of 14 KEGG pathways related to lipid metabolism were found, and 86 unigenes encoding enzymes involved in α-linolenic acid (ALA) biosynthesis were obtained including five unigenes encoding FATA (Unigene0008403), SAD (Unigene0012943), DHLAT (Unigene0014324), α-CT (Unigene0022151) and KAS II (Unigene0024371) that were significantly up-regulated in the final stage of seed development. A total of 66 unigenes encoding key enzymes involved in the synthesis of triacylglycerols (TAGs) were found, along with seven unigenes encoding PDCT (Unigene0000909), LPCAT (Unigene0007846), Oleosin3 (Unigene0010027), PDAT1 (Unigene0016056), GPDH (Unigene0022660), FAD2 (Unigene0037808) and FAD3 (Unigene0044238); these also proved to be up-regulated in the final stage of seed development.