Down-regulation of crambe fatty acid desaturase and elongase in Arabidopsis and crambe resulted in significantly increased oleic acid content in seed oil

Global Transcriptome and Co-Expression Network Analyses Revealed Hub Genes Controlling Seed Size/Weight and/or Oil Content in Peanut

Cultivated peanut (Arachis hypogaea L.) is an important economic and oilseed crop worldwide, providing high-quality edible oil and high protein content. Seed size/weight and oil content are two important determinants of yield and quality in peanut breeding. To identify key regulators controlling these two traits, two peanut cultivars with contrasting phenotypes were compared to each other, one having a larger seed size and higher oil content (Zhonghua16, ZH16 for short), while the second cultivar had smaller-sized seeds and lower oil content (Zhonghua6, ZH6). Whole transcriptome analyses were performed on these two cultivars at four stages of seed development. The results showed that ~40% of the expressed genes were stage-specific in each cultivar during seed development, especially at the early stage of development. In addition, we identified a total of 5356 differentially expressed genes (DEGs) between ZH16 and ZH6 across four development stages. Weighted gene co-expression network analysis (WGCNA) based on DEGs revealed multiple hub genes with potential roles in seed size/weight and/or oil content. These hub genes were mainly involved in transcription factors (TFs), phytohormones, the ubiquitin-proteasome pathway, and fatty acid synthesis. Overall, the candidate genes and co-expression networks detected in this study could be a valuable resource for genetic breeding to improve seed yield and quality traits in peanut.

Engineering Nutritionally Improved Edible Plant Oils

In contrast to traditional breeding, which relies on the identification of mutants, metabolic engineering provides a new platform to modify the oil composition in oil crops for improved nutrition. By altering endogenous genes involved in the biosynthesis pathways, it is possible to modify edible plant oils to increase the content of desired components or reduce the content of undesirable components. However, introduction of novel nutritional components such as omega-3 long-chain polyunsaturated fatty acids needs transgenic expression of novel genes in crops. Despite formidable challenges, significant progress in engineering nutritionally improved edible plant oils has recently been achieved, with some commercial products now on the market.

Progress in understanding and improving oil content and quality in seeds

The world's population is projected to increase by two billion by 2050, resulting in food and energy insecurity. Oilseed crops have been identified as key to address these challenges: they produce and store lipids in the seeds as triacylglycerols that can serve as a source of food/feed, renewable fuels, and other industrially-relevant chemicals. Therefore, improving seed oil content and composition has generated immense interest. Research efforts aiming to unravel the regulatory pathways involved in fatty acid synthesis and to identify targets for metabolic engineering have made tremendous progress. This review provides a summary of the current knowledge of oil metabolism and discusses how photochemical activity and unconventional pathways can contribute to high carbon conversion efficiency in seeds. It also highlights the importance of ¹³C-metabolic flux analysis as a tool to gain insights on the pathways that regulate oil biosynthesis in seeds. Finally, a list of key genes and regulators that have been recently targeted to enhance seed oil production are reviewed and additional possible targets in the metabolic pathways are proposed to achieve desirable oil content and quality.

Improved fatty acid composition of field cress (Lepidium campestre) by CRISPR/Cas9-mediated genome editing

The wild species field cress (Lepidium campestre) has the potential to become a novel cover and oilseed crop for the Nordic climate. Its seed oil is however currently unsuitable for most food, feed, and industrial applications, due to the high contents of polyunsaturated fatty acids (PUFAs) and erucic acid (C22:1). As the biosynthesis of these undesirable fatty acids is controlled by a few well-known major dominant genes, knockout of these genes using CRISPR/Cas9 would thus be more effective in improving the seed oil quality. In order to increase the level of the desirable oleic acid (C18:1), and reduce the contents of PUFAs and C22:1, we targeted three important genes FATTY ACID ELONGASE1 (FAE1), FATTY ACID DESATURASE2 (FAD2), and REDUCED OLEATE DESATURASE1 (ROD1) using a protoplast-based CRISPR/Cas9 gene knockout system. By knocking out FAE1, we obtained a mutated line with almost no C22:1, but an increase in C18:1 to 30% compared with 13% in the wild type. Knocking out ROD1 resulted in an increase of C18:1 to 23%, and a moderate, but significant, reduction of PUFAs. Knockout of FAD2, in combination with heterozygous FAE1fae1 genotype, resulted in mutated lines with up to 66% C18:1, very low contents of PUFAs, and a significant reduction of C22:1. Our results clearly show the potential of CRISPR/Cas9 for rapid trait improvement of field cress which would speed up its domestication process. The mutated lines produced in this study can be used for further breeding to develop field cress into a viable crop.

Biotechnological approach for improvement of Crambe species as valuable oilseed plants for industrial purposes

Boosting technological innovation for a sustainable and circular bioeconomy encompasses the use of renewable materials and development of highly effective biotechnological approaches to improve the quality of oilseed crops and facilitate their industrial deployment. The interest in cultivating Crambe as a potential crop is steadily growing due to its low propensity to crossbreeding with other oilseed crops, valuable seed oil composition and a high yield capacity. The main focus is located on Crambe abyssinica as the most adapted into the agriculture and well-studied Crambe species. At the same time, the Crambe genus is one of the most numerous of the Brassicaceae family featuring several underestimated (orphaned) species with useful traits (abiotic stress tolerance, wide range of practical applications). This review features progress in the biotechnological improvement of well-adapted and wild Crambe species starting with aseptic culture establishment and plant propagation in vitro reinforced with the use of genetic engineering and breeding techniques. The aim of the paper is to highlight and review the existing biotechnological methods of both underestimated and well-adapted Crambe species improvment, including the establishment of aseptic culture, in vitro cultivation, plant regeneration and genetic transformation to modify seed oil content and morphological traits of valuable species.

Plant monounsaturated fatty acids: Diversity, biosynthesis, functions and uses

Monounsaturated fatty acids are straight-chain aliphatic monocarboxylic acids comprising a unique carbon‑carbon double bond, also termed unsaturation. More than 50 distinct molecular structures have been described in the plant kingdom, and more remain to be discovered. The evolution of land plants has apparently resulted in the convergent evolution of non-homologous enzymes catalyzing the dehydrogenation of saturated acyl chain substrates in a chemo-, regio- and stereoselective manner. Contrasted enzymatic characteristics and different subcellular localizations of these desaturases account for the diversity of existing fatty acid structures. Interestingly, the location and geometrical configuration of the unsaturation confer specific characteristics to these molecules found in a variety of membrane, storage, and surface lipids. An ongoing research effort aimed at exploring the links existing between fatty acid structures and their biological functions has already unraveled the importance of several monounsaturated fatty acids in various physiological and developmental contexts. What is more, the monounsaturated acyl chains found in the oils of seeds and fruits are widely and increasingly used in the food and chemical industries due to the physicochemical properties inherent in their structures. Breeders and plant biotechnologists therefore develop new crops with high monounsaturated contents for various agro-industrial purposes.

CRISPR/Cas9-Induced fad2 and rod1 Mutations Stacked With fae1 Confer High Oleic Acid Seed Oil in Pennycress (Thlaspi arvense L.)

Pennycress (Thlaspi arvense L.) is being domesticated as an oilseed cash cover crop to be grown in the off-season throughout temperate regions of the world. With its diploid genome and ease of directed mutagenesis using molecular approaches, pennycress seed oil composition can be rapidly tailored for a plethora of food, feed, oleochemical and fuel uses. Here, we utilized Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology to produce knockout mutations in the FATTY ACID DESATURASE2 (FAD2) and REDUCED OLEATE DESATURATION1 (ROD1) genes to increase oleic acid content. High oleic acid (18:1) oil is valued for its oxidative stability that is superior to the polyunsaturated fatty acids (PUFAs) linoleic (18:2) and linolenic (18:3), and better cold flow properties than the very long chain fatty acid (VLCFA) erucic (22:1). When combined with a FATTY ACID ELONGATION1 (fae1) knockout mutation, fad2 fae1 and rod1 fae1 double mutants produced ∼90% and ∼60% oleic acid in seed oil, respectively, with PUFAs in fad2 fae1 as well as fad2 single mutants reduced to less than 5%. MALDI-MS spatial imaging analyses of phosphatidylcholine (PC) and triacylglycerol (TAG) molecular species in wild-type pennycress embryo sections from mature seeds revealed that erucic acid is highly enriched in cotyledons which serve as storage organs, suggestive of a role in providing energy for the germinating seedling. In contrast, PUFA-containing TAGs are enriched in the embryonic axis, which may be utilized for cellular membrane expansion during seed germination and seedling emergence. Under standard growth chamber conditions, rod1 fae1 plants grew like wild type whereas fad2 single and fad2 fae1 double mutant plants exhibited delayed growth and overall reduced heights and seed yields, suggesting that reducing PUFAs below a threshold in pennycress had negative physiological effects. Taken together, our results suggest that combinatorial knockout of ROD1 and FAE1 may be a viable route to commercially increase oleic acid content in pennycress seed oil whereas mutations in FAD2 will likely require at least partial function to avoid fitness trade-offs.

The Potential of Genome Editing for Improving Seed Oil Content and Fatty Acid Composition in Oilseed Crops

A continuous rise in demand for vegetable oils, which comprise mainly the storage lipid triacylglycerol, is fueling a surge in research efforts to increase seed oil content and improve fatty acid composition in oilseed crops. Progress in this area has been achieved using both conventional breeding and transgenic approaches to date. However, further advancements using traditional breeding methods will be complicated by the polyploid nature of many oilseed crops and associated time constraints, while public perception and the prohibitive cost of regulatory processes hinders the commercialization of transgenic oilseed crops. As such, genome editing using CRISPR/Cas is emerging as a breakthrough breeding tool that could provide a platform to keep pace with escalating demand while potentially minimizing regulatory burden. In this review, we discuss the technology itself and progress that has been made thus far with respect to its use in oilseed crops to improve seed oil content and quality. Furthermore, we examine a number of genes that may provide ideal targets for genome editing in this context, as well as new CRISPR-related tools that have the potential to be applied to oilseed plants and may allow additional gains to be made in the future.

Genome-wide mining and comparative analysis of fatty acid elongase gene family in Brassica napus and its progenitors

Very long chain fatty acids (VLCFAs) that are structural components of cell membrane lipid, cuticular waxes and seed oil, play crucial roles in plant growth, development and stress response. Fatty acid elongases (FAEs) comprising KCS and ELO, are key enzymes for VLCFA biosynthesis in plants. Although reference genomes of Brassica napus and its parental speices both have been sequenced, whole-genome analysis of FAE gene family in these Brassica speices is not reported. Here, 58, 33 and 30 KCS genes were identified in B. napus, B. rapa and B. oleracea genomes, respectively, whereas 14, 6 and 8 members were obtained for ELO genes. These KCS genes were unevenly located in 37 chromosomes and 3 scaffolds of 3 Brassica species, while these ELO genes were mapped to 19 chromosomes. The KCS and ELO proteins were divided into 8 and 4 subclasses, respectively. Gene structure and protein motifs remained highly conserved in each KCS or ELO subclass. Most promoters of KCS and ELO genes harbored various plant growth-, phytohormone-, and stress response-related cis-acting elements. 20 SSR loci existed in the KCS and ELO genes/promoters. The whole-genome duplication and segmental duplication mainly contributed to expansion of KCS and ELO genes in these genomes. Transcriptome analysis showed that KCS and ELO genes in 3 Brassica species were expressed in various tissues/organs with different levels, whereas 1 BnELO gene and 6 BnKCS genes might be pathogen-responsive genes. The qRT-PCR assay showed that BnKCS22 and BnELO04 responded to various phytohormone treatments and abiotic stresses. This work lays the foundation for further function identification of KCS and ELO genes in B. napus and its progenitors.

Genome-Wide Identification of Peanut KCS Genes Reveals That AhKCS1 and AhKCS28 Are Involved in Regulating VLCFA Contents in Seeds

The peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. Compared to other common edible vegetable oils, peanut oil contains a higher content of saturated fatty acids (SFAs), approximately 20-40% of which are very long chain fatty acids (VLCFAs). To understand the basis for this oil profile, we interrogated genes for peanut β-ketoacyl-CoA synthase (KCS), which is known to be a key enzyme in VLCFA biosynthesis. A total of 30 AhKCS genes were identified in the assembled genome of the peanut. Based on transcriptome data, nine AhKCS genes with high expression levels in developing seeds were cloned and expressed in yeast. All these AhKCSs could produce VLCFAs but result in different profiles, indicating that the AhKCSs catalyzed fatty acid elongation with different substrate specificities. Expression level analysis of these nine AhKCS genes was performed in developing seeds from six peanut germplasm lines with different VLCFA contents. Among these genes, the expression levels of AhKCS1 or AhKCS28 were, 4-10-fold higher than that of any other AhKCS. However, only the expression levels of AhKCS1 and AhKCS28 were significantly and positively correlated with the VLCFA content, suggesting that AhKCS1 and AhKCS28 were involved in the regulation of VLCFA content in the peanut seed. Further subcellular localization analysis indicated that AhKCS1 and AhKCS28 were located at the endoplasmic reticulum (ER). Overexpression of AhKCS1 or AhKCS28 in Arabidopsis increased the contents of VLCFAs in the seed, especially for very long chain saturated fatty acids (VLCSFAs). Taken together, this study suggests that AhKCS1 and AhKCS28 could be key genes in regulating VLCFA biosynthesis in the seed, which could be applied to improve the health-promoting and nutritional qualities of the peanut.

Development of Industrial Oil Crop Crambe abyssinica for Wax Ester Production through Metabolic Engineering and Cross Breeding

As an important industrial feedstock, wax esters (WEs) have been used as lubricants in a number of technical processes. There is however currently no large-scale biological source for WE production and alteration in metabolic pathways of plant oils for producing WEs could be attractive to the commercial markets. Here, we present the breeding results of long-term studies on successful development of new crambe lines producing WEs through genetic engineering and cross breeding. The transgenic crambe lines producing WEs at over 25% of the total seed oil were first generated by introduction of the jojoba WE biosynthetic genes ScFAR and ScWS. Further improvement of the lines aiming at improving oxidative stability of WEs was achieved through introducing the CaFAD2-RNAi gene into these lines by crossing. The hybrid lines possessed similar agronomic traits to the wild type and a stable level of WEs over several generations, suggesting a high potential of crambe as an industrial crop for WE production.

Harnessing Biotechnology for the Development of New Seed Lipid Traits in Brassica

The seed oil quality of Brassica oilseed species has been improved in the last few decades, using conventional breeding approaches. Modern biotechnology has enabled the significant development of new seed lipid traits in many oil crops. Alternation of seed lipid component with gene knockout by RNAi gene silencing, artificial microRNA or gene editing within the crop is relative straightforward. Introducing a new pathway from an exogenous source via biotechnology enables the creation of a new trait, where the biosynthetic pathway for such a new trait is not available in the host crop. This review updates the recent development of new seed lipid traits in six major Brassica species and highlights the capability of biotechnology to improve the composition of important fatty acids for both industrial and nutritional purposes.

An integrated omics analysis reveals molecular mechanisms that are associated with differences in seed oil content between Glycine max and Brassica napus

BACKGROUND

Rapeseed (Brassica napus L.) and soybean (Glycine max L.) seeds are rich in both protein and oil, which are major sources of biofuels and nutrition. Although the difference in seed oil content between soybean (~ 20%) and rapeseed (~ 40%) exists, little is known about its underlying molecular mechanism.

RESULTS

An integrated omics analysis was performed in soybean, rapeseed, Arabidopsis (Arabidopsis thaliana L. Heynh), and sesame (Sesamum indicum L.), based on Arabidopsis acyl-lipid metabolism- and carbon metabolism-related genes. As a result, candidate genes and their transcription factors and microRNAs, along with phylogenetic analysis and co-expression network analysis of the PEPC gene family, were found to be largely associated with the difference between the two species. First, three soybean genes (Glyma.13G148600, Glyma.13G207900 and Glyma.12G122900) co-expressed with GmPEPC1 are specifically enriched during seed storage protein accumulation stages, while the expression of BnPEPC1 is putatively inhibited by bna-miR169, and two genes BnSTKA and BnCKII are co-expressed with BnPEPC1 and are specifically associated with plant circadian rhythm, which are related to seed oil biosynthesis. Then, in de novo fatty acid synthesis there are rapeseed-specific genes encoding subunits β-CT (BnaC05g37990D) and BCCP1 (BnaA03g06000D) of heterogeneous ACCase, which could interfere with synthesis rate, and β-CT is positively regulated by four transcription factors (BnaA01g37250D, BnaA02g26190D, BnaC01g01040D and BnaC07g21470D). In triglyceride synthesis, GmLPAAT2 is putatively inhibited by three miRNAs (gma-miR171, gma-miR1516 and gma-miR5775). Finally, in rapeseed there was evidence for the expansion of gene families, CALO, OBO and STERO, related to lipid storage, and the contraction of gene families, LOX, LAH and HSI2, related to oil degradation.

CONCLUSIONS

The molecular mechanisms associated with differences in seed oil content provide the basis for future breeding efforts to improve seed oil content.

Seed-specific RNAi in safflower generates a superhigh oleic oil with extended oxidative stability

Vegetable oils extracted from oilseeds are an important component of foods, but are also used in a range of high value oleochemical applications. Despite being biodegradable, nontoxic and renewable current plant oils suffer from the presence of residual polyunsaturated fatty acids that are prone to free radical formation that limit their oxidative stability, and consequently shelf life and functionality. Many decades of plant breeding have been successful in raising the oleic content to ~90%, but have come at the expense of overall field performance, including poor yields. Here, we engineer superhigh oleic (SHO) safflower producing a seed oil with 93% oleic generated from seed produced in multisite field trials spanning five generations. SHO safflower oil is the result of seed-specific hairpin-based RNA interference of two safflower lipid biosynthetic genes, FAD2.2 and FATB, producing seed oil containing less than 1.5% polyunsaturates and only 4% saturates but with no impact on lipid profiles of leaves and roots. Transgenic SHO events were compared to non-GM safflower in multisite trial plots with a wide range of growing season conditions, which showed no evidence of impact on seed yield. The oxidative stability of the field-grown SHO oil produced from various sites was 50 h at 110°C compared to 13 h for conventional ~80% oleic safflower oils. SHO safflower produces a uniquely stable vegetable oil across different field conditions that can provide the scale of production that is required for meeting the global demands for high stability oils in food and the oleochemical industry.

Naturally occurring high oleic acid cottonseed oil: identification and functional analysis of a mutant allele of Gossypium barbadense fatty acid desaturase-2

Some naturally occurring cotton accessions contain commercially attractive seed oil fatty acid profiles. The likely causal factor for a high-oleate trait in pima cotton ( Gossypium barbadense ) accession GB-713 is described here. Vegetable oils are broadly used in the manufacture of many human and animal nutritional products, and in various industrial applications. Along with other well-known edible plant oils from soybean, corn, and canola, cottonseed oil is a valuable commodity. Cottonseed oil is a co-product derived from the processing of cottonseed fiber. In the past, it was used extensively in a variety of food applications. However, cottonseed oil has lost market share in recent years due to less than optimal ratios of the constituent fatty acids found in either traditional or partially hydrogenated oil. Increased awareness of the negative health consequences of dietary trans-fats, along with the public wariness associated with genetically modified organisms has created high demand for naturally occurring oil with high monounsaturate/polyunsaturate ratios. Here, we report the discovery of multiple exotic accessions of pima cotton that contain elevated seed oil oleate content. The genome of one such accession was sequenced, and a mutant candidate fatty acid desaturase-2 (FAD2-1D) gene was identified. The mutant protein produced significantly less linoleic acid in infiltrated Arabidopsis leaf assays, compared to a repaired version of the same enzyme. Identification of this gene provides a valuable resource. Development of markers associated with this mutant locus will be very useful in efforts to breed the high-oleate trait into agronomic fiber accessions of upland cotton.

Significant increase of oleic acid level in the wild species Lepidium campestre through direct gene silencing

Simultaneous RNAi silencing of the FAD2 and FAE1 genes in the wild species Lepidium campestre improved the oil quality with 80 % oleic acid content compared to 11 % in wildtype. Field cress (Lepidium campestre) is a wild biennial species within the Brassicaceae family with desirable agronomic traits, thus being a good candidate for domestication into a new oilseed and catch crop. However, it has agronomic traits that need to be improved before it can become an economically viable species. One of such traits is the seed oil composition, which is not desirable either for food use or for industrial applications. In this study, we have, through metabolic engineering, altered the seed oil composition in field cress into a premium oil for food processing, industrial, or chemical industrial applications. Through seed-specific RNAi silencing of the field cress fatty acid desaturase 2 (FAD2) and fatty acid elongase 1 (FAE1) genes, we have obtained transgenic lines with an oleic acid content increased from 11 % in the wildtype to over 80 %. Moreover, the oxidatively unstable linolenic acid was decreased from 40.4 to 2.6 %, and the unhealthy erucic acid was reduced from 20.3 to 0.1 %. The high oleic acid trait has been kept stable for three generations. This shows the possibility to use field cress as a platform for genetic engineering of oil compositions tailor-made for its end uses.