Transcriptome Analysis of Walnut (Juglans regia L.) Embryos Reveals Key Developmental Stages and Genes Involved in Lipid Biosynthesis and Polyunsaturated Fatty Acid Metabolism

AhFAD3-A01 enhances α-linolenic acid content in Arabidopsis and peanut

Alpha-linolenic acid (ALA, C18:3) is an essential fatty acid integral to human growth and development. Despite its significance, the ALA content in peanut seeds-a major global oilseed crop-is notably low. This study employed bioinformatics analysis, tissue expression, and promoter function evaluations to investigate AhFAD3, which encodes the microsomal omega-3 fatty acid desaturase that is directly responsible for ALA accumulation through converting linoleic acid (LA) to ALA. We identified the active AhFAD3 gene, AhFAD3-A01, with the functional protein encoded by AhFAD3-A01 localized in the endoplasmic reticulum (ER) and found to be pivotal in ALA synthesis in seeds. The low expression of AhFAD3 genes during the late stages of seed development, coupled with the specific activation by only AhFAD3-A01 and AhFAD3-B01 promoters in seeds, results in the low ALA levels in mature peanut seeds. To enhance ALA content, the constitutive promoter CaMV35S and the seed-specific promoter PAhWRI1 were utilized to overexpress AhFAD3-A01 in Arabidopsis and peanut. While the expression level of AhFAD3-A01 in PAhWRI1::AhFAD3-A01 transgenic Arabidopsis remained unchanged, it significantly increased under the CaMV35S::AhFAD3-A01 configuration, leading to an over a 40 % increase in ALA content of in T4 generation seeds, indicating that PAhWRI1 was unable to drive AhFAD3 overexpression in Arabidopsis. Similarly, the overexpression of AhFAD3-A01 using both promoters in peanuts resulted in enhanced expression and an increase in ALA content from 15.18 % to 30.65 % in CaMV35S::AhFAD3-A01 T1 generation seeds and from 11.23 % to 25.49 % in PAhWRI1::AhFAD3-A01 seeds. These results highlight the critical role of AhFAD3-A01 ALA synthesis in peanut seeds and provide a solid foundation for developing peanut varieties with elevated ALA content.

Protoplast transient transformation facilitates subcellular localization and functional analysis of walnut proteins

Walnut (Juglans regia L.), an important contributor to oil production among woody plants, encounters research constraints due to difficulties in the subcellular localization and functional analysis of its proteins. These limitations arise from the protracted fruiting cycle and the absence of a reliable transient gene transformation system and organelle markers. In this study, we established a transient expression system using walnut protoplasts and generated fluorescent-tagged organelle markers, whose localization was validated against Arabidopsis (Arabidopsis thaliana) organelle markers. The versatility of this system was demonstrated through pharmaceutical treatments, confirming its ability to determine the subcellular localization of endogenous proteins. We determined the subcellular localization of walnut oleosin proteins and explored protein-protein interactions through bimolecular fluorescence complementation analysis. We also explored the effects of abscisic acid signaling on oil body morphology and the regulation of walnut WRINKLED1 (JrWRI1) in lipid biosynthesis. Overall, this stable and versatile protoplast-based transient expression system, integrated with walnut organelle markers, enhances the subcellular localization and functional studies of uncharacterized walnut proteins. This advancement accelerates research into walnut gene function and streamlines molecular breeding processes with high-throughput efficiency.

Comparative transcriptome analysis of Cyperus esculentus and C. rotundus with contrasting oil contents in tubers defines genes and regulatory networks involved in oil accumulation

Plant vegetative organs present great potential for lipid storage, with tubers of Cyperus esculentus as a unique example. To investigate the genome and transcriptomic features of C. esculentus and related species, we sequenced and assembled the C. esculentus genome at the contig level. Through a comparative study of high-quality transcriptomes across 36 tissues from high-oil and intermediate-oil C. esculentus and low-oil Cyperus rotundus, we identified potential genes and regulatory networks related to tuber oil accumulation. First, we identified tuber-specific genes in two C. esculentus cultivars. Second, genes involved in fatty acid (FA) biosynthesis, triacylglycerol synthesis, and TAG packaging presented increased activity in the later stages of tuber development. Notably, tubers with high oil contents presented higher levels of these genes than those with intermediate oil contents did, whereas tubers with low oil contents presented minimal gene expression. Notably, a large fragment of the FA biosynthesis rate-limiting enzyme-encoding gene BCCP1 was missing from the C. rotundus transcript, which might be responsible for blocking FA biosynthesis in its tubers. WGCNA pinpointed a gene module linked to tuber oil accumulation, with a coexpression network involving the transcription factors WRI1, MYB4, and bHLH68. The ethylene-related genes in this module suggest a role for ethylene signaling in oil accumulation, which is supported by the finding that ethylene (ETH) treatment increases the oil content in C. esculentus tubers. This study identified potential genes and networks associated with tuber oil accumulation in C. esculentus, highlighting the role of specific genes, transcription factors, and ethylene signaling in this process.

The chromosome-level Elaeagnus mollis genome and transcriptomes provide insights into genome evolution, glycerolipid and vitamin E biosynthesis in seeds

Elaeagnus mollis, which has seeds with high lipid and vitamin E contents, is a valuable woody oil plant with potential for utilization. Currently, the biosynthesis and regulation mechanism of glycerolipids and vitamin E are still unknown in E. mollis. Here, we present the chromosome-level reference genome of E. mollis (scaffold N50: ~40.66Mbp, genome size: ~591.48Mbp) by integrating short-read, long-read, and Hi-C sequencing platforms. A total of 36,796 protein-coding sequences, mainly located on 14 proto-chromosomes, were predicted. Additionally, two whole genome duplication (WGD) events were suggested to have occurred ~54.07 and ~35.06 million years ago (MYA), with Elaeagnaceae plants probably experiencing both WGD events. Furthermore, the long terminal retrotransposons in E. mollis were active ~0.23MYA, and one of them was inferred to insert into coding sequence of the negative regulatory lipid synthesis gene, EMF2. Through transcriptomic and metabonomic analysis, key genes contributing to the high lipid and vitamin E levels of E. mollis seeds were identified, while miRNA regulation was also considered. This comprehensive work on the E. mollis genome not only provides a solid theoretical foundation and experimental basis for the efficient utilization of seed lipids and vitamin E, but also contributes to the exploration of new genetic resources.

Transcriptome analysis of lipid biosynthesis during kernel development in two walnut (Juglans regia L.) varieties of 'Xilin 3' and 'Xiangling'

BACKGROUND

Walnut is an oilseed tree species and an ecologically important woody tree species that is rich in oil and nutrients. In light of differences in the lipid content, fatty acid composition and key genes expression patterns in different walnut varieties, the key gene regulatory networks for lipid biosynthesis in different varieties of walnuts were intensively investigated.

RESULTS

The kernels of two walnut varieties, 'Xilin 3' (X3) and 'Xiangling' (XL) were sampled at 60, 90, and 120 days post-anthesis (DPA) to construct 18 cDNA libraries, and the candidate genes related to oil synthesis were identified via sequencing and expression analysis. A total of 106 differentially expressed genes associated with fatty acid biosynthesis, fatty acid elongation, unsaturated fatty acid biosynthesis, triglyceride assembly, and oil body storage were selected from the transcriptomes. Weighted gene co-expression network analysis (WGCNA), correlation analysis and quantitative validation confirmed the key role of the FAD3 (109002248) gene in lipid synthesis in different varieties.

CONCLUSIONS

These results provide valuable resources for future investigations and new insights into genes related to oil accumulation and lipid metabolism in walnut seed kernels. The findings will also aid future molecular studies and ongoing efforts to genetically improve walnut.

The identification and expression analysis of walnut Acyl-ACP thioesterases

Walnuts (Juglans regia L.), renowned for their nutritional potency, are a rich source of unsaturated fatty acids. Their regular intake plays a pivotal role in health maintenance and recuperation from a myriad of ailments. Fatty acyl-acyl carrier protein thioesterases, which orchestrate the hydrolysis of acyl-ACP thioester bonds, thereby yielding fatty acids of varying chain lengths, are instrumental in augmenting plant fatty acid content and modulating the balance between saturated and unsaturated fatty acids. Despite some investigative efforts into the synthesis and metabolic pathways of fatty acids in walnuts, our comprehension of Fat in walnuts remains rudimentary. This research undertook a comprehensive characterization of the JrFat family, predicated on the complete genome sequence of walnuts, leading to the identification of 8 JrFat genes and an exploration of their protein physicochemical properties. Utilizing Arabidopsis and soybean Fat genes as outgroups, JrFat genes can be categorized into 5 distinct subgroups, three of which encompass a pair of homologous gene pairs. These genes have demonstrated remarkable conservation throughout the evolutionary process, with highly analogous conserved base sequences. The promoter region of JrFats genes predominantly harbors light response and plant hormone response regulatory elements, with no discernible disparity in promoter elements among different JrFats. Predictive analyses indicate that JrFats proteins engage extensively with walnut fatty acid synthesis and metabolism-associated proteins. qRT-PCR analysis reveals an initial surge in the expression of JrFats during the development of walnut kernels, which either stabilizes or diminishes following the hard core period. Homologous gene pairs exhibit analogous expression patterns, and the expression trajectory of JrFats aligns with the dynamic accumulation of fatty acids in kernels. The expression of JrFatA2 exhibits a strong correlation with the content of Alpha-linolenic acid, while the expression of JrFatB2 is inversely correlated with the content of two saturated fatty acids. Collectively, these findings enrich our understanding of fatty acid synthesis and metabolism in walnuts and furnish gene resources for enhancing the content and ratio of fatty acids in walnuts.

Unveiling the "hidden quality" of the walnut pellicle: a precious source of bioactive lipids

Tree nut consumption has been widely associated with various health benefits, with walnuts, in particular, being linked with improved cardiovascular and neurological health. These benefits have been attributed to walnuts' vast array of phenolic antioxidants and abundant polyunsaturated fatty acids. However, recent studies have revealed unexpected clinical outcomes related to walnut consumption, which cannot be explained simply with the aforementioned molecular hallmarks. With the goal of discovering potential molecular sources of these unexplained clinical outcomes, an exploratory untargeted metabolomics analysis of the isolated walnut pellicle was conducted. This analysis revealed a myriad of unusual lipids, including oxylipins and endocannabinoids. These lipid classes, which are likely present in the pellicle to enhance the seeds' defenses due to their antimicrobial properties, also have known potent bioactivities as mammalian signaling molecules and homeostatic regulators. Given the potential value of this tissue for human health, with respect to its "bioactive" lipid fraction, we sought to quantify the amounts of these compounds in pellicle-enriched waste by-products of mechanized walnut processing in California. An impressive repertoire of these compounds was revealed in these matrices, and in notably significant concentrations. This discovery establishes these low-value agriculture wastes promising candidates for valorization and translation into high-value, health-promoting products; as these molecules represent a potential explanation for the unexpected clinical outcomes of walnut consumption. This "hidden quality" of the walnut pellicle may encourage further consumption of walnuts, and walnut industries may benefit from a revaluation of abundant pellicle-enriched waste streams, leading to increased sustainability and profitability through waste upcycling.

Integrated metabolomic and transcriptomic dynamic profiles of endopleura coloration during fruit maturation in three walnut cultivars

BACKGROUND

The color of endopleura is a vital factor in determining the economic value and aesthetics appeal of nut. Walnuts (Juglans) are a key source of edible nuts, high in proteins, amino acids, lipids, carbohydrates. Walnut had a variety endopleura color as yellow, red, and purple. However, the regulation of walnut endopleura color remains little known.

RESULTS

To understand the process of coloration in endopleura, we performed the integrative analysis of transcriptomes and metabolomes at two developmental stages of walnut endopleura. We obtained total of 4,950 differentially expressed genes (DEGs) and 794 metabolites from walnut endopleura, which are involved in flavonoid and phenolic biosynthesis pathways. The enrichment analysis revealed that the cinnamic acid, coniferyl alcohol, naringenin, and naringenin-7-O-glucoside were important metabolites in the development process of walnut endopleura. Transcriptome and metabolome analyses revealed that the DEGs and differentially regulated metabolites (DRMs) were significantly enriched in flavonoid biosynthesis and phenolic metabolic pathways. Through co-expression analysis, CHS (chalcone synthase), CHI (chalcone isomerase), CCR (cinnamoyl CoA reductase), CAD (cinnamyl alcohol dehydrogenase), COMT (catechol-Omethyl transferase), and 4CL (4-coumaroyl: CoA-ligase) may be the key genes that potentially regulate walnut endopleura color in flavonoid biosynthesis and phenolic metabolic pathways.

CONCLUSIONS

This study illuminates the metabolic pathways and candidate genes that underlie the endopleura coloration in walnuts, lay the foundation for further study and provides insights into controlling nut's colour.

Differential gene expression and potential regulatory network of fatty acid biosynthesis during fruit and leaf development in yellowhorn (Xanthoceras sorbifolium), an oil-producing tree with significant deployment values

Xanthoceras sorbifolium (yellowhorn) is a woody oil plant with super stress resistance and excellent oil characteristics. The yellowhorn oil can be used as biofuel and edible oil with high nutritional and medicinal value. However, genetic studies on yellowhorn are just in the beginning, and fundamental biological questions regarding its very long-chain fatty acid (VLCFA) biosynthesis pathway remain largely unknown. In this study, we reconstructed the VLCFA biosynthesis pathway and annotated 137 genes encoding relevant enzymes. We identified four oleosin genes that package triacylglycerols (TAGs) and are specifically expressed in fruits, likely playing key roles in yellowhorn oil production. Especially, by examining time-ordered gene co-expression network (TO-GCN) constructed from fruit and leaf developments, we identified key enzymatic genes and potential regulatory transcription factors involved in VLCFA synthesis. In fruits, we further inferred a hierarchical regulatory network with MYB-related (XS03G0296800) and B3 (XS02G0057600) transcription factors as top-tier regulators, providing clues into factors controlling carbon flux into fatty acids. Our results offer new insights into key genes and transcriptional regulators governing fatty acid production in yellowhorn, laying the foundation for efforts to optimize oil content and fatty acid composition. Moreover, the gene expression patterns and putative regulatory relationships identified here will inform metabolic engineering and molecular breeding approaches tailored to meet biofuel and bioproduct demands.

Lipid Metabolism and Improvement in Oilseed Crops: Recent Advances in Multi-Omics Studies

Oilseed crops are rich in plant lipids that not only provide essential fatty acids for the human diet but also play important roles as major sources of biofuels and indispensable raw materials for the chemical industry. The regulation of lipid metabolism genes is a major factor affecting oil production. In this review, we systematically summarize the metabolic pathways related to lipid production and storage in plants and highlight key research advances in characterizing the genes and regulatory factors influencing lipid anabolic metabolism. In addition, we integrate the latest results from multi-omics studies on lipid metabolism to provide a reference to better understand the molecular mechanisms underlying oil anabolism in oilseed crops.

Lipidomic and comparative transcriptomic analysis of fatty acid synthesis pathway in Carya illinoinensis embryo

Pecan (Carya illinoinensis (Wagenh.) K. Koch) is an important oilseed nut and is rich in fatty acids (FAs) and flavonols. Pecan FA has significantly edible, industrial and clinical value. To investigate the dynamic patterns and compositions of FA, and the molecular mechanism that controls FA accumulation in pecan, lipidomic and transcriptomic analyses were performed to determine lipid profiles and gene expression in pecan's FA biosynthesis pathway. In the present study, compared with cultivars 'Caddo' and 'Y-01', 'Mahan' formed larger and heavier embryos and accumulated higher oil content. Lipidomic analysis showed that FA and (O-acyl)-1-hydroxy FA contents were higher in 'Mahan' at the mature stage. Based on full-length and comparative RNA-Seq, differential expression gene enrichment analysis revealed that many functional genes participated in the pathways of 'fatty acid biosynthesis', 'fatty acid metabolism' and 'linoleic acid metabolism'. High FA accumulation model from 'Mahan' demonstrated that key enzyme-encoding genes played an important role in regulating FA biosynthesis. Co-expression module analysis indicated that several transcription factors (TFs; MYB, TCP, bHLH, Dof, ERF, NAC) were involved in FA accumulation by regulating the expression of functional genes, and real-time quantitative PCR verification proved that these TFs had a high correlation with the pecan FA accumulation pattern. These findings provided an insight into the molecular mechanism of FA accumulation in C. illinoinensis embryo, which contributes to pecan oil yielding and pecan molecular breeding.

Widely Targeted Metabolomic Profiling Combined with Transcriptome Analysis Provides New Insights into Lipid Biosynthesis in Seed Kernels of Pinus koraiensis

Lipid-rich Pinus koraiensis seed kernels are highly regarded for their nutritional and health benefits. To ascertain the molecular mechanism of lipid synthesis, we conducted widely targeted metabolomic profiling together with a transcriptome analysis of the kernels in P. koraiensis cones at various developmental stages. The findings reveal that 148 different types of lipid metabolites, or 29.6% of total metabolites, are present in kernels. Among those metabolites, the concentrations of linoleic acid, palmitic acid, and α-linolenic acid were higher, and they steadily rose as the kernels developed. An additional 10 hub genes implicated in kernel lipid synthesis were discovered using weighted gene co-expression network analysis (WGCNA), gene interaction network analysis, oil body biosynthesis, and transcriptome analysis. This study used lipid metabolome and transcriptome analyses to investigate the mechanisms of key regulatory genes and lipid synthesis molecules during kernel development, which served as a solid foundation for future research on lipid metabolism and the creation of P. koraiensis kernel food.

Molecular regulation of lipid metabolism in Suaeda salsa

Suaeda salsa is remarkable for its high oil content and abundant unsaturated fatty acids. In this study, the regulatory networks on fatty acid and lipid metabolism were constructed by combining the de novo transcriptome and lipidome data. Differentially expressed genes (DEGs) associated with lipids biosynthesis pathways were identified in the S. salsa transcriptome. DEGs involved in fatty acid and glycerolipids were generally up-regulated in leaf tissues. DEGs for TAG assembly were enriched in developing seeds, while DEGs in phospholipid metabolic pathways were enriched in root tissues. Polar lipids were extracted from S. salsa tissues and analyzed by lipidomics. The proportion of galactolipid MGDG was the highest in S. salsa leaves. The molar percentage of PG was high in the developing seeds, and the other main phospholipids had higher molar percentage in roots of S. salsa. The predominant C36:6 molecular species indicates that S. salsa is a typical 18:3 plant. The combined transcriptomic and lipidomic data revealed that different tissues of S. salsa were featured with DEGs associated with specific lipid metabolic pathways, therefore, represented unique lipid profiles. This study will be helpful on understanding lipid metabolism pathway and exploring the key genes involved in lipid synthesis in S. salsa.

Metabolomics and Transcriptomics Analyses Reveals the Molecular Regulatory Mechanisms of Walnut (Juglans regia L.) Embryos in Response to Shade Treatment

The walnut is an important nut that has numerous uses worldwide. However, due to dwarf and close plantation methods as well as continuous cloudy or rainy days that occur during periods of walnut oil accumulation, the walnut fruit exhibits varying degrees of stress under low-light conditions. However, the effects of shade on metabolites and genes in walnut embryos remain unclear in the literature. The purpose of this study is to investigate the lipid biosynthesis process that occurs in walnut embryos under shade treatment via the use of metabolomics and transcriptomics analyses. The results indicate that the oil content decreases significantly under shaded conditions, while the protein content increases significantly. The expression levels of fatty acid desaturase 2 (FAD2) and stearoyl-ACP-desaturase (SAD) involved in the lipid biosynthesis mechanism were significantly reduced in the shaded group, which resulted in reductions in oleic (C18:1), linoleic (C18:2), and α-linolenic (C18:3) acids. The reduced oil content was consistent with the downregulation of genes associated with the lipid biosynthesis mechanism. In the amino acid biosynthesis process, the upregulated cysteine synthase (cscK) and anthranilate synthase beta subunit 2 (trpG) genes promoted the accumulation of L-aspartic acid and L-citrulline. The increase in protein content was consistent with the upregulation of genes related to amino acid biosynthesis. Thus, our study provides new insights into the regulatory mechanisms of shade underlying overall walnut fruit quality.

Identification of Key Lipogenesis Stages and Proteins Involved in Walnut Kernel Development

Walnuts are abundant in oil content, especially for polyunsaturated fatty acids, but the understanding of their formation is limited. We collected walnut (Juglans regia L.) kernels at 60, 74, 88, 102, 116, 130, and 144 days after pollination (designated S1-S7). The ultrastructure and accumulation of oil bodies (OBs) were observed using transmission electron microscopy (TEM), and the oil content, fatty acid composition, and proteomic changes in walnut kernels were determined. The oil content and OB accumulation increased during the development and rose sharply from S1 to S3 stages, which are considered the key lipogenesis stage. A total of 5442 proteins were identified and determined as differentially expressed proteins (DEPs) using label-free proteomic analysis. Fatty acid desaturases (FAD) 2, FAD3, oleosin, and caleosin were essential and upregulated from the S1 to S3 stages. Furthermore, the highly expressed oleosin gene JrOLE14.7 from walnuts was cloned and overexpressed in transgenic Brassica napus. The overexpression of JrOLE14.7 increased the oil content, diameter, hundred weight of seeds and changed the fatty acid composition and OB size of Brassica napus seeds. These findings provide insights into the molecular mechanism of oil biosynthesis and the basis for the genetic improvement of walnuts.

Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)

Walnut (Juglans) species are used as nut crops worldwide. Eastern black walnut (EBW, Juglans nigra), a diploid, horticultural important woody species is native to much of eastern North America. Although it is highly valued for its wood and nut, there are few resources for understanding EBW genetics. Here, we present a high-quality genome assembly of J. nigra based on Illumina, Pacbio, and Hi-C technologies. The genome size was 540.8 Mb, with a scaffold N50 size of 35.1 Mb, and 99.0% of the assembly was anchored to 16 chromosomes. Using this genome as a reference, the resequencing of 74 accessions revealed the effective population size of J. nigra declined during the glacial maximum. A single whole-genome duplication event was identified in the J. nigra genome. Large syntenic blocks among J. nigra, Juglans regia, and Juglans microcarpa predominated, but inversions of more than 600 kb were identified. By comparing the EBW genome with those of J. regia and J. microcarpa, we detected InDel sizes of 34.9 Mb in J. regia and 18.3 Mb in J. microcarpa, respectively. Transcriptomic analysis of differentially expressed genes identified five presumed NBS-LRR (NUCLEOTIDE BINDING SITE-LEUCINE-RICH REPEAT) genes were upregulated during the development of walnut husks and shells compared to developing embryos. We also identified candidate genes with essential roles in seed oil synthesis, including FAD (FATTY ACID DESATURASE) and OLE (OLEOSIN). Our work advances the understanding of fatty acid bioaccumulation and disease resistance in nut crops, and also provides an essential resource for conducting genomics-enabled breeding in walnut.

Metabolomics and Transcriptomics Provide Insights into Lipid Biosynthesis in the Embryos of Walnut (Juglans regia L.)

Walnut (Juglans regia L.) is an important woody oilseed tree species due to its commercial value. However, the regulation mechanism of walnut oil accumulation is still poorly understood, which restricted the breeding and genetic improvement of high-quality oil-bearing walnuts. In order to explore the metabolic mechanism that regulates the synthesis of walnut oil, we used transcriptome sequencing technology and metabolome technology to comprehensively analyze the key genes and metabolites involved in oil synthesis of the walnut embryo at 60, 90, and 120 days after pollination (DAP). The results showed that the oil and protein contents increased gradually during fruit development, comprising 69.61% and 18.32% of the fruit, respectively, during ripening. Conversely, the contents of soluble sugar and starch decreased gradually during fruit development, comprising 2.14% and 0.84%, respectively, during ripening. Transcriptome sequencing generated 40,631 unigenes across 9 cDNA libraries. We identified 51 and 25 candidate unigenes related to the biosynthesis of fatty acid and the biosynthesis of triacylglycerol (TAG), respectively. The expression levels of the genes encoding Acetyl-CoA carboxylase (ACCase), long-chain acyl-CoA synthetases (LACS), 3-oxoacyl-ACP synthase II (KASII), and glycerol-3-phosphate acyl transfer (GPAT) were upregulated at 60 DAP relative to the levels at 90 and 120 DAP, while the stearoyl-ACP-desaturase (SAD) and fatty acid desaturase 2 (FAD2) genes were highly abundantly expressed during all walnut developmental periods. We found that ABSCISIC ACID INSENSEITIVE3 (ABI3), WRINKLEDl (WRI1), LEAFY COTYLEDON1 (LEC1), and FUSCA3 (FUS3) may be key transcription factors involved in lipid synthesis. Additionally, the metabolomics analysis detected 706 metabolites derived from 18 samples, among which, 4 are implicated in the TAG synthesis, 2 in the glycolysis pathway, and 5 in the tricarboxylic acid cycle (TCA cycle) pathway. The combined analysis of the related genes and metabolites in TAG synthesis showed that phospholipid:diacylglycerol acyltransferase (PDAT) genes were highly abundantly expressed across walnut fruit developmental periods, and their downstream metabolite TAG gradually accumulated with the progression of fruit development. The FAD2 gene showed consistently higher expression during fruit development, and its downstream metabolites 18:2-PC and 18:3-PC gradually accumulated. The ACCase, LACS, SAD, FAD2, and PDAT genes may be crucial genes required for walnut oil synthesis. Our data will enrich public databases and provide new insights into functional genes related to lipid metabolism in walnut.

Effects of Low Nighttime Temperature on Fatty Acid Content in Developing Seeds from Brassica napus L. Based on RNA-Seq and Metabolome

Brassica napus L. is a vital plant oil resource worldwide. The fatty acid biosynthesis and oil accumulation in its seeds are controlled by several genetic and environmental factors, including daytime and nighttime temperatures. We analyzed changes in oleic and erucic acid content in two double haploid (DH) lines, DH0729, a weakly temperature-sensitive line, and DH0815, a strongly temperature-sensitive line, derived from B. napus plants grown at different altitudes (1600, 1800, 2000, 2200, and 2400 m a.s.l., 28.85° N, 112.35° E) and nighttime temperatures (20/18, 20/16, 20/13 and 20/10 °C, daytime/nighttime temperature). Based on medium- and long-chain fatty acid metabolites, the total oleic acid content 35 and 43 days after flowering was significantly lower in low nighttime temperature (LNT, 20/13 °C) plants than in high nighttime temperature (HNT, 20/18 °C) plants (HNT: 58-62%; LNT: 49-54%; an average decrease of 9%), and the total erucic acid content was significantly lower in HNT than in LNT plants (HNT: 1-2%; LNT: 8-13%; an average increase of 10%). An RNA-seq analysis showed that the expression levels of SAD (LOC106366808), ECR (LOC106396280), KCS (LOC106419344), KAR (LOC106367337), HB1(LOC106430193), and DOF5 (LOC111211868) in STSL seeds increased under LNT conditions. In STSL seeds, a base mutation in the cis-acting element involved in low-temperature responsiveness (LTR), the HB1 and KCS promoter caused loss of sensitivity to low temperatures, whereas that of the KCS promoter caused increased sensitivity to low temperatures.

Transcriptome Analysis of Genes Involved in Fatty Acid and Lipid Biosynthesis in Developing Walnut (Juglans regia L.) Seed Kernels from Qinghai Plateau

Walnut (Juglans regia) is an important woody oil-bearing plant with high nutritional value. For better understanding of the underlying molecular mechanisms of its oil accumulation in the Qinghai Plateau, in this study we monitored walnut fruit development, and 15 cDNA libraries were constructed from walnut seed kernels collected at 72, 79, 93, 118 and 135 days after flowering (DAF). The candidate genes were identified using sequencing and expression analysis. The results showed that the oil content in the kernels increased dramatically in late July and reached the maximum value of 69% in mature seed. More than 90% of the oils were unsaturated fatty acids (UFAs) and linoleic acid (18:2) was the predominant UFA accumulated in mature seed. Differentially expressed genes (DEGs) in 15 KEGG pathways of lipid metabolism were detected. We identified 119 DEGs related to FA de novo biosynthesis (38 DEGs), FA elongation and desaturation (39 DEGs), triacylglycerol (TAG) assembly (24 DEGs), oil bodies (12 DEGs), and transcription factors (TFs, 6 DEGs). The abundantly expressed oleosins, caleosins and steroleosins may be important for timely energy reserve in oil bodies. Weighted gene coexpression network analysis (WGCNA) showed that AP2/ERF and bHLH were the key TFs, and were co-expressed with ACC1, α-CT, BCCP, MAT, KASII, LACS, FATA, and PDCT. Our transcriptome data will enrich public databases and provide new insights into functional genes related to the seed kernel lipid metabolism and oil accumulation in J. regia.

The Manchurian Walnut Genome: Insights into Juglone and Lipid Biosynthesis

BACKGROUND

Manchurian walnut (Juglans mandshurica Maxim.) is a tree with multiple industrial uses and medicinal properties in the Juglandaceae family (walnuts and hickories). J. mandshurica produces juglone, which is a toxic allelopathic agent and has potential utilization value. Furthermore, the seed of J. mandshurica is rich in various unsaturated fatty acids and has high nutritive value.

FINDINGS

Here, we present a high-quality chromosome-scale reference genome assembly and annotation for J. mandshurica (n = 16) with a contig N50 of 21.4 Mb by combining PacBio high-fidelity reads with high-throughput chromosome conformation capture data. The assembled genome has an estimated sequence size of 548.7 Mb and consists of 657 contigs, 623 scaffolds, and 40,453 protein-coding genes. In total, 60.99% of the assembled genome consists of repetitive sequences. Sixteen super-scaffolds corresponding to the 16 chromosomes were assembled, with a scaffold N50 length of 33.7 Mb and a BUSCO complete gene percentage of 98.3%. J. mandshurica displays a close sequence relationship with Juglans cathayensis, with a divergence time of 13.8 million years ago. Combining the high-quality genome, transcriptome, and metabolomics data, we constructed a gene-to-metabolite network and identified 566 core and conserved differentially expressed genes, which may be involved in juglone biosynthesis. Five CYP450 genes were found that may contribute to juglone accumulation. NAC, bZip, NF-YA, and NF-YC are positively correlated with the juglone content. Some candidate regulators (e.g., FUS3, ABI3, LEC2, and WRI1 transcription factors) involved in the regulation of lipid biosynthesis were also identified.

CONCLUSIONS

Our genomic data provide new insights into the evolution of the walnut genome and create a new platform for accelerating molecular breeding and improving the comprehensive utilization of these economically important tree species.

Metabolome and Transcriptome Profiling Unveil the Mechanisms of Polyphenol Synthesis in the Developing Endopleura of Walnut (Juglans regia L.)

Walnut (Juglans regia L.) is an important woody nut tree species, and its endopleura (the inner coating of a seed) is rich in many polyphenols. Thus far, the pathways and essential genes involved in polyphenol biosynthesis in developing walnut endopleura remain largely unclear. We compared metabolite differences between endopleura and embryo in mature walnuts, and analyzed the changes of metabolites in endopleura at 35, 63, 91, 119, and 147 days after pollination (DAP). A total of 760 metabolites were detected in the metabolome, and the polyphenol contents in endopleura were higher than those in embryos. A total of 15 types of procyanidins, 10 types of kaempferol glycosides, and 21 types of quercetin glycosides that accumulated during endopleura development were identified. The analysis of the phenylpropane metabolic pathway showed that phenylalanine was gradually transformed into proanthocyanidins and other secondary metabolites with the development of endopleura. A total of 49 unigenes related to polyphenol synthesis were identified by transcriptome analysis of endopleura. The expression patterns of PAL, C4H, 4CL, CHS, CHI, F3H, LDOX, and ANR were similar, and their expression levels were highest in endopleura at maturity. Transcriptome and metabolome analysis showed that endopleura rapidly synthesized and accumulated polyphenols during maturation. Moreover, the transcription factor MYB111 played an important role in synthesizing polyphenols in endopleura, and its expression pattern was positively correlated with the accumulation pattern of quercetin, kaempferol, and proanthocyanidins. MYB111 was co-expressed with NAP, NAC, ATR1, and other genes related to cell senescence and abiotic stress response. Our study analyzed the composition and molecular synthesis mechanism of polyphenols in walnut endopleura, and provided new perspectives and insights regarding the nutritional research of walnut nuts.

Transcriptome Analysis and GC-MS Profiling of Key Fatty Acid Biosynthesis Genes in Akebia trifoliata (Thunb.) Koidz Seeds

Simple Summary

Plant oil is an important renewable energy substance, and A. trifoliata seeds are of value in this regard. A. trifoliata fruits have many seeds with high oil content, but research progress on A. trifoliata seed oil is slow. Fatty acid biosynthesis is the most important factor affecting plant oil content. Therefore, analysis of the key genes for fatty acid biosynthesis is beneficial for breeding A. trifoliata varieties with high oil content. Here, we report changes in seed oil and key oil biosynthesis genes in the growth period of A. trifoliata based on transcriptome analysis. We found that the development of A. trifoliata seeds and fruits was not synchronized, and when the fruit was ripe, the seed oil content was not the highest. With the development of A. trifoliata seeds, linoleic and oleic acid content was found to decrease and increase, respectively. Subsequently, several key genes for oil biosynthesis in A. trifoliata were identified. These results further our understanding of the mechanism underlying oil biosynthesis in A. trifoliata seeds.

Abstract

Akebia trifoliata (Thunb.) Koidz is an important Chinese medicinal and economic crop. Its seeds, which are rich in fatty acids, are usually discarded. As of now, A. trifoliata lipid biosynthesis pathways and genes have not been clearly described. In this work, we found that seed and fruit development of A. trifoliata were not synchronized, and that when the fruit was ripe, seed oil content was not at its highest. As seeds developed, linoleic and oleic acid content was found to decrease and increase, respectively. RNA sequencing yielded 108.45 GB of clean reads from 15 cDNA libraries, containing 8756 differentially expressed genes. We identified 65 unigenes associated with lipid biosynthesis, including fatty acid and triacylglycerol biosynthesis. The 65 unigenes were mapped to the A. trifoliata lipid synthesis pathway. There were 20 AtrFAD family members in A. trifoliata, which could be divided into four sub-groups with the highest number of AtrSADs. Our study revealed the dynamic changes in A. trifoliata seed oil content and composition during its growth period and provides large-scale and comprehensive transcriptome data of A. trifoliata seeds. These findings provide a basis for the improvement of A. trifoliata seed oil yield and quality.

Multiomic analyses of two sorghum cultivars reveals the change of membrane lipids in their responses to water deficit

Drought is one of the main abiotic stresses influencing crop production all over the world. Membranes are sensitive to drought stress and easy to be degraded and modified. Lipidome and transcriptome analyses were applied to analyze the responses of membrane lipids to drought stress in two sorghum (Sorghum bicolor (L.) Moench) cultivars, drought-sensitive cv. Hongyingzi and drought-tolerant cv. Kangsi. In total, 156 lipid compounds were identified and the contents of the predominant ones changed significantly under drought stress. Drought significantly decreased the unsaturation indices (UI) of digalactosyl-diacylglycerol (DGDG), monogalactosyl-diacylglycerol (MGDG), phosphatidylglycerol (PG) and phosphatidylcholine (PC) in both cultivars, except for insignificant changes of UI for DGDG in cv. Kangsi. Transcriptome sequencing analysis identified genes related to membrane lipid remodeling such as phospholipase D α1 (PLDα1), phospholipase D δ (PLDδ), and phospholipase A 2 (PLA2). By integrating transcriptome data and lipidome data, weighted gene co-expression network analysis (WGCNA) identified hub genes, transcription factors and the genes involved in lipid metabolism. Then, the protein and protein interaction (PPI) was analyzed using STRING and the possible candidate genes regulating membrane lipids under drought stress were obtained, including CCT2, CER1, DGK1, DGK5, EMB3174, KCS4, LCB2, PAH1, PLDP1, PKP-β1, and KCS11. The results from this study have the potential to accelerate the process to breed drought-tolerant sorghum lines.

Integrated transcriptome and proteome analysis of developing embryo reveals the mechanisms underlying the high levels of oil accumulation in Carya cathayensis Sarg

Hickory (Carya cathayensis Sarg.) is an extraordinary nut-bearing deciduous arbor with high content of oil in its embryo. However, the molecular mechanism underlying high oil accumulation is mostly unknown. Here, we reported that the lipid droplets and oil accumulation gradually increased with the embryo development and the oil content was up to ~76% at maturity. Furthermore, transcriptome and proteome analysis of developing hickory embryo identified 32,907 genes and 9857 proteins. Time-series analysis of gene expressions showed that these genes were divided into 12 clusters and lipid metabolism-related genes were enriched in Cluster 3, with the highest expression levels at 95 days after pollination (S2). Differentially expressed genes and proteins indicated high correlation, and both were enriched in the lipid metabolism. Notably, the genes involved in biosynthesis, transport of fatty acid/lipid and lipid droplets formation had high expression levels at S2, while the expression levels of other genes required for suberin/wax/cutin biosynthesis and lipid degradation were very low at all the sampling time points, ultimately promoting the accumulation of oil. Quantitative reverse-transcription PCR analysis also verified the results of RNA-seq. The co-regulatory networks of lipid metabolism were further constructed and WRINKLED1 (WRI1) was a core transcriptional factor located in the nucleus. Of note, CcWRI1A/B could directly activate the expression of some genes (CcBCCP2A, CcBCCP2B, CcFATA and CcFAD3) required for fatty acid synthesis. These results provided in-depth evidence for revealing the molecular mechanism of high oil accumulation in hickory embryo.

A genome variation map provides insights into the genetics of walnut adaptation and agronomic traits

BACKGROUND

Common walnut (Juglans regia L.) is one of the top four most consumed nuts in the world due to its health benefits and pleasant taste. Despite its economic importance, the evolutionary history and genetic control of its adaptation and agronomic traits remain largely unexplored.

RESULTS

We report a comprehensive walnut genomic variation map based on whole-genome resequencing of 815 walnut accessions. Evolutionary analyses suggest that Chinese J. regia diverged from J. sigillata with extensive hybridizations after the split of the two species. In contrast to annual crops, the genetic diversity and heterozygous deleterious mutations of Chinese common walnut trees have continued to increase during the improvement process. Selective sweep analyses identify 902 genes uniquely selected in the improved common walnut compared to its progenitor population. Five major-effect loci are identified to be involved in walnut adaptations to temperature, precipitation, and altitude. Genome-wide association studies reveal 27 genomic loci responsible for 18 important agronomic traits, among which JrFAD2 and JrANR are the potentially major-effect causative genes controlling linoleic acid content and color of the endopleura of the nut, respectively.

CONCLUSIONS

The largest genomic resource for walnuts to date has been generated and explored in this study, unveiling their evolutionary history and cracking the genetic code for agronomic traits and environmental adaptation of this economically crucial crop tree.

Insights Into Walnut Lipid Metabolism From Metabolome and Transcriptome Analysis

Walnut oil is an excellent source of essential fatty acids. Systematic evaluation of walnut lipids has significance for the development of the nutritional and functional value of walnut. Ultra-performance liquid chromatography/Orbitrap high-resolution mass spectrometry (UHPLC-Orbitrap HRMS) was used to characterize the lipids of walnut. A total of 525 lipids were detected and triacylglycerols (TG) (18:2/18:2/18:3) and diacylglycerols (DG) (18:2/18:2) were the main glycerolipids present. Essential fatty acids, such as linoleic acid and linolenic acid, were the main DG and TG fatty acid chains. Many types of phospholipids were observed with phosphatidic acid being present in the highest concentration (5.58%). Using a combination of metabolome and transcriptome analysis, the present study mapped the main lipid metabolism pathway in walnut. These results may provide a theoretical basis for further study and specific gene targets to enable the development of walnut with increased oil content and modified fatty acid composition.

Analysis of lipidomics profile of Carya cathayensis nuts and lipid dynamic changes during embryonic development

Hickory (Carya cathayensis) nuts contain higher amount of lipids, and possess high nutritional value and substantial health benefits. However, their lipid composition and dynamic changes during embryogenesis have not been thoroughly investigated. Therefore, lipidomics profile and lipid dynamic changes during embryonic development were analyzed using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Totally, 544 kinds of lipids were identified in mature hickory nuts with higher proportions of glycerolipids (59.94%) and glycerophospholipids (38.66%). Notably, diacylglycerols showed gradual uptrends, which corresponded with total glycerolipid and glycerophospholipid at middle and late stage of embryogenesis, suggesting the pivotal role of diacylglycerols in the accumulation of glycerolipids and glycerophospholipids. Moreover, triacylglycerols, diacylglycerols, phosphatidylethanolamines and phosphatidylcholines had high relative content with abundance of unsaturated fatty acids, specifically oleic acid, linoleic acid and linolenic acid, localized mainly at sn-2 lipid position. Together, our study provides innovative perspectives for studying the nutritional benefits of hickory nut lipids.

Transcriptomic Analysis Reveals Key Genes Involved in Oil and Linoleic Acid Biosynthesis during Artemisia sphaerocephala Seed Development

Artemisia sphaerocephala seeds are rich in polysaccharides and linoleic acid (C18:2), which have been widely used as traditional medicine and to improve food quality. The accumulation patterns and molecular regulatory mechanisms of polysaccharides during A. sphaerocephala seed development have been studied. However, the related research on seed oil and C18:2 remain unclear. For this study, A. sphaerocephala seeds at seven different development stages at 10, 20, 30, 40, 50, 60, and 70 days after flowering (designated as S1~S7), respectively, were employed as experimental samples, the accumulation patterns of oil and fatty acids (FA) and the underlying molecular regulatory mechanisms were analyzed. The results revealed that oil content increased from 10.1% to 20.0% in the early stages of seed development (S1~S2), and up to 32.0% in mature seeds, of which C18:2 accounted for 80.6% of the total FA. FA and triacylglycerol biosynthesis-related genes jointly involved in the rapid accumulation of oil in S1~S2. Weighted gene co-expression network analysis showed that transcription factors FUS3 and bHLH played a critical role in the seed oil biosynthesis. The perfect harmonization of the high expression of FAD2 with the extremely low expression of FAD3 regulated the accumulation of C18:2. This study uncovered the gene involved in oil biosynthesis and molecular regulatory mechanisms of high C18:2 accumulation in A. sphaerocephala seeds; thus, advancing research into unsaturated fatty acid metabolism in plants while generating valuable genetic resources for optimal C18:2 breeding.

Integration of miRNAs, Degradome, and Transcriptome Omics Uncovers a Complex Regulatory Network and Provides Insights Into Lipid and Fatty Acid Synthesis During Sesame Seed Development

Sesame (Sesamum indicum L.) has always been known as a health-promoting oilseed crop because of its nutrient-rich oil. In recent years, studies have focused on lipid and fatty acid (FA) biosynthesis in various plants by high-throughput sequencing. Here, we integrated transcriptomics, small RNAs, and the degradome to establish a comprehensive reserve intensive on key regulatory micro RNA (miRNA)-targeting circuits to better understand the transcriptional and translational regulation of the oil biosynthesis mechanism in sesame seed development. Deep sequencing was performed to differentially express 220 miRNAs, including 65 novel miRNAs, in different developmental periods of seeds. GO and integrated KEGG analysis revealed 32 pairs of miRNA targets with negatively correlated expression profiles, of which 12 miRNA-target pairs were further confirmed by RT-PCR. In addition, a regulatory co-expression network was constructed based on the differentially expressed gene (DEG) profiles. The FAD2, LOC10515945, LOC105161564, and LOC105162196 genes were clustered into groups that regulate the accumulation of unsaturated fatty acid (UFA) biosynthesis. The results provide a unique advanced molecular platform for the study of lipid and FA biosynthesis, and this study may serve as a new theoretical reference to obtain increased levels of UFA from higher-quality sesame seed cultivars and other plants.