Integrated Analysis of Comparative Lipidomics and Proteomics Reveals the Dynamic Changes of Lipid Molecular Species in High-Oleic Acid Peanut Seed

ScRNA-seq reveals dark- and light-induced differentially expressed gene atlases of seedling leaves in Arachis hypogaea L

Although the regulatory mechanisms of dark and light-induced plant morphogenesis have been broadly investigated, the biological process in peanuts has not been systematically explored on single-cell resolution. Herein, 10 cell clusters were characterized using scRNA-seq-identified marker genes, based on 13 409 and 11 296 single cells from 1-week-old peanut seedling leaves grown under dark and light conditions. 6104 genes and 50 transcription factors (TFs) displayed significant expression patterns in distinct cell clusters, which provided gene resources for profiling dark/light-induced candidate genes. Further pseudo-time trajectory and cell cycle evidence supported that dark repressed the cell division and perturbed normal cell cycle, especially the PORA abundances correlated with 11 TFs highly enriched in mesophyll to restrict the chlorophyllide synthesis. Additionally, light repressed the epidermis cell developmental trajectory extending by inhibiting the growth hormone pathway, and 21 TFs probably contributed to the different genes transcriptional dynamic. Eventually, peanut AHL17 was identified from the profile of differentially expressed TFs, which encoded protein located in the nucleus promoted leaf epidermal cell enlargement when ectopically overexpressed in Arabidopsis through the regulatory phytohormone pathway. Overall, our study presents the different gene atlases in peanut etiolated and green seedlings, providing novel biological insights to elucidate light-induced leaf cell development at the single-cell level.

Omics-driven advances in the understanding of regulatory landscape of peanut seed development

Peanuts (Arachis hypogaea) are an essential oilseed crop known for their unique developmental process, characterized by aerial flowering followed by subterranean fruit development. This crop is polyploid, consisting of A and B subgenomes, which complicates its genetic analysis. The advent and progression of omics technologies-encompassing genomics, transcriptomics, proteomics, epigenomics, and metabolomics-have significantly advanced our understanding of peanut biology, particularly in the context of seed development and the regulation of seed-associated traits. Following the completion of the peanut reference genome, research has utilized omics data to elucidate the quantitative trait loci (QTL) associated with seed weight, oil content, protein content, fatty acid composition, sucrose content, and seed coat color as well as the regulatory mechanisms governing seed development. This review aims to summarize the advancements in peanut seed development regulation and trait analysis based on reference genome-guided omics studies. It provides an overview of the significant progress made in understanding the molecular basis of peanut seed development, offering insights into the complex genetic and epigenetic mechanisms that influence key agronomic traits. These studies highlight the significance of omics data in profoundly elucidating the regulatory mechanisms of peanut seed development. Furthermore, they lay a foundational basis for future research on trait-related functional genes, highlighting the pivotal role of comprehensive genomic analysis in advancing our understanding of plant biology.

Coordinated Lipid Mobilization during Seed Development and Germination in Peanut (Arachis hypogaea L.)

Peanut (Arachis hypogaea L.) is one of the most important oil crops in the world due to its lipid-rich seeds. Lipid accumulation and degradation play crucial roles in peanut seed maturation and seedling establishment, respectively. Here, we utilized lipidomics and transcriptomics to comprehensively identify lipids and the associated functional genes that are important in the development and germination processes of a large-seed peanut variety. A total of 332 lipids were identified; triacylglycerols (TAGs) and diacylglycerols were the most abundant during seed maturation, constituting 70.43 and 16.11%, respectively, of the total lipids. Significant alterations in lipid profiles were observed throughout seed maturation and germination. Notably, TAG (18:1/18:1/18:2) and (18:1/18:2/18:2) peaked at 23386.63 and 23392.43 nmol/g, respectively, at the final stage of seed development. Levels of hydroxylated TAGs (HO-TAGs) increased significantly during the initial stage of germination. Accumulation patterns revealed an inverse relationship between free fatty acids and TAGs. Lipid degradation was determined to be regulated by diacylglycerol acyltransferase, triacylglycerol lipase, and associated transcription factors, predominantly yielding oleic acid, linoleic acid, and linolenic acid. Collectively, the results of this study provide valuable insights into lipid dynamics during the development and germination of large-seed peanuts, gene resources, and guiding future research into lipid accumulation in an economically important crop.

scRNA-seq Reveals the Mechanism of Fatty Acid Desaturase 2 Mutation to Repress Leaf Growth in Peanut (Arachis hypogaea L.)

Fatty Acid Desaturase 2 (FAD2) controls the conversion of oleic acids into linoleic acids. Mutations in FAD2 not only increase the high-oleic content, but also repress the leaf growth. However, the mechanism by which FAD2 regulates the growth pathway has not been elucidated in peanut leaves with single-cell resolution. In this study, we isolated fad2 mutant leaf protoplast cells to perform single-cell RNA sequencing. Approximately 24,988 individual cells with 10,249 expressed genes were classified into five major cell types. A comparative analysis of 3495 differentially expressed genes (DEGs) in distinct cell types demonstrated that fad2 inhibited the expression of the cytokinin synthesis gene LOG in vascular cells, thereby repressing leaf growth. Further, pseudo-time trajectory analysis indicated that fad2 repressed leaf cell differentiation, and cell-cycle evidence displayed that fad2 perturbed the normal cell cycle to induce the majority of cells to drop into the S phase. Additionally, important transcription factors were filtered from the DEG profiles that connected the network involved in high-oleic acid accumulation (WRKY6), activated the hormone pathway (WRKY23, ERF109), and potentially regulated leaf growth (ERF6, MYB102, WRKY30). Collectively, our study describes different gene atlases in high-oleic and normal peanut seedling leaves, providing novel biological insights to elucidate the molecular mechanism of the high-oleic peanut-associated agronomic trait at the single-cell level.

A Comprehensive Review of Health-Benefiting Components in Rapeseed Oil

Rapeseed oil is the third most consumed culinary oil in the world. It is well-known for its high content of unsaturated fatty acids, especially polyunsaturated fatty acids, which make it of great nutritional value. There is increasing evidence that a diet rich in unsaturated fatty acids offers health benefits. Although the consumption of rapeseed oil cuts across many areas around the world, the nutritional elements of rapeseed oil and the exact efficacy of the nutrients remain unclear. In this review, we systematically summarized the latest studies on functional rapeseed components to ascertain which component of canola oil contributes to its function. Apart from unsaturated fatty acids, there are nine functional components in rapeseed oil that contribute to its anti-microbial, anti-inflammatory, anti-obesity, anti-diabetic, anti-cancer, neuroprotective, and cardioprotective, among others. These nine functional components are vitamin E, flavonoids, squalene, carotenoids, glucoraphanin, indole-3-Carbinol, sterols, phospholipids, and ferulic acid, which themselves or their derivatives have health-benefiting properties. This review sheds light on the health-benefiting effects of rapeseed oil in the hope of further development of functional foods from rapeseed.

Visualizing the Distribution of Lipids in Peanut Seeds by MALDI Mass Spectrometric Imaging

Peanut (also called groundnut, Arachis hypogaea L.) seeds are used for producing edible oils and functional foods, and offer a rich source of lipids, proteins and carbohydrates. However, the location of these metabolites has not yet been firmly established. In the present study, the matrix-assisted laser desorption/ionization mass spectrometric imaging (MALDI-MSI) technique was applied to investigate spatial distribution of lipids and other key components in seeds of three peanut cultivars (ZH9, KQBH, HP). A total of 103 metabolites, including 34 lipid compounds, were putatively identified by MALDI-MSI. The abundance and spatial distribution of glycerolipids (GLs) and glycerophospholipids (GPs) were compared among the three peanut cultivars. All the identified lysophosphatidylcholine (LPC), phosphatidylethanolamine (PE) and phosphatidylcholines (PCs) were distributed mainly in the inner part of seeds. The visualization of phosphatidic acids (PAs) and triacylglycerols (TGs) revealed a dramatic metabolic heterogeneity between the different tissues making up the seed. The non-homogeneous spatial distribution of metabolites appeared to be related to the different functions of particular tissue regions. These results indicated that MALDI-MSI could be useful for investigating the lipids of foodstuffs from a spatial perspective. The present study may contribute to the development of oil crops with higher oil yields, and to improvement of food processing.

A Comparison of Lipid Contents in Different Types of Peanut Cultivars Using UPLC-Q-TOF-MS-Based Lipidomic Study

Peanuts are a rich dietary source of lipids, which are essential for human health. In this study, the lipid contents of 13 peanut cultivars were analyzed using UPLC-Q-TOF-MS and GC–MS. The OXITEST reactor was used to test their lipid oxidation stabilities. A total of 27 subclasses, 229 individual lipids were detected. The combined analysis of lipid and oxidation stability showed that lipid unsaturation was inversely correlated with oxidation stability. Moreover, lipid profiles differed significantly among the different peanut cultivars. A total of 11 lipid molecules (TG 18:2/18:2/18:2, TG 24:0/18:2/18:3, TG 20:5/14:1/18:2, TG 18:2/14:1/18:2, PE 17:0/18:2, BisMePA 18:2/18:2, PG 38:5, PMe 18:1/18:1, PC 18:1/18:1, MGDG 18:1/18:1, TG 10:0/10:1/18:1) might be employed as possible indicators to identify high oleic acid (OA) and non-high OA peanut cultivars, based on the PLS-DA result of lipid molecules with a VIP value greater than 2. This comprehensive analysis will help in the rational selection and application of peanut cultivars.

Time-Series Lipidomics Insights into the Progressive Characteristics of Lipid Constituents of Fresh Walnut during Postharvest Storage

A high-throughput lipid profiling platform adopting an accurate quantification strategy was built based on Q-Orbitrap mass spectrometry. Lipid components of fresh walnut during postharvest storage were determined, and the fatty acid distributions in triacylglycerol and polar lipids were also characterized. A total of 554 individual lipids in fresh walnut were mainly glycerolipids (56.7%), glycerophospholipids (32.4%), and sphingolipids (11%). With the progress of postharvest storage, 16 lipid subclasses in the stored walnut sample were significantly degraded, in which 34 lipids changed significantly between the fresh and stored groups. The sphingolipid metabolism, glycerolipid metabolism, and linoleic acid metabolism pathways were significantly enriched. The oxidation and degradation mechanism of linoleic acid in walnut kernel during postharvest storage was proposed. The established lipidomics platform can supply reliable and traceable lipid profiling data, help to improve the understanding of lipid degradation in fresh walnut, and offer a framework for analyzing lipid metabolisms in other tree nuts.

Single-cell RNA-seq describes the transcriptome landscape and identifies critical transcription factors in the leaf blade of the allotetraploid peanut (Arachis hypogaea L.)

Single-cell RNA-seq (scRNA-seq) has been highlighted as a powerful tool for the description of human cell transcriptome, but the technology has not been broadly applied in plant cells. Herein, we describe the successful development of a robust protoplast cell isolation system in the peanut leaf. A total of 6,815 single cells were divided into eight cell clusters based on reported marker genes by applying scRNA-seq. Further, a pseudo-time analysis was used to describe the developmental trajectory and interaction network of transcription factors (TFs) of distinct cell types during leaf growth. The trajectory enabled re-investigation of the primordium-driven development processes of the mesophyll and epidermis. These results suggest that palisade cells likely differentiate into spongy cells, while the epidermal cells originated earlier than the primordium. Subsequently, the developed method integrated multiple technologies to efficiently validate the scRNA-seq result in a homogenous cell population. The expression levels of several TFs were strongly correlated with epidermal ontogeny in accordance with obtained scRNA-seq values. Additionally, peanut AHL23 (AT-HOOK MOTIF NUCLEAR LOCALIZED PROTEIN 23), which is localized in nucleus, promoted leaf growth when ectopically expressed in Arabidopsis by modulating the phytohormone pathway. Together, our study displays that application of scRNA-seq can provide new hypotheses regarding cell differentiation in the leaf blade of Arachis hypogaea. We believe that this approach will enable significant advances in the functional study of leaf blade cells in the allotetraploid peanut and other plant species.

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.

Comprehensive and High-Coverage Lipidomic Analysis of Oilseeds Based on Ultrahigh-Performance Liquid Chromatography Coupled with Electrospray Ionization Quadrupole Time-of-Flight Mass Spectrometry

Oilseeds are an important source of dietary lipids, and a comprehensive analysis of oilseed lipids is of great significance to human health, while information about the global lipidomes in oilseeds was limited. Herein, an ultrahigh-performance liquid chromatography coupled with electrospray ionization quadrupole time-of-flight mass spectrometry method for comprehensive lipidomic profiling of oilseeds was established and applied. First, the lipid extraction efficiency and lipid coverage of four different lipid extraction methods were compared. The optimized methyl tert-butyl ether extraction method was superior to isopropanol, Bligh-Dyer, and Folch extraction methods, in terms of the operation simplicity, lipid coverage, and number of identified lipids. Then, global lipidomic analysis of soybean, sesame, peanut, and rapeseed was conducted. A total of 764 lipid molecules, including 260 triacylglycerols, 54 diacylglycerols, 313 glycerophospholipids, 36 saccharolipids, 35 ceramides, 30 free fatty acids, 21 fatty esters, and 15 sphingomyelins were identified and quantified. The compositions and contents of lipids significantly varied among different oilseeds. Our results provided a theoretical basis for the selection and breeding of varieties of oilseed as well as deep processing of oilseed for the edible oil industry.

Characteristics of Metabolites by Seed-Specific Inhibition of FAD2 in Brassica napus L

Fatty acid desaturase-2 (FAD2) is a key enzyme in the production of polyunsaturated fatty acids in plants. RNAi technology can reduce the expression of FAD2 genes in Brassica napus seeds and acquire transgenic B. napus plants with a high oleic acid content, but the effect of seed-specific inhibition of FAD2 expression on B. napus seed metabolites is not clear. Here we use widely targeted metabolomics to investigate the metabolites of normal-oleic-acid rapeseed (OA) and high-oleic-acid rapeseed (HOA) seeds, resulting in a total of 726 metabolites being detected. Among them, 24 differential metabolites were significantly downregulated and 88 differential metabolites were significantly upregulated in HOA rapeseed. In further lipid profile experiments, more lipids in B. napus seeds were accurately quantified. The contents of glycolipids and phospholipids that contain C18:1 increased significantly and C18:2 decreased because FAD2 expression was inhibited. The changes in the expression of key genes in related pathways were also consistent with the changes in metabolites. The insertion site of the ihpRNA plant expression vector was reconfirmed through genomewide resequencing, and the transgenic event did not change the sequence of FAD2 genes. There was no significant difference in the germination rate and germination potential between OA and HOA rapeseed seeds because the seed-specific ihpRNA plant expression vector did not affect other stages of plant growth. This work provides a theoretical and practical guidance for subsequent molecular breeding of high OA B. napus.

Prokaryotic Expression of Phosphoenolpyruvate Carboxylase Fragments from Peanut and Analysis of Osmotic Stress Tolerance of Recombinant Strains

Phosphoenolpyruvate carboxylase (PEPC) is a ubiquitous cytosolic enzyme that catalyzes the irreversible β-carboxylation of phosphoenolpyruvate (PEP) in presence of HCO₃⁻ to produce oxaloacetate (OAA) during carbon fixation and photosynthesis. It is well accepted that PEPC genes are expressed in plants upon stress. PEPC also supports the biosynthesis of biocompatible osmolytes in many plant species under osmotic stress. There are five isoforms of PEPC found in peanut (Arachis hypogaea L.), namely, AhPEPC1, AhPEPC2, AhPEPC3, AhPEPC4, and AhPEPC5. Quantitative real-time polymerase chain reaction (qRT-PCR) analysis revealed that the gene expression patterns of these AhPEPC genes were different in mature seeds, stems, roots, flowers, and leaves. The expression of all the plant type PEPC (PTPCs) (AhPEPC1, AhPEPC2, AhPEPC3, and AhPEPC4) was relatively high in roots, while the bacterial type PEPC (BTPC) (AhPEPC5) showed a remarkable expression level in flowers. Principal component analysis (PCA) result showed that AhPEPC3 and AhPEPC4 are correlated with each other, indicating comparatively associations with roots, and AhPEPC5 have a very close relationship with flowers. In order to investigate the function of these AhPEPCs, the fragments of these five AhPEPC cDNA were cloned and expressed in Escherichia coli (E. coli). The recombinant proteins contained a conserved domain with a histidine site, which is important for enzyme catalysis. Results showed that protein fragments of AhPEPC1, AhPEPC2, and AhPEPC5 had remarkable expression levels in E. coli. These three recombinant strains were more sensitive at pH 9.0, and recombinant strains carrying AhPEPC2 and AhPEPC5 fragments exhibited more growth than the control strain with the presence of PEG6000. Our findings showed that the expression of the AhPEPC fragments may enhance the resistance of transformed E. coli to osmotic stress.

Identification of three new microsatellites and their effects on body measurement traits in pigs using time of flight-mass spectrometry (TOF-MS)

The body status of livestock affects their physiological function and productive performances. Microsatellites, one of the most used DNA markers, have been found to be associated with pig productive traits. However, their identifications and effects on body measurement traits of the Chinese Qinghai Bamei pig still uncovered. According to our previous sequencing data, in this study, three novel microsatellites were found in this breed. Using time of flight-mass spectrometry (TOF-MS) method, these microsatellites were further identified in a large Bamei pig population. TOF-MS spectra showed that there are three microsatellites loci, named P1, P2 and P3. These microsatellites were linkage equilibrium based on the values of D' and r² tests. Association results demonstrated that P1 locus was associated with the body length, body height and chest width and the beneficial genotype was 150-/150-bp (p < 0.05); and P2 locus was associated with the body height (p < 0.05), and the 145-/145-bp, 145-/147-bp and 145-/149-bp were claimed as favorable genotypes and 145-bp allele was considered as the favorable allele. These findings suggested that P1 and P2 microsatellites might be considered as the candidate genetic markers to select pigs with superior body sizes, especially in local breed.

Global Transcriptome and Correlation Analysis Reveal Cultivar-Specific Molecular Signatures Associated with Fruit Development and Fatty Acid Determination in Camellia oleifera Abel

Background

Oil-tea Camellia is a very important edible oil plant widely distributed in southern China. Tea oil extracted from the oil-tea Camellia seeds is beneficial to health and is considered as a health edible oil. We attempt to identify genes related to fatty acid biosynthesis in an oil-tea Camellia seed kernel, generated a comprehensive transcriptome analysis of the seed kernel at different developmental stages, and explore optimal picking time of fruit. Material and Methods. A gas chromatography-mass spectrometer was used to detect the content of various fatty acids in samples. Transcriptome analysis was performed to detect gene dynamics and corresponding functions.

Results

Multiple phenotypic data were counted in detail, including the oil content, oleic acid content, linoleic acid content, linolenic acid content, fruit weight, fruit height, fruit diameter, single seed weight, seed length, and seed width in different developmental stages, which indicate that a majority of indicators increased with the development of oil-tea Camellia. The transcriptomics was conducted to perform a comprehensive and system-level view on dynamic gene expression networks for different developmental stages. Short Time-series Expression Miner (STEM) analysis of XL106 (the 6 time points) and XL210 (8 time points) was performed to screen related fatty acid (FA) gene set, from which 1041 candidate genes related to FA were selected in XL106 and 202 related genes were screened in XL210 based on GO and KEGG enrichment. Then, candidate genes and trait dataset were combined to conduct correlation analysis, and 10 genes were found to be strongly connected with several key traits.

Conclusions

The multiple phenotypic data revealed the dynamic law of changes during the picking stage. Transcriptomic analysis identified a large number of potential key regulatory factors that can control the oil content of dried kernels, oleic acid, linoleic acid, linolenic acid, fresh seed rate, and kernel-to-seed ratio, thereby providing a new insight into the molecular networks underlying the picking stage of oil-tea Camellia, which provides a theoretical basis for the optimal fruit picking point.