Lipidomic and transcriptomic profiling of developing nodules reveals the essential roles of active glycolysis and fatty acid and membrane lipid biosynthesis in soybean nodulation

Three separate pathways in Rhizobium leguminosarum maintain phosphatidylcholine biosynthesis, which is required for symbiotic nitrogen fixation with clover

Phosphatidylcholine (PC) is critical for the nitrogen-fixing symbiosis between rhizobia and legumes. We characterized three PC biosynthesis pathways in Rhizobium leguminosarum and evaluated their impact on nitrogen fixation in clover nodules. In the presence of choline, a PC synthase catalyzes the condensation of cytidine diphosphate-diacylglycerol with choline to produce PC. In the presence of lyso-PC, acyltransferases acylate this mono-acylated phospholipid to PC. The third pathway relies on phospholipid N-methyltransferases (Pmts), which sequentially methylate phosphatidylethanolamine (PE) through three rounds of methylation, yielding PC via the intermediates monomethyl-PE and dimethyl-PE. In R. leguminosarum, at least three Pmts participate in this methylation cascade. To elucidate the functions of these enzymes, we recombinantly produced and biochemically characterized them. We moved on to determine the phospholipid profiles of R. leguminosarum mutant strains harboring single and combinatorial deletions of PC biosynthesis genes. The cumulative results show that PC production occurs through the combined action of multiple enzymes, each with distinct substrate and product specificities. The methylation pathway emerges as the dominant PC biosynthesis route, and we pinpoint PmtS2, which catalyzes all three methylation steps, as the enzyme responsible for providing adequate PC amounts for a functional nitrogen-fixing symbiosis with clover.

IMPORTANCE

Understanding the molecular mechanisms of symbiotic nitrogen fixation has important implications for sustainable agriculture. The presence of the phospholipid phosphatidylcholine (PC) in the membrane of rhizobia is critical for the establishment of productive nitrogen-fixing root nodules on legume plants. The reasons for the PC requirement are unknown. Here, we employed Rhizobium leguminosarum and clover as model system for a beneficial plant-microbe interaction. We found that R. leguminosarum produces PC by three distinct pathways. The relative contribution of these pathways to PC formation was determined in an array of single, double, and triple mutant strains. Several of the PC biosynthesis enzymes were purified and biochemically characterized. Most importantly, we demonstrated the essential role of PC formation by R. leguminosarum in nitrogen fixation and pinpointed a specific enzyme indispensable for plant-microbe interaction. Our study offers profound insights into bacterial PC biosynthesis and its pivotal role in biological nitrogen fixation.

Natural variation in Fatty Acid 9 is a determinant of fatty acid and protein content

Soybean is one of the most economically important crops worldwide and an important source of unsaturated fatty acids and protein for the human diet. Consumer demand for healthy fats and oils is increasing, and the global demand for vegetable oil is expected to double by 2050. Identification of key genes that regulate seed fatty acid content can facilitate molecular breeding of high-quality soybean varieties with enhanced fatty acid profiles. Here, we analysed the genetic architecture underlying variations in soybean seed fatty acid content using 547 accessions, including mainly landraces and cultivars from northeastern China. Through fatty acid profiling, genome re-sequencing, population genomics analyses, and GWAS, we identified a SEIPIN homologue at the FA9 locus as an important contributor to seed fatty acid content. Transgenic and multiomics analyses confirmed that FA9 was a key regulator of seed fatty acid content with pleiotropic effects on seed protein and seed size. We identified two major FA9 haplotypes in 1295 resequenced soybean accessions and assessed their phenotypic effects in a field planting of 424 accessions. Soybean accessions carrying FA9H2 had significantly higher total fatty acid contents and lower protein contents than those carrying FA9H1 . FA9H2 was absent in wild soybeans but present in 13% of landraces and 26% of cultivars, suggesting that it may have been selected during soybean post-domestication improvement. FA9 therefore represents a useful genetic resource for molecular breeding of high-quality soybean varieties with specific seed storage profiles.

Lipidomics, transcription analysis, and hormone profiling unveil the role of CsLOX6 in MeJA biosynthesis during black tea processing

Jasmonates, such as jasmonic acid (JA) and methyl jasmonate (MeJA), are crucial aspect of black tea quality. However, lipids species, hormones, and genes regulated mechanism in the jasmonate biosynthesis during black tea processing are lacking. In this study, we employed lipidomics, hormone metabolism analysis, and transcriptome profiling of genes associated with the MeJA biosynthesis pathway to investigate these factors. The contents of lipids GLs, PLs, and TAG are decreased, accompanied by the main lipids species reduced during black tea processing. Galactolipids, primarily 34:3/36:6/36:3 DGDG and 36:6/36:5/36:4 MGDG, are transformed into massive MeJA and JA in black tea processing, accompanied by the decreased SA, MeSA, IAA, and BA and increased zeatin. Additionally, the transcriptional activity of the primary genes in MeJA biosynthesis pathway exhibited downregulated trends except for AOS and OPR and non-primary genes tend to be a little high or have fluctuation of expression. Coordinated expression of main CsHPL (TEA008699), CsAOS (TEA001041), and CsJMT (TEA015791) control the flow of lipids degradation and MeJA production. A strong infected reduction of a key lipoxygenase gene, CsLOX6 (TEA009423), in tea buds significantly reduced the level of jasmonates and expression of downstream genes, accompanied by SA, MeSA level rising, and ABA declining. We have identified a key CsLOX6, as well as established galactolipids, mainly 34:3/36:6/36:3 DGDG and 36:6/36:5/36:4 MGDG, sources for MeJA biosynthesis regulated by dynamics hormone and controlled by coordinated expressed CsHPL (TEA008699), CsAOS (TEA001041), and CsJMT (TEA015791). Our findings provide a theoretical basis for breeding high-quality black tea and offer valuable insights for improving processing methods.

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.

Integrated lipidomic and transcriptomic analysis reveals diacylglycerol accumulation in olive of Longnan (China)

Background

Olive (Olea europaea L.) oil accumulate more diacylglycerols (DAG) than mostly vegetable oils. Unsaturated fatty acids-enriched DAG consumption enhanced wellness in subjects. However, the mechanism of DAG accumulation is not yet fully understood.

Methods

In this study, gene network of DAG accumulation and fatty acid composition in the two olive mesocarps ("Chenggu 32" (CG) and "Koroneiki" (QJ)) were investigated by integrating lipidome and transcriptome techniques.

Results

A total of 1,408 lipid molecules were identified by lipidomic analysis in olive mesocarp, of which DAG (DAG36:3, DAG36:4 and DAG36:5) showed higher content, and triacylglycerols (TAG54:3, TAG54:4) exhibited opposite trend in CG. Specifically, DAG was rich in polyunsaturated fatty acids (especially C18:2) at the sn-2 position, which was inconsistent with TAG at the same positions (Primarily C18:1). Transcriptomic analysis revealed that phospholipase C (NPC, EC 3.1.4.3) were up-regulated relative to QJ, whereas diacylglycerol kinase (ATP) (DGK, EC 2.7.1.107), diacylglycerol acyltransferase (DGAT, EC 2.3.1.20), and phospholipid: diacylglycerol acyltransferase (PDAT, EC 2.3.1.158) were down-regulated.

Conclusion

We speculated that the non-acyl coenzyme A pathway played a significant role in DAG biosynthesis. Additionally, fatty acyl-ACP thioesterase B (FATB, EC 3.1.2.14), stearoyl [acyl-carrier-protein] 9-desaturase (SAD, EC 1.14.19.2) and omega-6 fatty acid desaturase (FAD2, EC 1.14.19.6) were highly expressed in CG and may be involved in regulating fatty acid composition. Meanwhile, phospholipase A1 (LCAT, EC 3.1.1.32) involved in the acyl editing reaction facilitated PUFA linkage at the sn-2 position of DAG. Our findings provide novel insights to increase the DAG content, improve the fatty acid composition of olive oil, and identify candidate genes for the production of DAG-rich oils.

Soybean gene co-expression network analysis identifies two co-regulated gene modules associated with nodule formation and development

Gene co-expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait-associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co-expression network analysis. Two nodule-specific modules (NSM-1 and NSM-2, containing 304 and 203 genes, respectively) were identified. The NSM-1 gene promoters were significantly enriched in cis-binding elements for ERF, MYB, and C2H2-type zinc transcription factors, whereas NSM-2 gene promoters were enriched in cis-binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co-expressed genes. The co-expressed gene modules included genes with potential novel roles in nodulation, including those involved in xylem development, transmembrane transport, the ethylene signalling pathway, cytoskeleton organization, cytokinesis and regulation of the cell cycle, regulation of meristem initiation and growth, transcriptional regulation, DNA methylation, and histone modifications. Functional analysis of two co-expressed genes using TILLING mutants provided novel insight into the involvement of unsaturated fatty acid biosynthesis and folate metabolism in nodule formation and development. The identified gene co-expression modules provide valuable resources for further functional genomics studies to dissect the genetic basis of nodule formation and development in soybean.

Combined analysis of the metabolome and transcriptome provides insight into seed oil accumulation in soybean

BACKGROUND

Soybean (Glycine max (L.) Merr) is an important source of human food, animal feed, and bio-energy. Although the genetic network of lipid metabolism is clear in Arabidopsis, the understanding of lipid metabolism in soybean is limited.

RESULTS

In this study, 30 soybean varieties were subjected to transcriptome and metabolome analysis. In total, 98 lipid-related metabolites were identified, including glycerophospholipid, alpha-linolenic acid, linoleic acid, glycolysis, pyruvate, and the sphingolipid pathway. Of these, glycerophospholipid pathway metabolites accounted for the majority of total lipids. Combining the transcriptomic and metabolomic analyses, we found that 33 lipid-related metabolites and 83 lipid-related genes, 14 lipid-related metabolites and 17 lipid-related genes, and 12 lipid-related metabolites and 25 lipid-related genes were significantly correlated in FHO (five high-oil varieties) vs. FLO (five low-oil varieties), THO (10 high-oil varieties) vs. TLO (10 low-oil varieties), and HO (15 high-oil varieties) vs. LO (15 low-oil varieties), respectively.

CONCLUSIONS

The GmGAPDH and GmGPAT genes were significantly correlated with lipid metabolism genes, and the result revealed the regulatory relationship between glycolysis and oil synthesis. These results improve our understanding of the regulatory mechanism of soybean seed oil improvement.

Aluminum and Fluoride Stresses Altered Organic Acid and Secondary Metabolism in Tea (Camellia sinensis) Plants: Influences on Plant Tolerance, Tea Quality and Safety

Tea plants have adapted to grow in tropical acidic soils containing high concentrations of aluminum (Al) and fluoride (F) (as Al/F hyperaccumulators) and use secret organic acids (OAs) to acidify the rhizosphere for acquiring phosphorous and element nutrients. The self-enhanced rhizosphere acidification under Al/F stress and acid rain also render tea plants prone to accumulate more heavy metals and F, which raises significant food safety and health concerns. However, the mechanism behind this is not fully understood. Here, we report that tea plants responded to Al and F stresses by synthesizing and secreting OAs and altering profiles of amino acids, catechins, and caffeine in their roots. These organic compounds could form tea-plant mechanisms to tolerate lower pH and higher Al and F concentrations. Furthermore, high concentrations of Al and F stresses negatively affected the accumulation of tea secondary metabolites in young leaves, and thereby tea nutrient value. The young leaves of tea seedlings under Al and F stresses also tended to increase Al and F accumulation in young leaves but lower essential tea secondary metabolites, which challenged tea quality and safety. Comparisons of transcriptome data combined with metabolite profiling revealed that the corresponding metabolic gene expression supported and explained the metabolism changes in tea roots and young leaves via stresses from high concentrations of Al and F. The study provides new insight into Al- and F-stressed tea plants with regard to responsive metabolism changes and tolerance strategy establishment in tea plants and the impacts of Al/F stresses on metabolite compositions in young leaves used for making teas, which could influence tea nutritional value and food safety.

Lipidomic and transcriptomic profiles of glycerophospholipid metabolism during Hemerocallis citrina Baroni flowering

BACKGROUND

Hemerocallis citrina Baroni (daylily) is a horticultural ornamental plant and vegetable with various applications as a raw material in traditional Chinese medicine and as a flavouring agent. Daylily contains many functional substances and is rich in lecithin, which is mostly composed of glycerophospholipids. To study the comprehensive dynamic changes in glycerophospholipid during daylily flowering and the underlying signalling mechanisms, we performed comprehensive, time-resolved lipidomic and transcriptomic analyses of 'Datong Huanghua 6' daylily.

RESULTS

Labelling with PKH67 fluorescent antibodies clearly and effectively helped visualise lipid changes in daylily, while relative conductivity and malonaldehyde content detection revealed that the early stages of flowering were controllable processes; however, differences became non-significant after 18 h, indicating cellular damage. In addition, phospholipase D (PLD) and lipoxygenase (LOX) activities increased throughout the flowering process, suggesting that lipid hydrolysis and oxidation had intensified. Lipidomics identified 558 lipids that changed during flowering, with the most different lipids found 12 h before and 12 h after flowering. Transcriptome analysis identified 13 key functional genes and enzymes in the glycerophospholipid metabolic pathway. The two-way orthogonal partial least squares analysis showed that diacylglycerol diphosphate phosphatase correlated strongly and positively with phosphatidic acid (PA)(22:0/18:2), PA(34:2), PA(34:4), and diacylglycerol(18:2/21:0) but negatively with phospholipase C. In addition, ethanolamine phosphotransferase gene and phospholipid-N-methyltransferase gene correlated positively with phosphatidylethanolamine (PE)(16:0/18:2), PE(16:0/18:3), PE(33:2), and lysophosphatidylcholine (16:0) but negatively with PE(34:1).

CONCLUSIONS

Overall, this study elucidated changes in the glycerophospholipid metabolism pathway during the daylily flowering process, as well as characteristic genes, thus providing a basis for future studies of glycerophospholipids and signal transduction in daylilies.

GmWRI1c Increases Palmitic Acid Content to Regulate Seed Oil Content and Nodulation in Soybean (Glycine max)

Soybean (Glycine max) is an important oil crop, but the regulatory mechanisms underlying seed oil accumulation remain unclear. We identified a member of the GmWRI1s transcription factor family, GmWRI1c, that is involved in regulating soybean oil content and nodulation. Overexpression of GmWRI1c in soybean hairy roots increased the expression of genes involved in glycolysis and de novo lipogenesis, the proportion of palmitic acid (16:0), and the number of root nodules. The effect of GmWRI1c in increasing the number of root nodules via regulating the proportion of palmitic acid was confirmed in a recombinant inbred line (RIL) population. GmWRI1c shows abundant sequence diversity and has likely undergone artificial selection during domestication. An association analysis revealed a correlation between seed oil content and five linked natural variations (Hap1/Hap2) in the GmWRI1c promoter region. Natural variations in the GmWRI1c promoter were strongly associated with the GmWRI1c transcript level, with higher GmWRI1c transcript levels in lines carrying GmWRI1c^Hap1 than in those carrying GmWRI1c^Hap2. The effects of GmWRI1c alleles on seed oil content were confirmed in natural and RIL populations. We identified a favourable GmWRI1c allele that can be used to breed new varieties with increased seed oil content and nodulation.

Integrated analyses of transcriptome and metabolome provides new insights into the primary and secondary metabolism in response to nitrogen deficiency and soil compaction stress in peanut roots

Peanut (Arachis hypogaea L.) is an important oil crop globally because of its high edible and economic value. However, its yield and quality are often restricted by certain soil factors, especially nitrogen (N) deficiency, and soil compaction. To explore the molecular mechanisms and metabolic basis behind the peanut response to N deficiency and soil compaction stresses, transcriptome and metabolome analyses of peanut root were carried out. The results showed that N deficiency and soil compaction stresses clearly impaired the growth and development of peanut's aboveground and underground parts, as well as its root nodulation. A total of 18645 differentially expressed genes (DEGs) and 875 known differentially accumulated metabolites (DAMs) were identified in peanut root under differing soil compaction and N conditions. The transcriptome analysis revealed that DEGs related to N deficiency were mainly enriched in "amino acid metabolism", "starch and sucrose metabolism", and "TCA cycle" pathways, while DEGs related to soil compaction were mainly enriched in "oxidoreductase activity", "lipids metabolism", and "isoflavonoid biosynthesis" pathways. The metabolome analysis also showed significant differences in the accumulation of metabolisms in these pathways under different stress conditions. Then the involvement of genes and metabolites in pathways of "amino acid metabolism", "TCA cycle", "lipids metabolism", and "isoflavonoid biosynthesis" under different soil compaction and N deficiency stresses were well discussed. This integrated transcriptome and metabolome analysis study enhances our mechanistic knowledge of how peanut plants respond to N deficiency and soil compaction stresses. Moreover, it provides new leads to further investigate candidate functional genes and metabolic pathways for use in improving the adaptability of peanut to abiotic stress and accelerating its breeding process of new stress-resistant varieties.

Fatty acid desaturases (FADs) modulate multiple lipid metabolism pathways to improve plant resistance

BACKGROUND

Biological and abiotic stresses such as salt, extreme temperatures, and pests and diseases place major constraints on plant growth and crop yields. Fatty acids (FAs) and FA- derivatives are unique biologically active substance that show a wide range of functions in biological systems. They are not only participated in the regulation of energy storage substances and cell membrane plasm composition, but also extensively participate in the regulation of plant basic immunity, effector induced resistance and systemic resistance and other defense pathways, thereby improving plant resistance to adversity stress. Fatty acid desaturases (FADs) is involved in the desaturation of fatty acids, where desaturated fatty acids can be used as substrates for FA-derivatives.

OBJECTIVE

In this paper, the role of omega-FADs (ω-3 FADs and ω-6 FADs) in the prokaryotic and eukaryotic pathways of fatty acid biosynthesis in plant defense against stress (biological and abiotic stress) and the latest research progress were summarized. Moreover' the existing problems in related research and future research directions were also discussed.

RESULTS

Fatty acid desaturases are involved in various responses of plants during biotic and abiotic stress. For example, it is involved in regulating the stability and fluidity of cell membranes, reactive oxygen species signaling pathways, etc. In this review, we have collected several experimental studies to represent the differential effects of fatty acid desaturases on biotic and abiotic species.

CONCLUSION

Fatty acid desaturases play an important role in regulating biotic and abiotic stresses.

Progress in soybean functional genomics over the past decade

Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.

Foliar Application with Iron Oxide Nanomaterials Stimulate Nitrogen Fixation, Yield, and Nutritional Quality of Soybean

Sustainable strategies for the management of iron deficiency in agriculture are warranted because of the low use efficiency of commercial iron fertilizer, which confounds global food security and induces negative environmental consequences. The impact of foliar application of differently sized γ-Fe2O3 nanomaterials (NMs, 4-15, 8-30, and 40-215 nm) on the growth and physiology of soybean seedlings was investigated at different concentrations (10-100 mg/L). Importantly, the beneficial effects on soybean were size- and concentration-dependent. Foliar application with the smallest size γ-Fe2O3 NMs (S-Fe2O3 NMs, 4-15 nm, 30 mg/L) yielded the greatest growth promotion, significantly increasing the shoot and nodule biomass by 55.4 and 99.0%, respectively, which is 2.0- and 2.6-fold greater than the commercially available iron fertilizer (EDTA-Fe) with equivalent molar Fe. In addition, S-Fe2O3 NMs significantly enhanced soybean nitrogen fixation by 13.2% beyond that of EDTA-Fe. Mechanistically, transcriptomic and metabolomic analyses revealed that (1) S-Fe2O3 NMs increased carbon assimilation in nodules to supply more energy for nitrogen fixation; (2) S-Fe2O3 NMs activated the antioxidative system in nodules, with subsequent elimination of excess reactive oxygen species; (3) S-Fe2O3 NMs up-regulated the synthesis of cytokinin and down-regulated ethylene and jasmonic acid content in nodules, promoting nodule development and delaying nodule senescence. S-Fe2O3 NMs also improved 13.7% of the soybean yield and promoted the nutritional quality (e.g., free amino acid content) of the seeds as compared with EDTA-Fe with an equivalent Fe dose. Our findings demonstrate the significant potential of γ-Fe2O3 NMs as a high-efficiency and sustainable crop fertilizer strategy.

Phospholipase Ds in plants: Their role in pathogenic and symbiotic interactions

Phospholipase Ds (PLDs) are a heterogeneous group of enzymes that are widely distributed in organisms. These enzymes hydrolyze the structural phospholipids of the plasma membrane, releasing phosphatidic acid (PA), an important secondary messenger. Plant PLDs play essential roles in several biological processes, including growth and development, abiotic stress responses, and plant-microbe interactions. Although the roles of PLDs in plant-pathogen interactions have been extensively studied, their roles in symbiotic relationships are not well understood. The establishment of the best-studied symbiotic interactions, those between legumes and rhizobia and between most plants and mycorrhizae, requires the regulation of several physiological, cellular, and molecular processes. The roles of PLDs in hormonal signaling, lipid metabolism, and cytoskeletal dynamics during rhizobial symbiosis were recently explored. However, to date, the roles of PLDs in mycorrhizal symbiosis have not been reported. Here, we present a critical review of the participation of PLDs in the interactions of plants with pathogens, nitrogen-fixing bacteria, and arbuscular mycorrhizal fungi. We describe how PLDs regulate rhizobial and mycorrhizal symbiosis by modulating reactive oxygen species levels, hormonal signaling, cytoskeletal rearrangements, and G-protein activity.

Critical metabolic pathways and SAD/FADs, WRI1s, and DGATs cooperate for high-oleic acid oil production in developing oil tea (Camellia oleifera) seeds

Oil tea trees produce high-quality edible oils with desirably high oleic acid (18:1) and low linoleic (18:2) and linolenic (18:3) fatty acid (FA) levels, but limited understanding of tea oil biosynthesis and regulation has become a significant obstacle for the breeding of high-yield and -quality oil tea varieties. By integrating metabolite and transcriptome analyses of developing oil tea seeds, we dissected the critical metabolic pathways, including glycolysis, fatty acid, and triacylglycerol (TAG) biosynthesis, as well as genes essential for tea seed oil production. Two plastidic stearoyl-acyl carrier protein desaturases (CoSAD1 and 2) and two endoplasmic reticulum-localized FA desaturases (CoFAD2 and 3) were functionally characterized as responsible for high 18:1 and low 18:2 and 18:3 proportions in tea oils. Two diacylglycerol O-acyltransferases (CoDGAT1 and 2) that may prefer to synthesize 18:1-TAG were functionally characterized and might be also important for high 18:1-TAG production. The highly expressed CoWRI1a and b were identified and characterized as activators of glycolysis and regulators of directing source carbon flux into FA biosynthesis in developing oil tea seeds. The upregulated CoSADs with downregulated CoFAD2 and CoFAD3 at the late seed developmental stages mainly accounted for high 18:1 levels. Two CoDGATs might be responsible for assembling TAGs with oleoyl acyl chains, whilst two CoWRI1s regulated carbons from parental sources, partitioning into oil production in oil tea embryo sinks. This study provides a deep understanding of the biosynthesis of tea seed oils and information on genes that may be used as molecular markers to breed oil tea varieties with higher oil yield and quality.

Lipidomic, Transcriptomic, and BSA-660K Single Nucleotide Polymorphisms Profiling Reveal Characteristics of the Cuticular Wax in Wheat

Plant epidermal wax helps protect plants from adverse environmental conditions, maintains the function of tissues and organs, and ensures normal plant development. However, the constituents of epidermal wax and the regulatory mechanism of their biosynthesis in wheat have not been fully understood. Wheat varieties with different wax content, Jinmai47 and Jinmai84, were selected to comparatively analyze their waxy components and genetic characteristics, using a combination of lipidomic, transcriptomic, and BSA-Wheat 660K chip analysis. Through lipidomic analysis, 1287 lipid molecules were identified representing 31 lipid subclasses. Among these, Diacylglycerols (DG), (O-acyl)-ω-hydroxy fatty acids (OAHFA), wax ester (WE), Triacylglycerols (TG), and Monoradylglycerols (MG) accounted for 96.4% of the total lipids in Jinmai84 and 94.5% in Jinmai47. DG, OAHFA, and WE were higher in Jinmai84 than in Jinmai47 with the content of OAHFA 2.88-fold greater and DG 1.66-fold greater. Transcriptome sequence and bioinformatics analysis revealed 63 differentially expressed genes related to wax biosynthesis. Differentially expressed genes (DEGs) were found to be involved with the OAHFA, DG, and MG of synthesis pathways, which enriched the wax metabolism pathway. Non-glaucous and glaucous bulks from a mapping population were used to identify single nucleotide polymorphisms (SNP) via 660K chip analysis. Two loci centered on chromosomes 2D and 4B were detected and the locus on 4B is likely novel. These data improve understanding of complex lipid metabolism for cuticular wax biosynthesis in wheat and lay the foundation for future detailed investigation of mechanisms regulating wax metabolism.

The Metabolic Response of Brachypodium Roots to the Interaction with Beneficial Bacteria Is Affected by the Plant Nutritional Status

The potential of plant growth promoting (PGP) bacteria in improving the performance of plants in suboptimal environments is increasingly acknowledged, but little information is available on the mechanisms underlying this interaction, particularly when plants are subjected to a combination of stresses. In this study, we investigated the effects of the inoculation with the PGP bacteria Azospirillum brasilense (Azospirillum) on the metabolism of the model cereal Brachypodium distachyon (Brachypodium) grown at low temperatures and supplied with insufficient phosphorus. Investigating polar metabolite and lipid fluctuations during early plant development, we found that the bacteria initially elicited a defense response in Brachypodium roots, while at later stages Azospirillum reduced the stress caused by phosphorus deficiency and improved root development of inoculated plants, particularly by stimulating the growth of branch roots. We propose that the interaction of the plant with Azospirillum was influenced by its nutritional status: bacteria were sensed as pathogens while plants were still phosphorus sufficient, but the interaction became increasingly beneficial for the plants as their phosphorus levels decreased. Our results provide new insights on the dynamics of the cereal-PGP bacteria interaction, and contribute to our understanding of the role of beneficial microorganisms in the growth of cereal crops in suboptimal environments.

Phospholipase D- and phosphatidic acid-mediated phospholipid metabolism and signaling modulate symbiotic interaction and nodulation in soybean (Glycine max)

Symbiotic rhizobium-legume interactions, such as root hair curling, rhizobial invasion, infection thread expansion, cell division and proliferation of nitrogen-fixing bacteroids, and nodule formation, involve extensive membrane synthesis, lipid remodeling and cytoskeleton dynamics. However, little is known about these membrane-cytoskeleton interfaces and related genes. Here, we report the roles of a major root phospholipase D (PLD), PLDα1, and its enzymatic product, phosphatidic acid (PA), in rhizobium-root interaction and nodulation. PLDα1 was activated and the PA content transiently increased in roots after rhizobial infection. Levels of PLDα1 transcript and PA, as well as actin and tubulin cytoskeleton-related gene expression, changed markedly during root-rhizobium interactions and nodule development. Pre-treatment of the roots of soybean seedlings with n-butanol suppressed the generation of PLD-derived PA, the expression of early nodulation genes and nodule numbers. Overexpression or knockdown of GmPLDα1 resulted in changes in PA levels, glycerolipid profiles, nodule numbers, actin cytoskeleton dynamics, early nodulation gene expression and hormone levels upon rhizobial infection compared with GUS roots. The transcript levels of cytoskeleton-related genes, such as GmACTIN, GmTUBULIN, actin capping protein 1 (GmCP1) and microtubule-associating protein (GmMAP1), were modified in GmPLDα1-altered hairy roots compared with those of GUS roots. Phosphatidic acid physically bound to GmCP1 and GmMAP1, which could be related to cytoskeletal changes in rhizobium-infected GmPLDα1 mutant roots. These data suggest that PLDα1 and PA play important roles in soybean-rhizobium interaction and nodulation. The possible underlying mechanisms, including PLDα1- and PA-mediated lipid signaling, membrane remodeling, cytoskeleton dynamics and related hormone signaling, are discussed herein.

Soybean TILLING-by-Sequencing+ reveals the role of novel GmSACPD members in unsaturated fatty acid biosynthesis while maintaining healthy nodules

Developing soybean lines with high levels of stearic acid is a primary goal of the soybean industry. Most high-stearic-acid soybeans carry different GmSACPD-C mutated alleles. However, due to the dual role of GmSACPD-C in seeds and nodule development, all derived deleterious GmSACPD-C mutant alleles are of extremely poor agronomic value because of defective nodulation. The soybean stearoyl-acyl carrier protein desaturase (GmSACPD) gene family is composed of five members. Comparative genomics analysis indicated that SACPD genes were duplicated and derived from a common ancestor that is still present in chlorophytic algae. Synteny analysis showed the presence of segment duplications between GmSACPD-A/GmSACPD-B, and GmSACPD-C/GmSACPD-D. GmSACPD-E was not contained in any duplicated segment and may be the result of tandem duplication. We developed a TILLING by Target Capture Sequencing (Tilling-by-Sequencing+) technology, a versatile extension of the conventional TILLING by sequencing, and successfully identified 12, 14, and 18 ethyl methanesulfonate mutants at the GmSACPD-A, GmSACPD-B, and GmSACPD-D genes, respectively. Functional analysis of all identified mutants revealed an unprecedented role of GmSACPD-A, GmSACPD-B, and GmSACPD-D in unsaturated fatty acid biosynthesis without affecting nodule development and structure. This discovery will positively impact the development of high-stearic-acid lines to enhance soybean nutritional value without potential developmental tradeoffs.