Proteomic analysis of maize grain development using iTRAQ reveals temporal programs of diverse metabolic processes

Integrated Transcriptomic and Proteomic Characterization of a Chromosome Segment Substitution Line Reveals the Regulatory Mechanism Controlling the Seed Weight in Soybean

Soybean is the major global source of edible oils and vegetable proteins. Seed size and weight are crucial traits determining the soybean yield. Understanding the molecular regulatory mechanism underlying the seed weight and size is helpful for improving soybean genetic breeding. The molecular regulatory pathways controlling the seed weight and size were investigated in this study. The 100-seed weight, seed length, seed width, and seed weight per plant of a chromosome segment substitution line (CSSL) R217 increased compared with those of its recurrent parent 'Suinong14' (SN14). Transcriptomic and proteomic analyses of R217 and SN14 were performed at the seed developmental stages S15 and S20. In total, 2643 differentially expressed genes (DEGs) and 208 differentially accumulated proteins (DAPs) were detected at S15, and 1943 DEGs and 1248 DAPs were detected at S20. Furthermore, integrated transcriptomic and proteomic analyses revealed that mitogen-activated protein kinase signaling and cell wall biosynthesis and modification were potential pathways associated with seed weight and size control. Finally, 59 candidate genes that might control seed weight and size were identified. Among them, 25 genes were located on the substituted segments of R217. Two critical pathways controlling seed weight were uncovered in our work. These findings provided new insights into the seed weight-related regulatory network in soybean.

Cell-type proteomic and metabolomic resolution of early and late grain filling stages of wheat endosperm

The nutritional value of wheat grains, particularly their protein and metabolite composition, is a result of the grain-filling process, especially in the endosperm. Here, we employ laser microdissection (LMD) combined with shotgun proteomics and metabolomics to generate a cell type-specific proteome and metabolome inventory of developing wheat endosperm at the early (15 DAA) and late (26 DAA) grain-filling stages. We identified 1803 proteins and 41 metabolites from four different cell types (aleurone (AL), sub-aleurone (SA), starchy endosperm (SE) and endosperm transfer cells (ETCs). Differentially expressed proteins were detected, 67 in the AL, 31 in the SA, 27 in the SE and 50 in the ETCs between these two-time points. Cell-type accumulation of specific SUT and GLUT transporters, sucrose converting and starch biosynthesis enzymes correlate well with the respective sugar metabolites, suggesting sugar upload and starch accumulation via nucellar projection and ETC at 15 DAA in contrast to the later stage at 26 DAA. Changes in various protein levels between AL, SA and ETC support this metabolic switch from 15 to 26 DAA. The distinct spatial and temporal abundances of proteins and metabolites revealed a contrasting activity of nitrogen assimilation pathways, e.g. for GOGAT, GDH and glutamic acid, in the different cell types from 15 to 26 DAA, which can be correlated with specific protein accumulation in the endosperm. The integration of cell-type specific proteome and metabolome data revealed a complex metabolic interplay of the different cell types and a functional switch during grain development and grain-filling processes.

Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds

Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple-level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.

Reveal the kernel dehydration mechanisms in maize based on proteomic and metabolomic analysis

BACKGROUND

Kernel dehydration is an important factor for the mechanized harvest in maize. Kernel moisture content (KMC) and kernel dehydration rate (KDR) are important indicators for kernel dehydration. Although quantitative trait loci and genes related to KMC have been identified, where most of them only focus on the KMC at harvest, these are still far from sufficient to explain all genetic variations, and the relevant regulatory mechanisms are still unclear. In this study, we tried to reveal the key proteins and metabolites related to kernel dehydration in proteome and metabolome levels. Moreover, we preliminarily explored the relevant metabolic pathways that affect kernel dehydration combined proteome and metabolome. These results could accelerate the development of further mechanized maize technologies.

RESULTS

In this study, three maize inbred lines (KB182, KB207, and KB020) with different KMC and KDR were subjected to proteomic analysis 35, 42, and 49 days after pollination (DAP). In total, 8,358 proteins were quantified, and 2,779 of them were differentially expressed proteins in different inbred lines or at different stages. By comparative analysis, K-means cluster, and weighted gene co-expression network analysis based on the proteome data, some important proteins were identified, which are involved in carbohydrate metabolism, stress and defense response, lipid metabolism, and seed development. Through metabolomics analysis of KB182 and KB020 kernels at 42 DAP, 18 significantly different metabolites, including glucose, fructose, proline, and glycerol, were identified.

CONCLUSIONS

In sum, we inferred that kernel dehydration could be regulated through carbohydrate metabolism, antioxidant systems, and late embryogenesis abundant protein and heat shock protein expression, all of which were considered as important regulatory factors during kernel dehydration process. These results shed light on kernel dehydration and provide new insights into developing cultivars with low moisture content.

Phenotypic and Proteomic Insights into Differential Cadmium Accumulation in Maize Kernels

The contamination of agricultural soil with cadmium (Cd), a heavy metal, poses a significant environmental challenge, affecting crop growth, development, and human health. Previous studies have established the pivotal role of the ZmHMA3 gene, a P-type ATPase heavy metal transporter, in determining variable Cd accumulation in maize grains among 513 inbred lines. To decipher the molecular mechanism underlying mutation-induced phenotypic differences mediated by ZmHMA3, we conducted a quantitative tandem mass tag (TMT)-based proteomic analysis of immature maize kernels. This analysis aimed to identify differentially expressed proteins (DEPs) in wild-type B73 and ZmHMA3 null mutant under Cd stress. The findings demonstrated that ZmHMA3 accumulated higher levels of Cd compared to B73 when exposed to varying Cd concentrations in the soil. In comparison to soil with a low Cd concentration, B73 and ZmHMA3 exhibited 75 and 142 DEPs, respectively, with 24 common DEPs shared between them. ZmHMA3 showed a higher induction of upregulated genes related to Cd stress than B73. Amino sugar and nucleotide sugar metabolism was specifically enriched in B73, while phenylpropanoid biosynthesis, nitrogen metabolism, and glyoxylate and dicarboxylate metabolism appeared to play a more significant role in ZmHMA3. This study provides proteomics insights into unraveling the molecular mechanism underlying the differences in Cd accumulation in maize kernels.

Effects of 6-Benzyladenine (6-BA) on the Filling Process of Maize Grains Placed at Different Ear Positions under High Planting Density

Increasing grain weight under dense planting conditions can further improve maize yield. 6-BA is known to be involved in regulating grain development and influencing grain weight. Maize grain development is closely linked to starch accumulation and hormone levels. In this work, the effects of applying 6-BA at the flowering stage under high density on the grain filling characteristics, starch content, starch synthesis critical enzyme activity, and endogenous hormones levels of maize grains (including inferior grains (IGs) and superior grains (SGs)) of two high-yielding summer maize varieties widely cultivated in China were investigated. The findings indicated that applying 6-BA significantly improved maize yield compared to the control, mainly as a result of increased grain weight due to a faster grain filling rate. Additionally, the activities of enzymes associated with starch synthesis, including sucrose synthase (SuSy), ADP-glucose pyrophosphorylase (AGPase), granule-bound starch synthase (GBSS), soluble starch synthase (SSS), and starch branching enzyme (SBE), were all increased following 6-BA application, thus facilitating starch accumulation in the grains. Applying 6-BA also increased the zeatin riboside (ZR), indole-3-acetic acid (IAA), and abscisic acid (ABA) levels, and reduced the gibberellin (GA3) level in the grains, which further improved grain filling. It is worth noting that IG had a poorer filling process than SG, possibly due to the low activities of critical enzymes for starch synthesis and imbalanced endogenous hormones levels. However, IG responded more strongly to exogenous 6-BA than SG. It appears that applying 6-BA is beneficial in improving filling characteristics, promoting starch accumulation by enhancing the activities of critical enzymes for starch synthesis, and altering endogenous hormones levels in the grains, thus improving grain filling and increasing the final grain weight and yield of maize grown under crowded conditions. These results provide theoretical and technical support for the further utilization of exogenous hormones in high-density maize production.

Genome-wide identification and characterization of 14-3-3 gene family related to negative regulation of starch accumulation in storage root of Manihot esculenta

The 14-3-3 protein family is a highly conservative member of the acid protein family and plays an important role in regulating a series of important biological activities and various signal transduction pathways. The role of 14-3-3 proteins in regulating starch accumulation still remains largely unknown. To investigate the properties of 14-3-3 proteins, the structures and functions involved in starch accumulation in storage roots were analyzed, and consequently, 16 Me14-3-3 genes were identified. Phylogenetic analysis revealed that Me14-3-3 family proteins are split into two groups (ε and non-ε). All Me14-3-3 proteins contain nine antiparallel α-helices. Me14-3-3s-GFP fusion protein was targeted exclusively to the nuclei and cytoplasm. In the early stage of starch accumulation in the storage root, Me14-3-3 genes were highly expressed in high-starch cultivars, while in the late stage of starch accumulation, Me14-3-3 genes were highly expressed in low-starch cultivars. Me14-3-3 I, II, V, and XVI had relatively high expression levels in the storage roots. The transgenic evidence from Me14-3-3II overexpression in Arabidopsis thaliana and the virus-induced gene silencing (VIGS) in cassava leaves and storage roots suggest that Me14-3-3II is involved in the negative regulation of starch accumulation. This study provides a new insight to understand the molecular mechanisms of starch accumulation linked with Me14-3-3 genes during cassava storage root development.

Genome-Wide Identification of 14-3-3 gene family reveals their diverse responses to abiotic stress by interacting with StABI5 in Potato (Solanum tuberosum L.)

The 14-3-3 genes are widely present in plants and participate in a wide range of cellular and physiological processes. In the current study, twelve 14-3-3s were identified from potato genome. According to phylogenetic evolutionary analysis, potato 14-3-3s were divided into ϵ and non-ϵ groups. Conserved motif and gene structure analysis displayed a distinct class-specific divergence between the ϵ group and non-ϵ group. Multiple sequence alignments and three-dimensional structure analysis of 14-3-3 proteins indicated all the members contained nine conservative antiparallel α-helices. The majority of 14-3-3s had transcript accumulation in each detected potato tissue, implying their regulatory roles across all stages of potato growth and development. Numerous cis-acting elements related to plant hormones and abiotic stress response were identified in the promoter region of potato 14-3-3s, and the transcription levels of these genes fluctuated to different degrees under exogenous ABA, salt and drought stress, indicating that potato 14-3-3s may be involved in different hormone signaling pathways and abiotic stress responses. In addition, eight potato 14-3-3s were shown to interact with StABI5, which further demonstrated that potato 14-3-3s were involved in the ABA-dependent signaling pathway. This study provides a reference for the identification of the 14-3-3 gene family in other plants, and provides important clues for cloning potential candidates in response to abiotic stresses in potato.

A community resource to mass explore the wheat grain proteome and its application to the late-maturity alpha-amylase (LMA) problem

BACKGROUND

Late-maturity alpha-amylase (LMA) is a wheat genetic defect causing the synthesis of high isoelectric point alpha-amylase following a temperature shock during mid-grain development or prolonged cold throughout grain development, both leading to starch degradation. While the physiology is well understood, the biochemical mechanisms involved in grain LMA response remain unclear. We have applied high-throughput proteomics to 4,061 wheat flours displaying a range of LMA activities. Using an array of statistical analyses to select LMA-responsive biomarkers, we have mined them using a suite of tools applicable to wheat proteins.

RESULTS

We observed that LMA-affected grains activated their primary metabolisms such as glycolysis and gluconeogenesis; TCA cycle, along with DNA- and RNA- binding mechanisms; and protein translation. This logically transitioned to protein folding activities driven by chaperones and protein disulfide isomerase, as well as protein assembly via dimerisation and complexing. The secondary metabolism was also mobilized with the upregulation of phytohormones and chemical and defence responses. LMA further invoked cellular structures, including ribosomes, microtubules, and chromatin. Finally, and unsurprisingly, LMA expression greatly impacted grain storage proteins, as well as starch and other carbohydrates, with the upregulation of alpha-gliadins and starch metabolism, whereas LMW glutenin, stachyose, sucrose, UDP-galactose, and UDP-glucose were downregulated.

CONCLUSIONS

To our knowledge, this is not only the first proteomics study tackling the wheat LMA issue but also the largest plant-based proteomics study published to date. Logistics, technicalities, requirements, and bottlenecks of such an ambitious large-scale high-throughput proteomics experiment along with the challenges associated with big data analyses are discussed.

Maize ear growth is stimulated at the fourth day after pollination by cell wall remodeling and changes in lipid and hormone signaling

BACKGROUND

Stimulating maize ear development is an effective way of improving yield. However, limited information is available regarding the regulation of sink strength change from weak to strong at the same position of maize plants. Here, a novel method for stimulating development combined with physiological assays and proteomics was applied to explore the regulation of ear strengthened development.

RESULTS

By blocking pollination of the upper ear of maize hybrid Suyu 41, the adjacent lower ear was dramatically stimulated at 4 days after pollination (DAP). Tandem mass tag (TMT)-based proteomics identified 173 differentially expressed proteins (fold change >1.2 or <0.83, P < 0.05) from 7793 total proteins. Gene ontology annotations indicated that several pathways showed noticeable changes, with a preferential distribution to cell wall remodeling, hormone signals and lipid metabolism in the stimulated kernels. Cell wall remodeling was highly mediated by chitinase, exhydrolase II and xyloglucan enotransglucosylase/hydrolase, and accompanied by increased sucrose and glucose content. A series of lipoxygenase proteins were significantly upregulated, causing a significant alteration in lipid metabolism. Hormone signals were influenced by the expression of the proteins involved in indole-3-acetic acid (IAA) transport, zeatin (ZT) biosynthesis and abscisic acid (ABA) signal response, and increased IAA, ZT and ABA content.

CONCLUSION

The critical time for understanding the mechanism by which ear growth is stimulated is 4 DAP. Comparative proteomics and physiological analysis revealed that lipid metabolism enhancement, cell wall remodeling and changes in hormone signaling (IAA, ZT and ABA) were all important in stimulating early ear development. Proper regulation of these pathways may improve ear development, resulting in increased maize yield. © 2022 Society of Chemical Industry.

The molecular basis of cereal grain proteostasis

Storage proteins deposited in the endosperm of cereal grains are both a nitrogen reserve for seed germination and seedling growth and a primary protein source for human nutrition. Detailed surveys of the patterns of storage protein accumulation in cereal grains during grain development have been undertaken, but an in-depth understanding of the molecular mechanisms that regulate these patterns is still lacking. Accumulation of storage proteins in cereal grains involves a series of subcellular compartments, a set of energy-dependent events that compete with other cellular processes, and a balance of protein synthesis and protein degradation rates at different times during the developmental process. In this review, we focus on the importance of rates in cereal grain storage protein accumulation during grain development and outline the potential implications and applications of this information to accelerate modern agriculture breeding programmes and optimize energy use efficiency in proteostasis.

Spatial distribution of proteins and metabolites in developing wheat grain and their differential regulatory response during the grain filling process

Grain filling and grain development are essential biological processes in the plant's life cycle, eventually contributing to the final seed yield and quality in all cereal crops. Studies of how the different wheat (Triticum aestivum L.) grain components contribute to the overall development of the seed are very scarce. We performed a proteomics and metabolomics analysis in four different developing components of the wheat grain (seed coat, embryo, endosperm, and cavity fluid) to characterize molecular processes during early and late grain development. In-gel shotgun proteomics analysis at 12, 15, 20, and 26 days after anthesis (DAA) revealed 15 484 identified and quantified proteins, out of which 410 differentially expressed proteins were identified in the seed coat, 815 in the embryo, 372 in the endosperm, and 492 in the cavity fluid. The abundance of selected protein candidates revealed spatially and temporally resolved protein functions associated with development and grain filling. Multiple wheat protein isoforms involved in starch synthesis such as sucrose synthases, starch phosphorylase, granule-bound and soluble starch synthase, pyruvate phosphate dikinase, 14-3-3 proteins as well as sugar precursors undergo a major tissue-dependent change in abundance during wheat grain development suggesting an intimate interplay of starch biosynthesis control. Different isoforms of the protein disulfide isomerase family as well as glutamine levels, both involved in the glutenin macropolymer pattern, showed distinct spatial and temporal abundance, revealing their specific role as indicators of wheat gluten quality. Proteins binned into the functional category of cell growth/division and protein synthesis/degradation were more abundant in the early stages (12 and 15 DAA). At the metabolome level all tissues and especially the cavity fluid showed highly distinct metabolite profiles. The tissue-specific data are integrated with biochemical networks to generate a comprehensive map of molecular processes during grain filling and developmental processes.

The Pyruvate-Phosphate Dikinase (C4-SmPPDK) Gene From Suaeda monoica Enhances Photosynthesis, Carbon Assimilation, and Abiotic Stress Tolerance in a C3 Plant Under Elevated CO2 Conditions

A pyruvate-phosphate dikinase (C4-PPDK) gene was cloned from Suaeda monoica, which had a single-cell C4 photosynthesis pathway without Kranz anatomy and was functionally validated in a C3 model plant under different abiotic stress conditions in an ambient and elevated CO2 environment. Overexpression of SmPPDK promoted growth of C3 transgenic plants, enhancing their photosynthesis (CO2 assimilation) by lowering photorespiration under stress conditions. Transgenic plants also showed an improved physiological status, with higher relative water content (RWC), membrane integrity, concentration of glycine betaine, total soluble sugars, free amino acids, polyphenols and antioxidant activity, and lower electrolyte leakage, lipid peroxidation, free radical accumulation, and generation of reactive oxygen species (ROS), compared to control plants. Moreover, SmPPDK transgenic plants exhibited earlier flowering and higher dry biomass compared to controls. These results suggested that the C4-PPDK gene was appropriate for improvement of carbon assimilation, and it also played an important role in adaption to salinity and severe drought-induced stress. More intriguingly, an elevated CO2 environment alleviated the adverse effects of abiotic stress, particularly caused by drought through coordination of osmoprotectants and antioxidant defense systems. The molecular, physiological, metabolic, and biochemical indicators ameliorated the overall performance of model C3 plants overexpressing the C4-PPDK gene in an elevated CO2 environment, by lowering photorespiration metabolic processes, however, further studies are needed to confirm its precise role in C3 plants as protection against future climate change.

Label-Free Comparative Proteomic Analysis Combined with Laser-Capture Microdissection Suggests Important Roles of Stress Responses in the Black Layer of Maize Kernels

The black layer (BL) is traditionally used as an indicator for kernel harvesting in maize, as it turns visibly dark when the kernel reaches physiological maturity. However, the molecular roles of BL in kernel development have not been fully elucidated. In this work, microscopy images showed that BL began to appear at a growth stage earlier than 10 days after pollination (DAP), and its color gradually deepened to become dark as the development period progressed. Scanning electron microscopy observations revealed that BL is a tissue structure composed of several layers of cells that are gradually squeezed and compressed during kernel development. Laser-capture microdissection (LCM) was used to sample BL and its neighboring inner tissue, basal endosperm transfer layer (BETL), and outer tissue, inner epidermis (IEP), from 20 DAP of kernels. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry profiling (MALDI-TOF MS profiling) detected 41, 104, and 120 proteins from LCM-sampled BL, BETL, and IEP, respectively. Gene ontology (GO) analysis indicated that the 41 BL proteins were primarily involved in the response to stress and stimuli. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis found that the BL proteins were enriched in several defense pathways, such as the ascorbate and aldarate metabolic pathways. Among the 41 BL proteins, six were BL-specific proteins that were only detected from BL. Annotations of five BL-specific proteins were related to stress responses. During kernel development, transcriptional expression of most BL proteins showed an increase, followed by a decrease, and reached a maximum zero to 20 DAP. These results suggest a role for BL in stress responses for protecting filial tissue against threats from maternal sides, which helps to elucidate the biological functions of BL.

ACT001 modulates the NF-κB/MnSOD/ROS axis by targeting IKKβ to inhibit glioblastoma cell growth

Glioblastomas are high-grade brain tumors with poor prognoses, and new therapeutic approaches for these tumors are critically needed. This study revealed the underlying mechanisms of a new orphan drug, ACT001, that is currently in clinical trials for the treatment of advanced glioblastoma in Australia and China. ACT001 significantly suppressed glioma cell proliferation and induced apoptosis and cell cycle arrest in vitro, as determined by Cell Counting Kit-8 assays and flow cytometry. In addition, U-118 MG cells with high expression of p-IKKβ were sensitive to ACT001. Changes in the oxidative stress pathway in U-118 MG cells were detected with the isobaric tags for relative and absolute quantitation (iTRAQ) method. We further verified that ACT001 elevated the levels of reactive oxygen species (ROS) by regulating NF-κB-targeted MnSOD. ACT001 markedly inhibited NF-κB activation by directly binding IKKβ and inhibiting its phosphorylation. Overexpression of IKKβ markedly attenuated the changes in MnSOD and NOX1, indicating that ACT001 increased the levels of ROS by reducing the protein expression of p-IKKβ. Furthermore, ACT001 reduced cyclin B1/CDC2 expression and triggered G₂/M phase arrest by increasing ROS production. ACT001 also upregulated the expression of Bax and Bim and induced apoptosis in a ROS-dependent manner. ACT001 effectively suppressed the growth of U-118 MG tumors in BALB/c nude mice and GL-261-luciferase tumors in C57BL/6 J mice. Finally, ACT001 downregulated the expression of p-p65, MnSOD, cyclin B1, CDC2, and Ki67 in U-118 MG tumor tissues. Patients with activated NF-κB signaling should thus be given priority for enrollment in future phase II clinical trials. KEY MESSAGES: ACT001 directly bind to IKKβ and inhibited its phosphorylation. The inhibition of p-IKKβ induced the generation of ROS. ACT001 promoted the generation of ROS by regulating MnSOD expression to induce G₂/M phase arrest.

Cytological, Biochemical and Molecular Events of the Embryogenic State in Douglas-fir (Pseudotsuga menziesii [Mirb.])

Somatic embryogenesis techniques have been developed for most coniferous species, but only using very juvenile material. To extend the techniques' scope, better integrated understanding of the key biological, physiological and molecular characteristics of embryogenic state is required. Therefore, embryonal masses (EMs) and non-embryogenic calli (NECs) have been compared during proliferation at multiple levels. EMs and NECs originating from a single somatic embryo (isogenic lines) of each of three unrelated genotypes were used in the analyses, which included comparison of the lines' anatomy by transmission light microscopy, transcriptomes by RNAseq Illumina sequencing, proteomes by free-gel analysis, contents of endogenous phytohormones (indole-3-acetic acid, cytokinins and ABA) by LC-MS analysis, and soluble sugar contents by HPLC. EMs were characterized by upregulation (relative to levels in NECs) of transcripts, proteins, transcription factors and active cytokinins associated with cell differentiation accompanied by histological, carbohydrate content and genetic markers of cell division. In contrast, NECs were characterized by upregulation (relative to levels in EMs) of transcripts, proteins and products associated with responses to stimuli (ABA, degradation forms of cytokinins, phenols), oxidative stress (reactive oxygen species) and carbohydrate storage (starch). Sub-Network Enrichment Analyses that highlighted functions and interactions of transcripts and proteins that significantly differed between EMs and NECs corroborated these findings. The study shows the utility of a novel approach involving integrated multi-scale transcriptomic, proteomic, biochemical, histological and anatomical analyses to obtain insights into molecular events associated with embryogenesis and more specifically to the embryogenic state of cell in Douglas-fir.

Comprehensive transcriptomics and proteomics analyses of pollinated and parthenocarpic litchi (Litchi chinensis Sonn.) fruits during early development

Litchi (Litchi chinensis Sonn.) is an important fruit that is widely cultivated in tropical and subtropical areas. In this study, we used RNA-Seq and iTRAQ technologies to compare the transcriptomes and proteomes of pollinated (polLFs) and parthenocarpic (parLFs) litchi fruits during early development (1 day, 2 days, 4 days and 6 days). We identified 4,864 DEGs in polLFs and 3,672 in parLFs, of which 2,835 were shared and 1,051 were specifically identified in parLFs. Compared to po1LFs, 768 DEGs were identified in parLFs. iTRAQ analysis identified 551 DEPs in polLFs and 1,021 in parLFs, of which 305 were shared and 526 were exclusively identified in parLFs. We found 1,127 DEPs in parLFs compared to polLFs at different stages. Further analysis revealed some DEGs/DEPs associated with abscisic acid, auxin, ethylene, gibberellin, heat shock protein (HSP), histone, ribosomal protein, transcription factor and zinc finger protein (ZFP). WGCNA identified a large set of co-expressed genes/proteins in polLFs and parLFs. In addition, a cross-comparison of transcriptomic and proteomic data identified 357 consistent DEGs/DEPs in polLFs and parLFs. This is the first time that protein/gene changes have been studied in polLFs and parLFs, and the findings improve our understanding of litchi parthenocarpy.

Photosynthetic Properties and Potentials for Improvement of Photosynthesis in Pale Green Leaf Rice under High Light Conditions

Light is the driving force of plant growth, providing the energy required for photosynthesis. However, photosynthesis is also vulnerable to light-induced damage caused by the production of reactive oxygen species (ROS). Plants have therefore evolved various protective mechanisms such as non-photochemical quenching (NPQ) to dissipate excessively absorbed solar energy as heat; however, photoinhibition and NPQ represent a significant loss in solar energy and photosynthetic efficiency, which lowers the yield potential in crops. To estimate light capture and light energy conversion in rice, a genotype with pale green leaves (pgl) and a normally pigmented control (Z802) were subjected to high (HL) and low light (LL). Chlorophyll content, light absorption, chloroplast micrographs, abundance of light-harvesting complex (LHC) binding proteins, electron transport rates (ETR), photochemical and non-photochemical quenching, and generation of ROS were subsequently examined. Pgl had a smaller size of light-harvesting chlorophyll antenna and absorbed less photons than Z802. NPQ and the generation of ROS were also low, while photosystem II efficiency and ETR were high, resulting in improved photosynthesis and less photoinhibition in pgl than Z802. Chlorophyll synthesis and solar conversion efficiency were higher in pgl under HL compared to LL treatment, while Z802 showed an opposite trend due to the high level of photoinhibition under HL. In Z802, excessive absorption of solar energy not only increased the generation of ROS and NPQ, but also exacerbated the effects of increases in temperature, causing midday depression in photosynthesis. These results suggest that photosynthesis and yield potential in rice could be enhanced by truncated light-harvesting chlorophyll antenna size.

Proteomics analysis of maize (Zea mays L.) grain based on iTRAQ reveals molecular mechanisms of poor grain filling in inferior grains

In maize, inferior grains (IG) located on the upper part of the ear have poor grain filling process compared to superior grains (SG) located on the middle and lower parts of the ear. This difference limits satisfactory yield and quality; however, the underlying molecular mechanisms remain unknown. Here, using the isobaric tag for relative and absolute quantification (iTRAQ) technology, the proteomes of IG and SG during early and middle grain filling stages were investigated. In total, 4720 proteins were identified in maize grain and 305 differentially accumulated proteins (DiAPs) were detected between IG and SG. These DiAPs were involved in diverse cellular and metabolic processes with preferred distribution in protein synthesis/destination and metabolism. Compared to SG, DiAPs related to cell growth/division and starch synthesis were lag-accumulated and down-regulated in IG, respectively, resulting in smaller sink sizes and lower sink activities in IG. Meanwhile, impediment of the glycolysis pathway in IG may lead to reduce energy supply and building materials for substance synthesis. Additionally, reactive oxygen species (ROS) homeostasis and the defense system were disturbed in IG, which might lead to reduce protection against various environmental stresses. The present study provides new information on the proteomic differences between IG and SG, and explains possible molecular mechanisms for poor grain filling in IG.