GWAS unravels acid phosphatase ACP2 as a photosynthesis regulator under phosphate starvation condition through modulating serine metabolism in rice.

Inorganic phosphorus (Pi) deficiency significantly impacts plant growth, development and photosynthetic efficiency (Asat). This study evaluated 206 rice accessions from a MiniCore population under both Pi sufficient (Pi+) and Pi starvation (Pi-) conditions in the field to assess photosynthetic phosphorus use efficiency (PPUE), defined as the ratio of AsatPi- to AsatPi+. A genome-wide association study (GWAS) and differential gene expression analyses identified an acid phosphatase (ACP2) gene that responds strongly to phosphate availability. Overexpress and knock out ACP2 led to 67% increase and 32% decrease in PPUE, respectively, compared to WT. Introduction of an elite allele A, by substituting v5 SNP from G to A, resulted in 18% increase in PPUE in gene-edited ACP2 rice lines. The phosphate-responsive gene PHR2 was found to transcriptionally activate ACP2 in parallel with PHR2 overexpression resulting in 11% increase in PPUE. Biochemical assays indicated that ACP2 primarily catalyzes the hydrolysis of phosphoethanolamine and phospho-L-serine. Additionally, serine levels were found to increase significantly in ACP2v8G OE line, along with a concomitant decrease in the expression of all nine genes involved in the photorespiratory pathway. Application of serine was shown to enhance PPUE and reduce photorespiration rates (PR) in ACP2 mutant under Pi-starvation conditions. In deduction, ACP2 plays a crucial role in promoting photosynthesis adaptation to Pi starvation by regulating serine metabolism in rice.

The MRE11-ATM-SOG1 DNA damage signaling pathway confers rice immunity to Xanthomonas oryzae.

Plants are constantly exposed to microbial pathogens in the environment. One branch of innate plant immunity is mediated by cell-membrane-localized receptors, but less is known about associations between DNA damage and plant immune responses. Here, we show that rice (Oryza sativa) mesophyll cells are prone to DNA double-stranded breaks (DSBs) in response to ZJ173, a strain of Xanthomonas oryzae pv. oryzae (Xoo). The DSB signal transducer ataxia telangiectasia mutated (ATM), but not the ATM and Rad3-related branch, confers resistance against Xoo. Mechanistically, the MRE11-ATM module phosphorylates suppressor of gamma response 1 (SOG1), which activates several phenylpropanoid pathway genes and prompts downstream phytoalexin biosynthesis during Xoo infection. Intriguingly, overexpression of the topoisomerase gene TOP6A3 causes a switch from the classic non-homologous end joining (NHEJ) pathway to the alternative NHEJ and homologous recombination pathways at Xoo-induced DSBs. The enhanced ATM signaling of the alternative NHEJ pathway strengthens the SOG1-regulated phenylpropanoid pathway and thereby boosts Xoo-induced phytoalexin biosynthesis in TOP6A3-OE1 overexpression lines. Overall, the MRE11-ATM-SOG1 pathway serves as a prime example of plant-pathogen interactions that occur via host non-specific recognition. The function of TOP6-facilitated ATM signaling in the defense response makes it a promising target for breeding of rice germplasm that exhibits resistance to bacterial blight disease without a growth penalty.

The Molecular Mechanism of GhbHLH121 in Response to Iron Deficiency in Cotton Seedlings.

Iron deficiency caused by high pH of saline-alkali soil is a major source of abiotic stress affecting plant growth. However, the molecular mechanism underlying the iron deficiency response in cotton (Gossypium hirsutum) is poorly understood. In this study, we investigated the impacts of iron deficiency at the cotton seedling stage and elucidated the corresponding molecular regulation network, which centered on a hub gene GhbHLH121. Iron deficiency induced the expression of genes with roles in the response to iron deficiency, especially GhbHLH121. The suppression of GhbHLH121 with virus-induced gene silence technology reduced seedlings' tolerance to iron deficiency, with low photosynthetic efficiency and severe damage to the structure of the chloroplast. Contrarily, ectopic expression of GhbHLH121 in Arabidopsis enhanced tolerance to iron deficiency. Further analysis of protein/protein interactions revealed that GhbHLH121 can interact with GhbHLH IVc and GhPYE. In addition, GhbHLH121 can directly activate the expression of GhbHLH38, GhFIT, and GhPYE independent of GhbHLH IVc. All told, GhbHLH121 is a positive regulator of the response to iron deficiency in cotton, directly regulating iron uptake as the upstream gene of GhFIT. Our results provide insight into the complex network of the iron deficiency response in cotton.

Cold-induced inhibition of photosynthesis-related genes integrated by a TOP6 complex in rice mesophyll cells.

Photosynthesis is the most temperature-sensitive process in the plant kingdom, but how the photosynthetic pathway responds during low-temperature exposure remains unclear. Herein, cold stress (4°C) induced widespread damage in the form DNA double-stranded breaks (DSBs) in the mesophyll cells of rice (Oryza sativa), subsequently causing a global inhibition of photosynthetic carbon metabolism (PCM) gene expression. Topoisomerase genes TOP6A3 and TOP6B were induced at 4°C and their encoded proteins formed a complex in the nucleus. TOP6A3 directly interacted with KU70 to inhibit its binding to cold-induced DSBs, which was facilitated by TOP6B, finally blocking the loading of LIG4, a component of the classic non-homologous end joining (c-NHEJ) pathway. The repression of c-NHEJ repair imposed by cold extended DSB damage signaling, thus prolonging the inhibition of photosynthesis in leaves. Furthermore, the TOP6 complex negatively regulated 13 crucial PCM genes by directly binding to their proximal promoter regions. Phenotypically, TOP6A3 overexpression exacerbated the γ-irradiation-triggered suppression of PCM genes and led to the hypersensitivity of photosynthesis parameters to cold stress, dependent on the DSB signal transducer ATM. Globally, the TOP6 complex acts as a signal integrator to control PCM gene expression and synchronize cold-induced photosynthesis inhibition, which modulates carbon assimilation rates immediately in response to changes in ambient temperature.

Integrative analysis of transcriptome and metabolism reveals potential roles of carbon fixation and photorespiratory metabolism in response to drought in Shanlan upland rice.

Shanlan upland rice is an important landrace rice resource and is characterized with high drought stress (DS) tolerance relative to cultivated rice. However, the molecular mechanism of DS response in Shanlan upland rice remains unclear. In this study, we performed an integrated analysis of transcriptome and targeted metabolism to decipher the key biological pathways that responded to drought tolerance using two Shanlan upland rice lines. Results show that SL10 possesses 64% higher photosynthetic efficiency (Pn) and 2-fold higher water use efficiency (WUE) than that in SL1 exposed to DS. The decrease in Pn by DS is not due to stomatal limitation effects for SL1. Transcriptome analysis suggests photosynthesis relevant pathways (photosynthesis-antenna proteins and carbon fixation) and photorespiration relevant pathway (glycine, serine and threonine metabolism) in SL1 under DS were significantly enriched in the down-regulated and up-regulated DEGs list, respectively. There are 412 up-regulated and 233 down-regulated drought responsive genes (DRGs) in SL10 relative to SL1 induced by DS. Targeted metabolism results suggest that the contents across five metabolites related to carbon fixation pathway were declined by 36 and 8% in SL1 and SL10 caused by DS, respectively. We finally summarized the both gene expression and metabolites involved in photorespiration and carbon fixation pathways in response to DS in both rice lines. This study provides valuable information for better understanding the molecular mechanism underlying drought tolerance in Shanlan rice.

The Ethylene Response Factor ERF5 Regulates Anthocyanin Biosynthesis in 'Zijin' Mulberry Fruits by Interacting with MYBA and F3H Genes.

Ethylene promotes ripening in fruits as well as the biosynthesis of anthocyanins in plants. However, the question of which ethylene response factors (ERFs) interact with the genes along the anthocyanin biosynthesis pathway is yet to be answered. Herein, we conduct an integrated analysis of transcriptomes and metabolome on fruits of two mulberry genotypes ('Zijin', ZJ, and 'Dashi', DS, with high and low anthocyanin abundance, respectively) at different post-flowering stages. In total, 1035 upregulated genes were identified in ZJ and DS, including MYBA in the MBW complex and anthocyanin related genes such as F3H. A KEGG analysis suggested that flavonoid biosynthesis and plant hormone signaling transduction pathways were significantly enriched in the upregulated gene list. In particular, among 103 ERF genes, the expression of ERF5 showed the most positive correlation with the anthocyanin change pattern across both genotypes and in the post-flowering stages, with a Pearson correlation coefficient (PCC) of 0.93. Electrophoresis mobility shift assay (EMSA) and luciferase assay suggested that ERF5 binds to the promoter regions of MYBA and F3H and transcriptionally activates their gene expression. We elucidated a potential mechanism by which ethylene enhances anthocyanin accumulation in mulberry fruits and highlighted the importance of the ERF5 gene in controlling the anthocyanin content in mulberry species. This knowledge could be used for engineering purposes in future mulberry breeding programs.

An Evidence Theory and Fuzzy Logic Combined Approach for the Prediction of Potential ARF-Regulated Genes in Quinoa.

Quinoa constitutes among the tolerant plants to the challenging and harmful abiotic environmental factors. Quinoa was selected as among the model crops destined for bio-saline agriculture that could contribute to the staple food security for an ever-growing worldwide population under various climate change scenarios. The auxin response factors (ARFs) constitute the main contributors in the plant adaptation to severe environmental conditions. Thus, the determination of the ARF-binding sites represents the major step that could provide promising insights helping in plant breeding programs and improving agronomic traits. Hence, determining the ARF-binding sites is a challenging task, particularly in species with large genome sizes. In this report, we present a data fusion approach based on Dempster-Shafer evidence theory and fuzzy set theory to predict the ARF-binding sites. We then performed an "In-silico" identification of the ARF-binding sites in Chenopodium quinoa. The characterization of some known pathways implicated in the auxin signaling in other higher plants confirms our prediction reliability. Furthermore, several pathways with no or little available information about their functions were identified to play important roles in the adaptation of quinoa to environmental conditions. The predictive auxin response genes associated with the detected ARF-binding sites may certainly help to explore the biological roles of some unknown genes newly identified in quinoa.

Evaluation on reprogramed biological processes in transgenic maize varieties using transcriptomics and metabolomics.

Genetic engineering (GM) has great potential to improve maize productivity, but rises some concerns on unintended effects, and equivalent as their comparators. There are some limitations through targeted analysis to detect the UE in genetically modified organisms in many previous studies. We here reported a case-study on the effects of introducing herbicides and insect resistance (HIR) gene cassette on molecular profiling (transcripts and metabolites) in a popular maize variety Zhengdan958 (ZD958) in China. We found that introducing HIR gene cassette bring a limited numbers of differential abundant genes (DAGs) or differential abundant metabolites (DAMs) between transgenic events and non-transgenic control. In contrast, averaged 10 times more DAGs and DAMs were observed when performed comparison under different growing environments in three different ecological regions of China than the numbers induced by gene effects. Major biological pathways relating to stress response or signaling transduction could explain somehow the effects of growing environments. We further compared two transgenic events mediated ZD958 (GM-ZD958) with either transgenic parent GM-Z58, and other genetic background nonGM-Z58, nonGM-ZD958, and Chang7-2. We found that the numbers of DAGs and DAMs between GM-ZD958 and its one parent maize variety, Z58 or GM-Z58 is equivalent, but not Chang7-2. These findings suggest that greater effects due to different genetic background on altered molecular profiling than gene modification itself. This study provides a case evidence indicating marginal effects of gene pleiotropic effects, and environmental effects should be emphasized.

Knocking out NEGATIVE REGULATOR OF PHOTOSYNTHESIS 1 increases rice leaf photosynthesis and biomass production in the field.

Improving photosynthesis is a major approach to increasing crop yield potential. Here we identify a transcription factor as a negative regulator of photosynthesis, which can be manipulated to increase rice photosynthesis and plant biomass in the field. This transcription factor, named negative regulator of photosynthesis 1 (NRP1; Os07g0471900), was identified through a co-expression analysis using rice leaf RNA sequencing data. NRP1 expression showed significantly negative correlation with the expression of many genes involved in photosynthesis. Knocking out NRP1 led to greater photosynthesis and increased biomass in the field, while overexpression of NRP1 decreased photosynthesis and biomass. Transcriptomic data analysis shows that NRP1 can negatively regulate the expression of photosynthetic genes. Protein transactivation experiments show that NRP1 is a transcription activator, implying that NRP1 may indirectly regulate photosynthetic gene expression through an unknown regulator. This study shows that combination of bioinformatics analysis with transgenic testing can be used to identify new regulators to improve photosynthetic efficiency in crops.

Natural variation in the fast phase of chlorophyll a fluorescence induction curve (OJIP) in a global rice minicore panel.

Photosynthesis can be probed through Chlorophyll a fluorescence induction (FI), which provides detailed insight into the electron transfer process in Photosystem II, and beyond. Here, we have systematically studied the natural variation of the fast phase of the FI, i.e. the OJIP phase, in rice. The OJIP phase of the Chl a fluorescence induction curve is referred to as "fast transient" lasting for less than a second; it is obtained after a dark-adapted sample is exposed to saturating light. In the OJIP curve, "O" stands for "origin" (minimal fluorescence), "P" for "peak" (maximum fluorescence), and J and I for inflection points between the O and P levels. Further, Fo is the fluorescence intensity at the "O" level, whereas Fm is the intensity at the P level, and Fv (= Fm - Fo) is the variable fluorescence. We surveyed a set of quantitative parameters derived from the FI curves of 199 rice accessions, grown under both field condition (FC) and growth room condition (GC). Our results show a significant variation between Japonica (JAP) and Indica (IND) subgroups, under both the growth conditions, in almost all the parameters derived from the OJIP curves. The ratio of the variable to the maximum (Fv/Fm) and of the variable to the minimum (Fv/Fo) fluorescence, the performance index (PIabs), as well as the amplitude of the I-P phase (AI-P) show higher values in JAP compared to that in the IND subpopulation. In contrast, the amplitude of the O-J phase (AO-J) and the normalized area above the OJIP curve (Sm) show an opposite trend. The performed genetic analysis shows that plants grown under GC appear much more affected by environmental factors than those grown in the field. We further conducted a genome-wide association study (GWAS) using 11 parameters derived from plants grown in the field. In total, 596 non-unique significant loci based on these parameters were identified by GWAS. Several photosynthesis-related proteins were identified to be associated with different OJIP parameters. We found that traits with high correlation are usually associated with similar genomic regions. Specifically, the thermal phase of FI, which includes the amplitudes of the J-I and I-P subphases (AJ-I and AI-P) of the OJIP curve, is, in turn, associated with certain common genomic regions. Our study is the first one dealing with the natural variations in rice, with the aim to characterize potential candidate genes controlling the magnitude and half-time of each of the phases in the OJIP FI curve.

Alterations in stomatal response to fluctuating light increase biomass and yield of rice under drought conditions.

The acceleration of stomatal closure upon high to low light transition could improve plant water use efficiency and drought tolerance. Herein, using genome-wide association study, we showed that the genetic variation in OsNHX1 was strongly associated with the changes in τcl , the time constant of stomatal closure, in 206 rice accessions. OsNHX1 overexpression in rice resulted in a decrease in τcl , and an increase in biomass, grain yield under drought. Conversely, OsNHX1 knockout by CRISPR/CAS9 shows opposite trends for these traits. We further found three haplotypes spanning the OsNHX1 promoter and CDS regions. Two among them, HapII and HapIII, were found to be associated with a high and low τcl , respectively. A near-isogenic line (NIL, S464) was developed through replacing the genomic region harboring HapII (~10 kb) from MH63 (recipient) rice cultivar by the same sized genomic region containing Hap III from 02428 (donor). Compared with MH63, S464 shows a reduction by 35% in τcl and an increase by 40% in the grain yield under drought. However, under normal conditions, S464 maintains closely similar grain yield as MH63. The global distribution of the two OsNHX1 haplotypes is associated with the local precipitation. Taken together, the natural variation in OsNHX1 could be utilized to manipulate the stomatal dynamics for an improved rice drought tolerance.

Photosynthetic and transcriptomic responses of two C4 grass species with different NaCl tolerance.

This report reveals the effects of salt on the photosynthetic electron transport and transcriptome of the glycophyte Setaria viridis (S. viridis) and its salt-tolerant close relative halophyte Spartina alterniflora (S. alterniflora). S. viridis was unable to survive exposed to sodium chloride (NaCl) levels higher than 100 mM, in contrast, S. alterniflora could tolerate NaCl up to 550 mM, with negligible effect on gas exchange related parameters and conductance of electrons transport chain (gETC). Under salt, the prompt fluorescence (OJIP-curves) exhibits an increase in the O- and J-steps in S. viridis and much less for S. alterniflora. Flowing NaCl stress, a dramatic decline in the photosystem II (PSII) primary photochemistry was observed for S. viridis, as reflected by the drastic drop in Fv/Fm, Fv/Fo and ΦPSII; however, no substantial change was recorded for these parameters in S. alterniflora. Interestingly, we found an increase in the primary PSII photochemistry (ΦPSII) for S. alterniflora with increasing either NaCl concentration or NaCl treatment duration. The NPQ magnitude was strongly enhanced for S. viridis even at a low NaCl (50 mM); however, it remains unchangeable or slightly increased for S. alterniflora at NaCl levels above 400 mM. After NaCl treatment, we found an increase in both the proportion of oxidized P700 and the amount of active P700 in S. viridis and almost no change for S. alterniflora. Under salt, the net photosynthetic rate (A) and stomatal conductance (gs) measurements demonstrate that A decreases earlier in S. viridis, even after one week exposure to only 50 mM NaCl; in contrast, in S. alterniflora, the effect of NaCl on A and gs was minor even after exposure for two weeks to high NaCl levels. For S. viridis exposed to 50 mM NaCl for 12 d, carbon dioxide (CO2) at a concentration of 2000 µL L-1 could not fully restore A to the control (Ctrl) level. Conversely, in S. alterniflora, high CO2 can fully restore A for all NaCl treatments except at 550 mM. RNA-seq data shows a major impact of NaCl on metabolic pathways in S. viridis and we found a number of transcription factors potentially related to NaCl responses. For S. alterniflora, no major changes in the transcriptomic levels were recorded under NaCl stress. To confirm our data analysis of RNA-seq, we performed quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis for randomly selected four genes for each species (8 genes in total) and we found that our results (up- and/or down-regulated genes) are fully consistent and match well our RNA-seq data. Overall, this study showed drastically different photosynthetic and transcriptomic responses of a salt-tolerant C4 grass species and one salt-sensitive C4 grass species to NaCl stress, which suggests that S. alterniflora could be used as a promising model species to study salt tolerance in C4 or monocot species.

Contrasting Responses of Plastid Terminal Oxidase Activity Under Salt Stress in Two C4 Species With Different Salt Tolerance.

The present study reveals contrasting responses of photosynthesis to salt stress in two C4 species: a glycophyte Setaria viridis (SV) and a halophyte Spartina alterniflora (SA). Specifically, the effect of short-term salt stress treatment on the photosynthetic CO2 uptake and electron transport were investigated in SV and its salt-tolerant close relative SA. In this experiment, at the beginning, plants were grown in soil then were exposed to salt stress under hydroponic conditions for two weeks. SV demonstrated a much higher susceptibility to salt stress than SA; while, SV was incapable to survive subjected to about 100 mM, SA can tolerate salt concentrations up to 550 mM with slight effect on photosynthetic CO2 uptake rates and electrons transport chain conductance (gETC ). Regardless the oxygen concentration used, our results show an enhancement in the P700 oxidation with increasing O2 concentration for SV following NaCl treatment and almost no change for SA. We also observed an activation of the cyclic NDH-dependent pathway in SV by about 2.36 times upon exposure to 50 mM NaCl for 12 days (d); however, its activity in SA drops by about 25% compared to the control without salt treatment. Using PTOX inhibitor (n-PG) and that of the Qo-binding site of Cytb6/f (DBMIB), at two O2 levels (2 and 21%), to restrict electrons flow towards PSI, we successfully revealed the presence of a possible PTOX activity under salt stress for SA but not for SV. However, by q-PCR and western-blot analysis, we showed an increase in PTOX amount by about 3-4 times for SA under salt stress but not or very less for SV. Overall, this study provides strong proof for the existence of PTOX as an alternative electron pathway in C4 species (SA), which might play more than a photoprotective role under salt stress.

An in situ approach to characterizing photosynthetic gas exchange of rice panicle.

BACKGROUND: Photosynthesis of reproductive organs in C3 cereals is generally regarded as important to crop yield. Whereas, photosynthetic characteristics of reproductive organs are much less understood as compared to leaf photosynthesis, mainly due to methodological limitations. To date, many indirect methods have been developed to study photosynthesis of reproductive organs and its contribution to grain yield, such as organ shading, application of herbicides and photosynthetic measurement of excised organs or tissues, which might be intrusive and cause biases. Thus, a robust and in situ approach needs to be developed. RESULTS: Here we report the development of a custom-built panicle photosynthesis chamber (P-chamber), which can be connected to standard infrared gas analyzers to study photosynthetic/respiratory rate of a rice panicle. With the P-chamber, we measured panicle photosynthetic characteristics of seven high-yielding elite japonica, japonica-indica hybrid and indica rice cultivars. Results show that, (1) rice panicle is photosynthetically active during grain filling, and there are substantial inter-cultivar variations in panicle photosynthetic and respiratory rates, no matter on a whole panicle basis, on an area basis or on a single spikelet basis; (2) among the seven testing cultivars, whole-panicle gross photosynthetic rates are 17-54 nmol s-1 5 days after heading under photon flux density (PFD) of 2000 µmol (photons) m-2 s-1, which represent some 20-38% of that of the corresponding flag leaves; (3) rice panicle photosynthesis has higher apparent CO2 compensation point, light compensation point and apparent CO2 saturation point, as compared to that of a typical leaf; (4) there is a strong and significant positive correlation between gross photosynthetic rate 5 days after heading on a single spikelet basis and grain setting rate at harvest (Pearson correlation coefficient r = 0.93, p value < 0.0001). CONCLUSIONS: Rice panicle gross photosynthesis is significant, has great natural variation, and plays an underappreciated role in grain yield formation. The P-Chamber can be used as a tool to study in situ photosynthetic characteristics of irregular non-foliar plant organs, such as ears, culms, leaf sheaths, fruits and branches, which is a relatively less explored area in current cereal breeding community.

Genome-Wide Association Study Unravels LRK1 as a Dark Respiration Regulator in Rice (Oryza sativa L.).

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (Rd) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with Rd. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that Rd shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. Rd also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of Rd collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high Rd. Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% Rd of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of Rd in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature.

Proteome and transcriptome reveal the involvement of heat shock proteins and antioxidant system in thermotolerance of Clematis florida.

Clematis florida Thun (CfT) is an ornamental and medicinal plant. It is a cold resistant but heat sensitive species and deserves to be further investigated to improve its adaptability to heat stress. Exploring the molecular mechanism potential via an omic-analysis constitutes a promising approach towards improving heat tolerance of CfT. Two CfT lines, heat resistance (HR) and heat sensitive (HS), with differential thermotolerance capacities were used for the integrative analyses of proteomics and transcriptomes. Transcriptomes analysis showed that various pathways were significantly enriched including plant hormone signal transduction and carbon fixation pathways in prokaryotes. Proteomics study revealed the enrichment of some other pathways comprising antioxidant activity and carbohydrates metabolism. Based on combined transcriptomes and proteomics analyses and following heat stress treatment, a total of 1724 annotated genes were overlapped between both CfT lines. Particularly, 84 differential expressed genes (DEGs) were overlapped in both CfT lines. Fifteen out of these 84 genes were up-regulated solely for HR line (PS) but not for HS one (SG). This strongly suggests a potential prominent role for these genes in the thermotolerance process in PS line. We corroborate that two Hsps (Hsp18 and Hsp70) out of 20 detected proteins with higher expression levels in PS than in SG based on either global transcripts or proteins levels. According to the transcriptomes and proteomics analyses, 6 proteins and their corresponding genes were found to be significantly abundant in HR line (PS). Data are available via ProteomeXchange with identifier PXD018192. The expressions levels of these 6 genes were checked also for both CfT lines to evaluate their potential contributions in the heat tolerance process. Thus, their expression levels were approximately 2~4 times higher in HR than in HS line. We provided as well a representative schematic model to highlight the key genes involved in ROS scavenging and photorespiratory pathway in CfT. This model could be helpful also in understanding the mechanism of heat tolerance in CfT.

Overexpression of maize transcription factor mEmBP-1 increases photosynthesis, biomass, and yield in rice.

Identifying new options to improve photosynthetic capacity is a major approach to improve crop yield potential. Here we report that overexpression of the gene encoding the transcription factor mEmBP-1 led to simultaneously increased expression of many genes in photosynthesis, including genes encoding Chl a,b-binding proteins (Lhca and Lhcb), PSII (PsbR3 and PsbW) and PSI reaction center subunits (PsaK and PsaN), chloroplast ATP synthase subunit, electron transport reaction components (Fd1 and PC), and also major genes in the Calvin-Benson-Bassham cycle, including those encoding Rubisco, glyceraldehyde phosphate dehydrogenase, fructose bisphosphate aldolase, transketolase, and phosphoribulokinase. These increased expression of photosynthesis genes resulted in increased leaf chlorophyll pigment, photosynthetic rate, biomass growth, and grain yield both in the greenhouse and in the field. Using EMSA experiments, we showed that mEmBP-1a protein can directly bind to the promoter region of photosynthesis genes, suggesting that the direct binding of mEmBP-1a to the G-box domain of photosynthetic genes up-regulates expression of these genes. Altogether, our results show that mEmBP-1a is a major regulator of photosynthesis, which can be used to increase rice photosynthesis and yield in the field.

Combined Proteomics and Metabolism Analysis Unravels Prominent Roles of Antioxidant System in the Prevention of Alfalfa (Medicago sativa L.) against Salt Stress.

Alfalfa is the most extensively cultivated forage legume worldwide, and salinity constitutes the main environmental scourge limiting its growth and productivity. To unravel the potential molecular mechanism involved in salt tolerance in alfalfa, we accomplished a combined analysis of parallel reaction monitoring-based proteomic technique and targeted metabolism. Based on proteomic analysis, salt stress induced 226 differentially abundant proteins (DAPs). Among them, 118 DAPs related to the antioxidant system, including glutathione metabolism and oxidation-reduction pathways, were significantly up-regulated. Data are available via ProteomeXchange with identifier PXD017166. Overall, 107 determined metabolites revealed that the tricarboxylic acid (TCA) cycle, especially the malate to oxaloacetate conversion step, was strongly stimulated by salt stress. This leads to an up-regulation by about 5 times the ratio of NADPH/NADP+, as well as about 3 to 5 times in the antioxidant enzymes activities, including those of catalase and peroxidase and proline contents. However, the expression levels of DAPs related to the Calvin-Benson-Bassham (CBB) cycle and photorespiration pathway were dramatically inhibited following salt treatment. Consistently, metabolic analysis showed that the metabolite amounts related to carbon assimilation and photorespiration decreased by about 40% after exposure to 200 mM NaCl for 14 d, leading ultimately to a reduction in net photosynthesis by around 30%. Our findings highlighted also the importance of the supplied extra reducing power, thanks to the TCA cycle, in the well-functioning of glutathione to remove and scavenge the reactive oxygen species (ROS) and mitigate subsequently the oxidative deleterious effect of salt on carbon metabolism including the CBB cycle.

Analytical dataset of short-term heat stress induced reshuffling of metabolism and transcriptomes in maize grown under elevated CO2.

This data article describes the analysis of sudden heat stress (SHS) induced transcriptomes and metabolism in SQ maize cultivar (Zea mays L. cv. Silver Queen). Plants were grown under elevated CO2 in both field based open top chambers (OTCs) and indoor growth chamber conditions [1]. After 20 days after radicle emergence, intact leaf section of maize was exposed for 2 hours to SHS treatment. Samples were stored in liquid nitrogen immediately and used thereafter for metabolism and transcriptomes determinations. Metabolism consisting of 37 targeted metabolites together with corresponding reference standard were determined by gas chromatography coupled to mass spectrometry (GC-MS). Total RNA was extracted using TRIzol® reagent according to the manufacturer's instructions (Invitrogen, Carlsbad, CA). RNA integrity was assessed using RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA). Transcriptomes were determined by Illumina Hiseq 4000 platform. Further interpretation and discussion on these datasets can be found in the related article entitled "Elevated CO2 concentrations may alleviate the detrimental effects of sudden heat stress on photosynthetic carbon metabolism in maize" [1].