Expression Of Photosynthesis-related Genes Research Articles

Transcriptomic insights into the dominance of two phototrophs throughout the water column of a tropical hypersaline-alkaline crater lake (Dziani Dzaha, Mayotte).

Saline-alkaline lakes often shelter high biomasses despite challenging conditions, owing to the occurrence of highly adapted phototrophs. Dziani Dzaha (Mayotte) is one such lake characterized by the stable co-dominance of the cyanobacterium Limnospira platensis and the picoeukaryote Picocystis salinarum throughout its water column. Despite light penetrating only into the uppermost meter, the prevailing co-dominance of these species persists even in light- and oxygen-deprived zones. Here, a depth profile of phototrophs metatranscriptomes, annotated using genomic data from isolated strains, is employed to identify expression patterns of genes related to carbon processing pathways including photosynthesis, transporters and fermentation. The findings indicate a prominence of gene expression associated with photosynthesis, with a peak of expression around 1 m below the surface, although the light intensity is very low and only red and dark red wavelengths can reach it, given the very high turbidity linked to the high biomass of L. platensis. Experiments on strains confirmed that both species do grow under these wavelengths, at rates comparable to those obtained under white light. A decrease in the expression of photosynthesis-related genes was observed in L. platensis with increasing depth, whereas P. salinarum maintained a very high pool of psbA transcripts down to the deepest point as a possible adaptation against photodamage, in the absence and/or very low levels of expression of genes involved in protection. In the aphotic/anoxic zone, expression of genes involved in fermentation pathways suggests active metabolism of reserve or available dissolved carbon compounds. Overall, L. platensis seems to be adapted to the uppermost water layer, where it is probably maintained thanks to gas vesicles, as evidenced by high expression of the gvpA gene. In contrast, P. salinarum occurs at similar densities throughout the water column, with a peak in abundance and gene expression levels which suggests a better adaptation to lower light intensities. These slight differences may contribute to limited inter-specific competition, favoring stable co-dominance of these two phototrophs.

Astaxanthin induces plant tolerance against cadmium by reducing cadmium uptake and enhancing carotenoid metabolism for antioxidant defense in wheat (Triticum aestivum L.)

Soil cadmium (Cd) contamination poses a significant threat to global food security and the environment. Astaxanthin (AX), a potent biological antioxidant belonging to the carotenoid group, has been demonstrated to confer tolerance against diverse abiotic stresses in plants. This study investigated the potential of AX in mitigating Cd-induced damage in wheat seedlings. Morpho-physiological, ultrastructural, and biochemical analyses were conducted to evaluate the impact of AX on Cd-exposed wheat seedlings. Illumina-based gene expression profiling was employed to uncover the molecular mechanisms underlying the protective effects of AX. The addition of 100 μM AX alleviated Cd toxicity by enhancing various parameters: growth, photosynthesis, carotenoid content, and total antioxidant capacity (T-AOC), while reducing Cd accumulation, malondialdehyde (MDA), and hydrogen peroxide (H2O2) levels. RNA sequencing analysis revealed differentially expressed genes associated with Cd uptake and carotenoid metabolism, such as zinc/iron permease (ZIP), heavy metal-associated protein (HMA), 3-beta hydroxysteroid dehydrogenase/isomerase (3-beta-HSD), and thiolase. These findings suggest that AX enhances Cd tolerance in wheat seedlings by promoting the expression of detoxification and photosynthesis-related genes. This research offers valuable insights into the potential use of AX to address Cd contamination in agricultural systems, highlighting the significance of antioxidant supplementation in plant stress management.

Potential molecular mechanism of photosynthesis regulation by PeMPK7 in poplar under para-hydroxybenzoic acid stress

Due to continuous plantation of poplar, its growth and biomass accumulation may be negatively affected by the accumulation of allelochemicals such as para-hydroxybenzoic acid (pHBA) in soil. As photosynthesis is the most fundamental process in plants, it can be negatively impacted by pHBA stress. Therefore, it is crucial to improve photosynthetic capacity under pHBA stress to facilitate poplar plant growth. The mitogen-activated protein kinase (MAPK) cascade pathway is widely involved in environmental stress responses in plants. However, the regulation mechanisms of photosynthesis-related pathways by MAPK pathway genes under pHBA stress are still unclear. In this study, through transcriptome analysis and weighted gene co-expression network analysis, we observed that PeMPK7 overexpression in poplar can regulate the expression of photosynthesis-related genes and transcription factor genes, namely, WRKY1, WRKY33, and ERF3, during the early stage of pHBA stress. In addition, PeMPK7 can improve photosynthesis in poplar under long-term pHBA stress. Moreover, yeast two-hybrid and pull-down assays confirmed the interaction between PeMPK7 and PeMKK7/10. Based on these results, a schematic diagram of the pathways involved in the regulation of photosynthesis by PeMPK7 was constructed. This study provided novel insights into the molecular mechanisms of regulation of pHBA stress via MAPK cascade pathway.

Direct and indirect responses of the Arabidopsis transcriptome to an induced increase in trehalose 6-phosphate.

Trehalose 6-phosphate (Tre6P) is an essential signal metabolite that regulates the level of sucrose, linking growth and development to the metabolic status. We hypothesized that Tre6P plays a role in mediating the regulation of gene expression by sucrose. To test this, we performed transcriptomic profiling on Arabidopsis (Arabidopsis thaliana) plants that expressed a bacterial TREHALOSE 6-PHOSPHATE SYNTHASE (TPS) under the control of an ethanol-inducible promoter. Induction led to a 4-fold rise in Tre6P levels, a concomitant decrease in sucrose, significant changes (FDR ≤ 0.05) of over 13,000 transcripts, and two-fold or larger changes of over 5000 transcripts. Comparison with nine published responses to sugar availability allowed some of these changes to be linked to the rise in Tre6P, while others were probably due to lower sucrose or other indirect effects. Changes linked to Tre6P included repression of photosynthesis-related gene expression and induction of many growth-related processes including ribosome biogenesis. About 500 starvation-related genes are known to be induced by SUCROSE-NON-FERMENTING-1-RELATED KINASE 1 (SnRK1). They were largely repressed by Tre6P in a manner consistent with SnRK1 inhibition by Tre6P. SnRK1 also represses many genes that are involved in biosynthesis and growth. These responded to Tre6P in a more complex manner, pointing toward Tre6P interacting with other C-signaling pathways. Additionally, elevated Tre6P modified the expression of genes encoding regulatory subunits of the SnRK1 complex and TPS class II and FCS-LIKE ZINC FINGER proteins that are thought to modulate SnRK1 function and genes involved in circadian, TARGET OF RAPAMYCIN-, light, abscisic acid, and other hormone signaling.

Bioprospecting of Chlamydomonas reinhardtii for boosting biofuel-related products production based on novel aggregation-induced emission active extracellular polymeric substances nanoprobes

Biofuel production from microalgae has been greatly restricted by low biomass productivity and long-term photosynthetic efficacy. Here, a novel strategy for selecting high-growing, stress-resistant algal strains with high photosynthetic capacity was proposed based on biocompatible extracellular polymeric substances (EPS) probes with aggregation-induced emission (AIE) properties. Specifically, AIE active EPS probes were synthesized for in-situ long-term monitoring of the EPS productivity at different algal growth stages. By coupling the AIE-based fluorescent techniques, algal cells were classified into four diverse populations based on their chlorophyll and EPS signals. Mechanistic studies on the sorted algal cells revealed their remarkable stress resistance and high expression of cell division, biopolymer production and photosynthesis-related genes. The sorted and subcultured algal cells consistently exhibited relatively higher growth rates and photosynthetic capacities, resulting in an increased (1.2 to 1.8-fold) algal biomass production, chlorophyll, and lipids. This study can potentially open new strategies to boost microalgal-based biofuel production.

Acyl-homoserine lactones regulate the photosynthesis of Chlorella sorokiniana to promote biomass and lipid

In the phycosphere, quorum sensing molecules (QSMs) might mediate an intricate interaction between microalgae and specified bacteria, yet little research had been reported in this area. In this study, the impacts of QSMs excreted by microalgae growth-promotion bacteria (MGPB) on Chlorellla sorokiniana were analyzed from phenotype and genes expression. In the control, the biomass and lipid content of C. sorokiniana were 93.06 mg/L and 37.58% after 15 days of cultivation. By adding 50 nmol L−1 of N-Octanoyl-dl-homoserine lactone (C8-HSL) and N-Tetradecanoyl-dl-homoserine lactone (C14-HSL) to the microalgae cultivation medium respectively, the biomass was raised by 7.42% and 13.86%, and the lipid contents were raised by 11.31% and 21.87%. The C8-HSL and C14-HSL could also enhance the photosynthesis of C. sorokiniana. After treated by 50 nmol L−1 of C8-HSL and C14-HSL, the maximum photosynthetic rates (Pm) were 17.80% and 28.81% higher than the control (the Pm was 2.36 μmol O2 mg−1 Chla min−1), and the light compensation points (Ic) were 1.88- and 1.67-fold increases compared to the control (the Ic was 27.23 μmol m−2 s−1). Furthermore, a total of 753 genes showed significant difference in expression, and the analysis of gene related to photosystem, chlorophyll synthesis and electron transport chains verified that acyl-homoserine lactones mediated the expression of photosynthesis-related genes. This study revealed the signaling communication mechanism between microalgae and bacteria, thereby guiding the regulation depending on QSMs.

Transcriptomic and proteomic analyses of distinct Arabidopsis organs reveal high PSI-NDH complex accumulation in stems.

In addition to leaves, the main site of photosynthetic reactions, active photosynthesis also takes place in stems, siliques and tree trunks. Although non-foliar photosynthesis has a marked effect on plant growth and yield, only limited information on the expression patterns of photosynthesis-related genes and the structure of photosynthetic machinery in different plant organs has been available. Here, we report the results of transcriptomic analysis of various organs of Arabidopsis thaliana and compare the gene expression profiles of young and mature leaves with a special focus on photosynthetic genes. Further, we analyzed the composition and organization of the photosynthetic electron transfer machinery in leaves, stems and green siliques at the protein level using BN-PAGE. RNA-Seq analysis revealed unique gene expression profiles in different plant organs and showed major differences in the expression of photosynthesis-related genes in young as compared to mature rosettes. Gel-based proteomic analysis of the thylakoid protein complex organization further showed that all studied plant organs contain the necessary components of the photosynthetic electron transfer chain. Intriguingly, stems accumulate high amounts of PSI-NDH complex, which has previously been implicated in cyclic electron transfer.

Effects of polystyrene nanoplastics and PCB-44 exposure on growth and physiological biochemistry of Chlorella vulgaris

Both NPs and PCBs are emerging contaminants widely distributed in the environment, and it is worth exploring whether the combination of the two contaminants causes serious pollution and harm. Therefore, we studied the effects of PS-NPs and PCB-44 alone and together after 96 h and 21 d of exposure to C. pyrenoidosa. The results showed that PS-NPs and PCB-44 affected the cell cycle of C. pyrenoidosa and inhibited its normal growth. Under PS-NPs and PCB-44 stress, the relative conductivity of the algal solution increased, the hydrophobicity of the algal cell surface decreased, and the synthesis of chlorophyll a and chlorophyll b was reduced. In addition to physiological, there are biochemical effects on C. pyrenoidosa. PS-NPs and PCB-44 exposure induced oxidative stress with significant changes in the enzymatic activities of SOD and CAT together with MDA content. Moreover, the relative expression of photosynthesis-related genes (psbA, rbcL, rbcS) all responded, negatively affecting photosynthesis. In particular, significant toxic effects were observed with single exposure to PCB-44 and co-exposure to PS-NPs and PCB-44, with similar trends of effects in acute and chronic experiments. Taken together, exposure to PS-NPs and PCB-44 caused negative effects on the growth and physiological biochemistry of C. pyrenoidosa. These results provide scientific information to further explore the effects of NPs and PCBs on aquatic organisms and ecosystems.

Investigating the impact of silencing an RNA-binding protein gene SlRBP1 on tomato photosynthesis through RNA-sequencing analysis

Photosynthesis in plants directly affects the synthesis and accumulation of organic matter, which directly influences crop yield. RNA-binding proteins (RBPs) are involved in the regulation of a variety of physiological functions in plants, while the functions of RBPs in photosynthesis have not been clearly elucidated. To investigate the effect of a glycine-rich RNA-binding protein (SlRBP1) in tomato on plant photosynthesis, a stably inherited SlRBP1 silenced plant in Alisa Craig was obtained by plant tissue culture using artificial small RNA interference. It turns out that the size of the tomato fruit was reduced and leaves significantly turned yellow. Chlorophyll(Chl) content measurement, Chl fluorescence imaging and chloroplast transmission electron microscopy revealed that the chloroplast morphology and structure of the leaves of tomato amiR-SlRBP1 silenced plants were disrupted, and the chlorophyll content was significantly reduced. Measurement of photosynthesis rate of wild-type and amiR-SlRBP1 silenced plants in the same period demonstrated that the photosynthetic rate of these plants was significantly reduced, and analysis of RNA-seq data indicated that silencing of SlRBP1 significantly reduced the expression of photosynthesis-related genes, such as PsaE, PsaL, and PsbY, and affected the yield of tomato fruits through photosynthesis.

Leaf variegation caused by plastome structural variation: an example from Dianella tasmanica.

Variegated plants often exhibit plastomic heteroplasmy due to single-nucleotide mutations or small insertions/deletions in their albino sectors. Here, however, we identified a plastome structural variation in albino sectors of the variegated plant Dianella tasmanica (Asphodelaceae), a perennial herbaceous plant widely cultivated as an ornamental in tropical Asia. This structural variation, caused by intermolecular recombination mediated by an 11-bp inverted repeat flanking a 92-bp segment in the large single-copy region (LSC), generates a giant plastome (228 878bp) with the largest inverted repeat of 105 226bp and the smallest LSC of 92bp known in land plants. It also generates an ~7-kb deletion on the boundary of the LSC, which eliminates three protein coding genes (psbA, matK, and rps16) and one tRNA gene (trnK). Albino sectors exhibit dramatic changes in expression of many plastid genes, including negligible expression of psbA, matK, and rps16, reduced expression of photosynthesis-related genes, and increased expression of genes related to the translational apparatus. Microscopic and ultrastructure observations showed that albino tissues were present in both green and albino sectors of the variegated individuals, and chloroplasts were poorly developed in the mesophyll cells of the albino tissues of the variegated individuals. These poorly developed chloroplasts likely carry the large and rearranged plastome, which is likely responsible for the loss of photosynthesis and albinism in the leaf margins. Considering that short repeats are relatively common in plant plastomes and that photosynthesis is not necessary for albino sectors, structural variation of this kind may not be rare in the plastomes of variegated plants.

Genome-wide transcriptome profiling of mulberry (Morus alba) response to boron deficiency and toxicity reveal candidate genes associated with boron tolerance in leaves

Mulberry (Morus alba) is an essential plant with countless economic benefits; however, its growth and metabolic processes are hampered by boron (B) stresses. Very little research has been performed to elucidate boron tolerance and detoxification mechanisms in this species. The M. alba cultivar, Yu-711, was exposed to five different concentrations of boric acid (H3BO3), including deficient (T1; 0 mM) moderate B deficiency (T2; 0.02 mM), sufficient (CK; 0.1 mM) and toxic (T3 and T4; 0.5 and 1 mM) levels for 18 days of growth in pots experiment. Transcriptome analysis of B deficiency and toxicity treatments was performed on mulberry leaves. The transcriptome data reveal that a total of 6114 genes were differentially expressed (DEGs), of which 3830 were up-regulated and 2284 were down-regulated. A comparative analysis between treatment groups CK-vs-T1 (deficiency) and CK-vs-T4 (toxicity) indicates that 590 and 1383 genes were down-regulated in both deficiency and B toxicity, respectively. The results show that 206 genes were differentially expressed in all treatments. B deficiency and toxicity significantly altered the expression of the key aquaporins (PIP2-1, PIP2-7, PIP2-4 and NIP3-1) and high-affinity boron transporter genes (BOR1 and BOR7). In addition, boron stress also altered the expression of antioxidants and photosynthesis-related genes. B stresses were found to alter several transcription factors including ERF1B, which is associated with the regulation of boron uptake and the synthesis and signaling of phytohormones. Unravelling the mechanisms of B tolerance and detoxification is important and would give us further insight into how B stresses affect mulberry plants.

Graphene oxide-based aerogel stimulates growth, mercury accumulation, photosynthesis-related gene expression, antioxidant efficiency and redox status in wheat under mercury exposure

Mercury (Hg) pollution is a global concern in cropland systems. Hg contamination causes a disruption in the growth, energy metabolism, redox balance, and photosynthetic activity of plants. In the removal of Hg toxicity, a recent critical strategy is the use of aerogels with biodegradability and biocompatibility. However, it is unknown how graphene oxide-based aerogels stimulate the defense systems in wheat plants exposed to Hg toxicity. Therefore, in this study, the photosynthetic, genetic, and biochemical effects of reduced graphene oxide aerogel treatments (gA; 50-100-250 mg L−1) were examined in wheat (Triticum aestivum) under Hg stress (50 μM HgCl2). The relative growth rate (RGR) significantly decreased (84%) in response to Hg stress. However, the reduced RGR and water relations (RWC) of wheat were improved by gA treatments. The impaired gas exchange levels (stomatal conductance, carbon assimilation rate, intercellular CO2 concentrations, and transpiration rate) caused by stress were reversed under Hg plus gAs. Additionally, stress hampered chlorophyll fluorescence (Fv/Fo, Fv/Fm), and under Hg toxicity the expression of psaA genes was reduced (>0.4-fold), but psaB gene was significantly up-regulated (>3-fold) which are the genes involved in PSI. By increasing expression patterns of both genes relating to PSI, gAs reversed the adverse consequences on Fv/Fo and Fv/Fm in the presence of excessive Hg concentration. The activities of glutathione S-transferase (GST), glutathione reductase (GR), catalase (CAT), ascorbate peroxidase (APX) and dehydroascorbate reductase (DHAR) decreased under Hg toxicity. On the other hand, the activities of superoxide dismutase (SOD), APX, GST, and glutathione peroxidase (GPX) increased following gA treatments against stress, leading to the successful elimination of toxic levels of H2O2 and lipid peroxidation (TBARS content) by decreasing the levels by about 30%, and 40%, respectively. By modulating enzyme/non-enzyme activity/contents including the AsA-GSH cycle, gAs contributed to the protection of the cellular redox state. Most important of all, gA applications were able to reduce Hg intake by approximately 66%. Therefore, these results showed that gAs were effective in highly inhibiting Hg uptake and could significantly increase wheat tolerance to toxicity by eliminating Hg-induced oxidative damage and inhibiting metabolic processes involved in photosynthesis. The findings obtained from the study provide a new perspective on the alleviation roles of reduced graphene oxide aerogels as an effective adsorbent for decreasing damages of mercury toxicity in wheat plants.

Consequences of light spectra for pigment composition and gene expression in the cryptophyte Rhodomonas salina.

Algae with a more diverse suite of pigments can, in principle, exploit a broader swath of the light spectrum through chromatic acclimation, the ability to maximize light capture via plasticity of pigment composition. We grew Rhodomonas salina in wide-spectrum, red, green, and blue environments and measured how pigment composition differed. We also measured expression of key light-capture and photosynthesis-related genes and performed a transcriptome-wide expression analysis. We observed the highest concentration of phycoerythrin in green light, consistent with chromatic acclimation. Other pigments showed trends inconsistent with chromatic acclimation, possibly due to feedback loops among pigments or high-energy light acclimation. Expression of some photosynthesis-related genes was sensitive to spectrum, although expression of most was not. The phycoerythrin α-subunit was expressed two-orders of magnitude greater than the β-subunit even though the peptides are needed in an equimolar ratio. Expression of genes related to chlorophyll-binding and phycoerythrin concentration were correlated, indicating a potential synthesis relationship. Pigment concentrations and expression of related genes were generally uncorrelated, implying post-transcriptional regulation of pigments. Overall, most differentially expressed genes were not related to photosynthesis; thus, examining associations between light spectrum and other organismal functions, including sexual reproduction and glycolysis, may be important.

High light and temperature enhancing astaxanthin production in Microcystis aeruginosa—Providing a potential thought for controlling cyanobacterial blooms through resource utilization

Artificial salvage is the common method to control cyanobacterial blooms that easily outbreak in summer, but the salvaged cyanobacteria are not effectively utilized. Microcystis aeruginosa is a typical species in cyanobacterial blooms and can accumulate astaxanthin. To promote cyanobacterial blooms control through producing astaxanthin as resource utilization manner, the algal cell growth, photosynthetic abilities, astaxanthin and its precursor levels as well as related gene expression in M. aeruginosa was investigated under high light (HL) and high temperature (HT), the typical conditions in summer. Under HL and HT conditions, M. aeruginosa cell growth and photosynthetic abilities were reduced, due to the declined chlorophyll content and down-regulated photosynthesis-related gene expression. During the 5 days, the astaxanthin content was gradually increased with elevating the light intensity and temperature, reaching the maximum level under HL at 1000 μmol·m−2·s−1 and HT at 35 °C. However, the precursor (β-carotene and zeaxanthin) levels were gradually decreased. This indicated that HL and HT can promote astaxanthin generation and the precursor transformation, as the expression of the genes related with methylerythritol-4-phosphate pathway and astaxanthin formation was up-regulated. Therefore, summer weather can promote astaxanthin accumulation in cyanobacteria by raising related gene expression. During cyanobacterial blooms in summer, their enormous biomass and high astaxanthin level provide a potential for astaxanthin production, while the cyanobacteria salvaged in other seasons can be cultured under HL (1000 μmol·m−2·s−1) and HT (35 °C) conditions to improve astaxanthin content for extracting the high-value compound, which are beneficial to promoting cyanobacterial blooms control through salvage and resource utilization.

OsTHA8 encodes a pentatricopeptide repeat protein required for RNA editing and splicing during rice chloroplast development

In higher plants, the chloroplast is the most important organelle for photosynthesis and for numerous essential metabolic processes in the cell. Although many genes involved in chloroplast development have been identified, the mechanisms underlying such development are not fully understood. In this study, a rice (Oryza sativa) mutant exhibiting pale green color and seedling lethality was isolated from a mutant library. The mutated gene was identified as an ortholog of THA8 (thylakoid assembly 8) in Arabidopsis and maize. This gene is designated as OsTHA8 hereafter. OsTHA8 showed a typical pentatricopeptide repeat (PPR) characteristic of only four PPR motifs. Inactivation of OsTHA8 led to a deficiency in chloroplast development in the rice seedling stage. OsTHA8 was expressed mainly in young leaves and leaf sheaths. The OsTHA8 protein was localized to the chloroplast. Loss of function of OsTHA8 weakened the editing efficiency of ndhB-611/737 and rps8-182 transcripts under normal conditions. Y2H and BiFC indicated that OsTHA8 facilitates RNA editing by forming an editosome with multiple organellar RNA editing factor (OsMORF8) and thioredoxin z (OsTRXz), which function in RNA editing in rice chloroplasts. Defective OsTHA8 impaired chloroplast ribosome assembly and resulted in reduced expression of PEP-dependent genes and photosynthesis-related genes. Abnormal splicing of the chloroplast gene ycf3 was detected in ostha8. These findings reveal a synergistic regulatory mechanism of chloroplast biogenesis mediated by RNA, broaden the function of the PPR family, and shed light on the RNA editing complex in rice.

Magnesium chelatase subunit D is not only required for chlorophyll biosynthesis and photosynthesis, but also affecting starch accumulation in Manihot esculenta Crantz

BackgroundMagnesium chelatase plays an important role in photosynthesis, but only a few subunits have been functionally characterized in cassava.ResultsHerein, MeChlD was successfully cloned and characterized. MeChlD encodes a magnesium chelatase subunit D, which has ATPase and vWA conservative domains. MeChlD was highly expressed in the leaves. Subcellular localization suggested that MeChlD:GFP was a chloroplast-localized protein. Furthermore, the yeast two-hybrid system and BiFC analysis indicated that MeChlD interacts with MeChlM and MePrxQ, respectively. VIGS-induce silencing of MeChlD resulted in significantly decreased chlorophyll content and reduction the expression of photosynthesis-related nuclear genes. Furthermore, the storage root numbers, fresh weight and the total starch content in cassava storage roots of VIGS-MeChlD plants was significantly reduced.ConclusionTaken together, MeChlD located at the chloroplast is not only required for chlorophyll biosynthesis and photosynthesis, but also affecting the starch accumulation in cassava. This study expands our understanding of the biological functions of ChlD proteins.

Comparative analysis of drought-responsive biochemical and transcriptomic mechanisms in two Dendrobium officinale genotypes

Drought stress is one of the most sever natural disaster, threatening to plant growth and global crop security. Dendrobium officinale is a drought-tolerance crop with effective defense mechanisms against drought stress, as well as an important economic plant for medicinal, cosmetic, or ornamental purposes. Revealing the regulatory mechanisms conferring drought resistance upon D. officinale is thus crucial for genetic breeding and water-saving agriculture. In this study, the biochemical and transcriptomic profiles of two D. officinale genotypes were comprehensively analyzed under three drought stress conditions. The M genotype has a relative weaker drought tolerance, as shown by withered leaves, rapidly accumulated malondialdehyde, and severely repressed expression of photosynthesis-related genes under water deficit. In the O genotype (drought-tolerant genotype), proline content, ascorbate peroxidase and catalase activities significantly increased with intensifying drought stress, showing a higher level than that in the M genotype, especially under severe drought stress. By contrast, superoxide dismutase and peroxidase activities were higher in the M genotype under moderate and severe water deficient. Transcriptome analysis demonstrated that mild water deficit initiated the plant hormone signal transduction pathway, while severe drought stress launched the flavonoid biosynthesis pathway in both D. officinale genotypes. Notably, high expression of most protein phosphatases type 2 C in the M genotype, a negative regulator of abscisic acid signaling, may partially explain the relative weaker drought tolerance of the M genotype. Moreover, the higher flavonoid content corresponding with the highly expressed PAL and DFR in the O genotype than in the M genotype, may confer a stronger drought tolerance upon the O genotype under water deficit. Additionally, the biased expression pattern of heat shock proteins, late embryogenesis abundant proteins, and dehydrins may also be linked to the different drought responses of the two D. officinale genotypes. Our results provide a theoretical basis for drought-tolerant crops breeding and water-sparing agriculture.

Identification and characterization of the chalkiness endosperm gene CHALK-H in rice (Oryza sativa L.)

Chalkiness is one of the most important agronomic traits in rice breeding, which directly affects the quality of rice seed. In this study, we identified a chalkiness endosperm mutant, chalk-h, from N-methyl-N-nitrosourea (MNU)-induced japonica rice cultivar Hwacheong (HC). Compared with wild type (WT)-HC, chalk-h showed severe chalkiness in the endosperm, yellowish green leaves, as well as reduced plant height. Scanning electron microscopy (SEM) analysis showed that starch grains in the chalk-h mutant were irregular in size and loosely arranged, with large gaps between granules, forming ovoid or orbicular shapes. MutMap analysis revealed that the phenotype of chalk-h is controlled by a single recessive gene LOC_Os11g39670 encoding seryl-tRNA synthetase, which is renamed as CHALK-H. A point mutation occurs in chalk-h on the sixth exon (at nucleotide 791) of CHALK-H, in which adenine (A) is replaced by thymidine (T), resulting in an amino acid codon change from glutamine (Glu) to valine (Val). The chalk-h mutant exhibited a heat-sensitive phenotype from the 3-leaf stage, including yellow-green leaves and reduced pigment content. The transcriptional expression of starch synthesis-related genes was down-regulated in the chalk-h mutants compared to WT-HC at different grain-filling stages. With an increase in temperature, the expression of photosynthesis-related genes was down-regulated in the chalk-h mutant compared to WT-HC. Overexpression of CHALK-H rescued the phenotype of chalk-h, with endosperm and leaf color similar to those of WT-HC. Our findings reveal that CHALK-H is a causative gene controlling chalkiness and leaf color of the chalk-h mutant. CHALK-H is the same gene locus as TSCD11, which was reported to be involved in chloroplast development under high temperature. We suggest that CHALK-H/TSCD11 plays important roles not only in chloroplast development, but also in photosynthesis and starch synthesis during rice growth and development, so it has great application potential in rice breeding for high quality and yield.

Integrative analysis of transcriptome and yeast screening system identified heat stress-responding genes in ryegrass

Heat stress threatens plant survival and productivity as global warming continues. Thus, it is urgent to understand heat tolerance genetically, especially in cool-season plants. Herein, ryegrass, a cool season grass, was subjected to two heat-temperature treatments (acquired and basal thermotolerances), followed by heat response gene identification using a transcriptome and yeast screening system. A total of 2730 and 8087 differentially expressed genes (DEGs) were identified by transcriptome in AT (acquired thermotolerance) and BT (basal thermotolerance) treatments, while 124 potential heat tolerance genes were identified by yeast screening. This study is the first to reveal the continuous changes in gene expression levels in ryegrass at the whole-genome level during the process of high temperature response. Our findings indicate that, in both the AT and BT experiments, there was a general inhibition of photosynthesis-related gene expression levels over time, whereas the expression levels of endoplasmic reticulum protein processing-related genes were primarily induced. The analysis of the yeast screening system indicated that the ryegrass ribosomal protein genes may play an essential role in high temperature response. Our study identified some genes and proteins related to heat tolerance in ryegrass and provided new and crucial clues to understand the resistance of ryegrass to heat stress.

Population transcriptomics uncover the relative roles of positive selection and differential expression in Batrachium bungei adaptation to the Qinghai-Tibetan plateau.

Positive selection genes are related to metabolism, while differentially expressed genes are related to photosynthesis, suggesting that genetic adaptation and expression regulation may play independent roles in different gene classes. Genome-wide investigation of the molecular mechanisms for high-altitude adaptation is an intriguing topic in evolutionary biology. The Qinghai-Tibet Plateau (QTP) with its extremely variable environments is an ideal site for studying high-altitude adaptation. Here, we used transcriptome data of 100 individuals from 20 populations collected from various altitudes on the QTP to investigate the adaptive mechanisms of the aquatic plant Batrachium bungei at both the genetic and transcriptional level. To explore genes and biological pathways that may contribute to QTP adaptation, we employed a two-step approach, in which we identified positively selected genes and differentially expressed genes using the landscape genomic and differential expression approaches. The positive selection analysis showed that genes involved in metabolic regulation played a crucial role in B. bungei adaptation to the extreme environments of the QTP, especially intense ultraviolet radiation. Altitude-based differential expression analysis suggested that B. bungei could increase the rate of energy dissipation or reduce the efficiency of light energy absorption by down regulating the expression of photosynthesis-related genes to adapt to the strong ultraviolet radiation. Weighted gene co-expression network analysis identified ribosomal genes as hubs of altitude adaptation in B. bungei. Only a small part of genes (about 10%) overlapped between positively selected genes and differentially expressed genes in B. bungei, suggesting that genetic adaptation and gene expression regulation might play relatively independent roles in different categories of functional genes. Taken together, this study enriches our understanding of the high-altitude adaptation mechanism of B. bungei on the QTP.