Photosynthesis-related Genes Research Articles

Transcriptomic landscape of tomato traditional long shelf-life landraces under low water regimes

‘Corbarino’ (COR) and ‘Lucariello’ (LUC) belong to the family of Mediterranean long shelf-life tomato landraces, producing high quality fruits under low water input cultivation regime in their traditional cultivation area. Understanding the morpho-physiological and molecular details of the peculiar drought stress tolerance of these two genotypes may be key to their valorization as breeding material. RNA sequencing of leaf samples of COR and LUC subjected to drought stress by water withholding in a semi-controlled greenhouse identified 3089 and 2135 differentially expressed genes respectively. These included COR- and LUC-specific annotated genes, as well as genes containing single nucleotide polymorphisms as compared to reference genome. Enriched Gene Ontology categories showed that categories such as response to water, oxidoreductase activity, nucleotide salvation and lipid biosynthesis-related processes were enriched among up-regulated DEGs. By contrast, growth and photosynthesis related genes were down-regulated after drought stress, consistent with leaf gas exchange and biomass accumulation measurements. Genes encoding cell wall degrading enzymes of the pectinase family were also down-regulated in drought stress conditions and upregulated in rewatering, indicating that cell wall composition/hardness is important for drought stress responses. Globally our results contribute to understanding the transcriptomic and physiological responses of representative tomato genotypes from Southern Italy, highlighting a promising set of genes to be investigated to improve tomato tolerance to drought.

BnGLO4 gene cloning and bioinformatics analysis in Brassica napus L

High oleic acid rapeseed oil offers superior nutritional and health benefits, but its mass production is limited due to poor resistance and slightly lower yield. Photosynthesis serves as the foundation of biological survival and closely correlates with crop resistance to stresses, yield, and quality. To identify photosynthesis-related genes, transcriptome sequencing was conducted on high oleic acid rapeseed Gaoyousuan No. 1 and low oleic acid rapeseed Xiangyou 15 resulting in the identification of a total of 9396 differentially expressed genes (4669 up-regulated and 4727 down-regulated). From these genes nine candidate genes were screened using GO and KEGG analysis with BnGLO4 being selected for cloning purposes. The BnGLO4 gene fragment has a length of 1161 bp with an ORF sequence of 1092 bp encoding a theoretical isoelectric point of pI 7.60; it encodes an unstable lipid-soluble protein localized in peroxisomes without transmembrane structural domains or signal peptides. Its amino acid sequence homology was highest with that of BnaA01G0355200ZS, BnaA01G0355600ZS, BnaA05G0410400ZS, BnaC01G0441800ZS, and Brassica rapa (XP_0091171 45.1), Brassica napus (CDY39100.1), Brassica cretica (KAF3533604.1) and Brassica oleracea var. oleracea (XP_0136106 44.1) belonging to the same cruciferous family.The BnGLO4 gene may be associated with responses to abiotic stresses such as salt, drought, and temperature extremes along with photosynthesis and growth in rapeseed plants. The expression levels of the GLO4 gene (BnaA01G0355200 ZS) were highest in filaments while being higher at each stage in seeds and siliques with the highest expression level at day 14 in seeds. Expression was significantly upregulated after 3 ​h of salt stress treatment, reaching a maximum at 12 ​h before slightly decreasing at 24 ​h. The findings of this study lay a foundation for further investigation on photosynthesis and stress response in high oleic rapeseed.

Elevated CO2 increases biomass of Sorghum bicolor green prop roots under drought conditions via soluble sugar accumulation and photosynthetic activity.

Elevated [CO2 ] (E[CO2 ]) mitigates agricultural losses of C4 plants under drought. Although several studies have described the molecular responses of the C4 plant species Sorghum bicolor during drought exposure, few have reported the combined effects of drought and E[CO2 ] (E[CO2 ]/D) on the roots. A previous study showed that, among plant organs, green prop roots (GPRs) under E[CO2 ]/D presented the second highest increase in biomass after leaves compared with ambient [CO2 ]/D. GPRs are photosynthetically active and sensitive to drought. To understand which mechanisms are involved in the increase in biomass of GPRs, we performed transcriptome analyses of GPRs under E[CO2 ]/D. Whole-transcriptome analysis revealed several pathways altered under E[CO2 ]/D, among which photosynthesis was strongly affected. We also used previous metabolome data to support our transcriptome data. Activities associated with photosynthesis and central metabolism increased, as seen by the upregulation of photosynthesis-related genes, a rise in glucose and polyol contents, and increased contents of chlorophyll a and carotenoids. Protein-protein interaction networks revealed that proliferation, biogenesis, and homeostasis categories were enriched and contained mainly upregulated genes. The findings suggest that the previously reported increase in GPR biomass of plants grown under E[CO2 ]/D is mainly attributed to glucose and polyol accumulation, as well as photosynthesis activity and carbon provided by respiratory CO2 refixation. Our findings reveal that an intriguing and complex metabolic process occurs in GPRs under E[CO2 ]/D, showing the crucial role of these organs in plant drought /tolerance.

Chlorophyll contents and expression profiles of photosynthesis-related genes in water-stressed banana plantlets

Chlorophyll contents and expression profiles of photosynthesis-related genes in water-stressed banana plantlets

Metal Toxicity across Different Thallus Sections of the Green Macroalga, Ulva australis.

We aimed to identify functional differences between different sections of the thallus of Ulva australis and develop tissue-endpoint combinations to assess the toxicity of six metals (i.e., Ag, As, Cd, Cr, Cu, and Ni). EC50 values for these metals in three sections of the thallus of Ulva were obtained for multiple endpoints: relative growth rate (RGR), chlorophyll a fluorescence, pigment contents, and the expression of the photosynthesis-related gene, rbcL. The responses of the endpoints varied across the respective thallus sections; overall, the most toxic metals were Ag and Cu. These endpoints were the best for evaluating metal toxicity: ETRmax of the middle thallus sections for Ag toxicity; RGR of the middle thallus section for As and Cd; ETRmax of the marginal thallus section for Cr; Chl b contents of the marginal thallus section for Cu; RGR of the basal thallus section for Ni. The EC50 values for the inhibition of ETRmax in middle (0.06 mg∙L-1) and Chl b in the marginal thallus sections (0.06 mg∙L-1) were all lower than those of the quality standard for wastewater discharge values of Ag and Cu in Republic of Korea and the US, pointing to the suitability of U. australis-based endpoints for risk assessment.

H3K79 methylation promotes rapid growth of Alexandrium pacificum under high light intensity via increased photosynthesis

Alexandrium pacificum is one of the main species responsible for harmful algal blooms, posing serious threats to coastal ecosystems, economies, and public health. Light intensity is an important abiotic factor affecting the occurrence of red tides. In a certain range, increasing light intensity can promote the rapid growth of A. pacificum. This study aimed to elucidate the molecular mechanisms of H3K79 methylation (H3K79me) in response to high light intensity during the rapid growth of A. pacificum and the formation of toxic red tides. The research found that the abundance of H3K79me increased 2.1-fold under high light (HL, 60 μmol photon m−2 s−l) compared to control light conditions (CT, 30 μmol photon m−2 s−l), which was consistent with the trend of rapid growth under HL, and both can be inhibited by EPZ5676. Then effector genes of H3K79me under HL were identified using ChIP-seq and a virtual genome constructed based on transcriptome data of A. pacificum for the first time. The results showed that the differential modification-associated genes were primarily enriched in the pathways of “energy metabolism”, “carbon metabolism”, and “amino acid metabolism”. These findings were confirmed through ChIP-qPCR. Subsequently, H3K79me-associated genes CP43 and GOGAT were identified by combined analysis of ChIP-seq and differentially expressed genes. Finally, pharmacological experiments using the H3K79me inhibitor EPZ5676 showed that the expression of the photosynthesis-related gene CP43 was significantly reduced by 2.5-fold and the maximum photochemical quantum efficiency of A. pacificum was reduced by 1.2 to 1.8-fold in HL compared with CT, leading to inhibited growth of A. pacificum. These results suggest that H3K79me plays a role in regulating the rapid growth of A. pacificum and photosynthesis is likely an important regulatory pathway, which is the first to provide epigenetic evidence underlying the formation of toxic red tides from the perspective of H3K79me.

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.

Characterization and development of a plastid genome base editor, ptpTALECD.

The modification of photosynthesis-related genes in plastid genomes may improve crop yields. Recently, we reported that a plastid-targeting base editor named ptpTALECD, in which a cytidine deaminase DddA functions as the catalytic domain, can homoplasmically substitute a targeted C to T in plastid genomes of Arabidopsis thaliana. However, some target Cs were not substituted. In addition, although ptpTALECD could substitute Cs on the 3' side of T and A, it was unclear whether it could also substitute Cs on the 3' side of G and C. In this study, we identified the preferential positions of the substituted Cs in ptpTALECD-targeting sequences in the Arabidopsis plastid genome. We also found that ptpTALECD could substitute Cs on the 3' side of all four bases in plastid genomes of Arabidopsis. More recently, a base editor containing an improved version of DddA (DddA11) was reported to substitute Cs more efficiently, and to substitute Cs on the 3' side of more varieties of bases in human mitochondrial genomes than a base editor containing DddA. Here, we also show that ptpTALECD_v2, in which a modified version of DddA11 functions as the catalytic domain, more frequently substituted Cs than ptpTALECD in the Arabidopsis plastid genome. We also found that ptpTALECD_v2 tended to substitute Cs at more positions than ptpTALECD. Our results reveal that ptpTALECD can cause a greater variety of codon changes and amino acid substitutions than previously thought, and that ptpTALECD and ptpTALECD_v2 are useful tools for the targeted base editing of plastid genomes.

Leaf Color Classification and Expression Analysis of Photosynthesis-Related Genes in Inbred Lines of Chinese Cabbage Displaying Minor Variations in Dark-Green Leaves.

The leaves of the Chinese cabbage which is most widely consumed come in a wide variety of colors. Leaves that are dark green can promote photosynthesis, effectively improving crop yield, and therefore hold important application and cultivation value. In this study, we selected nine inbred lines of Chinese cabbage displaying slight differences in leaf color, and graded the leaf color using the reflectance spectra. We clarified the differences in gene sequences and the protein structure of ferrochelatase 2 (BrFC2) among the nine inbred lines, and used qRT-PCR to analyze the expression differences of photosynthesis-related genes in inbred lines with minor variations in dark-green leaves. We found expression differences among the inbred lines of Chinese cabbage in photosynthesis-related genes involved in the porphyrin and chlorophyll metabolism, as well as in photosynthesis and photosynthesis-antenna protein pathway. Chlorophyll b content was significantly positively correlated with the expression of PsbQ, LHCA1_1 and LHCB6_1, while chlorophyll a content was significantly negatively correlated with the expression PsbQ, LHCA1_1 and LHCA1_2. Our results provide an empirical basis for the precise identification of candidate genes and a better understanding of the molecular mechanisms responsible for the production of dark-green leaves in Chinese cabbage.

Physiological and Transcriptome Analyses of Photosynthesis in Three Mulberry Cultivars within Two Propagation Methods (Cutting and Grafting) under Waterlogging Stress.

Mulberry is a valuable woody plant with significant economic importance. It can be propagated through two main methods: cutting and grafting. Waterlogging can have a major impact on mulberry growth and can significantly reduce production. In this study, we examined gene expression patterns and photosynthetic responses in three waterlogged mulberry cultivars propagated through cutting and grafting. Compared to the control group, waterlogging treatments reduced levels of chlorophyll, soluble protein, soluble sugars, proline, and malondialdehyde (MDA). Additionally, the treatments significantly decreased the activities of ascorbate peroxidase (APX), peroxidase (POD), and catalase (CAT) in all three cultivars, except for superoxide dismutase (SOD). Waterlogging treatments also affected the rate of photosynthesis (Pn), stomatal conductance (Gs), and transpiration rate (Tr) in all three cultivars. However, no significant difference in physiological response was observed between the cutting and grafting groups. Gene expression patterns in the mulberry changed dramatically after waterlogging stress and varied between the two propagation methods. A total of 10,394 genes showed significant changes in expression levels, with the number of differentially expressed genes (DEGs) varying between comparison groups. GO and KEGG analysis revealed important DEGs, including photosynthesis-related genes that were significantly downregulated after waterlogging treatment. Notably, these genes were upregulated at day 10 in the cutting group compared to the grafting group. In particular, genes involved in carbon fixation were significantly upregulated in the cutting group. Finally, cutting propagation methods displayed better recovery capacity from waterlogging stress than grafting. This study provides valuable information for improving mulberry genetics in breeding programs.

New Insight into the Function of Dopamine (DA) during Cd Stress in Duckweed (Lemna turionifera 5511).

Dopamine (DA), a kind of neurotransmitter in animals, has been proven to cause a positive influence on plants during abiotic stress. In the present study, the function of DA on plants under cadmium (Cd) stress was revealed. The yellowing of duckweed leaves under Cd stress could be alleviated by an exogenous DA (10/20/50/100/200 μM) supplement, and 50 μM was the optimal concentration to resist Cd stress by reducing root breakage, restoring photosynthesis and chlorophyll content. In addition, 24 h DA treatment increased Cd content by 1.3 times in duckweed under Cd stress through promoting the influx of Cd2+. Furthermore, the gene expression changes study showed that photosynthesis-related genes were up-regulated by DA addition under Cd stress. Additionally, the mechanisms of DA-induced Cd detoxification and accumulation were also investigated; some critical genes, such as vacuolar iron transporter 1 (VIT1), multidrug resistance-associated protein (MRP) and Rubisco, were significantly up-regulated with DA addition under Cd stress. An increase in intracellular Ca2+ content and a decrease in Ca2+ efflux induced by DA under Cd stress were observed, as well as synchrony with changes in the expression of cyclic nucleotide-gated ion channel 2 (CNGC2), predicting that, in plants, CNGC2 may be an upstream target for DA action and trigger the change of intracellular Ca2+ signal. Our results demonstrate that DA supplementation can improve Cd resistance by enhancing duckweed photosynthesis, changing intracellular Ca2+ signaling, and enhancing Cd detoxification and accumulation. Interestingly, we found that exposure to Cd reduced endogenous DA content, which is the result of a blocked shikimate acid pathway and decreased expression of the tyrosine aminotransferase (TAT) gene. The function of DA in Cd stress offers a new insight into the application and study of DA to Cd phytoremediation in aquatic systems.

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.

Submergence Stress Alters the Expression of Clock Genes and Configures New Zeniths and Expression of Outputs in Brachypodium distachyon.

Plant networks of oscillating genes coordinate internal processes with external cues, contributing to increased fitness. We hypothesized that the response to submergence stress may dynamically change during different times of the day. In this work, we determined the transcriptome (RNA sequencing) of the model monocotyledonous plant, Brachypodium distachyon, during a day of submergence stress, low light, and normal growth. Two ecotypes of differential tolerance, Bd21 (sensitive) and Bd21-3 (tolerant), were included. We submerged 15-day-old plants under a long-day diurnal cycle (16 h light/8 h dark) and collected samples after 8 h of submergence at ZT0 (dawn), ZT8 (midday), ZT16 (dusk), ZT20 (midnight), and ZT24 (dawn). Rhythmic processes were enriched both with up- and down-regulated genes, and clustering highlighted that the morning and daytime oscillator components (PRRs) show peak expression in the night, and a decrease in the amplitude of the clock genes (GI, LHY, RVE) was observed. Outputs included photosynthesis-related genes losing their known rhythmic expression. Up-regulated genes included oscillating suppressors of growth, hormone-related genes with new late zeniths (e.g., JAZ1, ZEP), and mitochondrial and carbohydrate signaling genes with shifted zeniths. The results highlighted genes up-regulated in the tolerant ecotype such as METALLOTHIONEIN3 and ATPase INHIBITOR FACTOR. Finally, we show by luciferase assays that Arabidopsis thaliana clock genes are also altered by submergence changing their amplitude and phase. This study can guide the research of chronocultural strategies and diurnal-associated tolerance mechanisms.

The plastome reveals new insights into the evolutionary and domestication history of peonies in East Asia

BackgroudPaeonia holds considerable value in medicinal, ornamental horticultural, and edible oil industries, but the incomplete state of phylogenetic research in this genus poses a challenge to the effective conservation and development of wild germplasm, and also impedes the practical utilization of existing cultivars. Due to its uniparental inheritance and lack of recombination, the plastome (i.e., plastid genome), which is a valuable molecular marker for phylogenetic analyses, is characterized by an appropriate rate of nucleotide evolution.MethodsIn this study, 10 newly assembled data and available reported data were combined to perform a comparative genomics and phylogenetics analysis of 63 plastomes of 16 Paeonia species, primarily from East Asia, which is the origin and diversity center of Paeonia.ResultsRanging between 152,153 and 154,405 bp, most plastomes displayed a conserved structure and relatively low nucleotide diversity, except for six plastomes, which showed obvious IR construction or expansion. A total of 111 genes were annotated in the Paeonia plastomes. Four genes (rpl22, rps3, rps19 and ycf1) showed different copy numbers among accessions while five genes (rpl36, petN, psbI, rpl33 and psbJ) showed strong codon usage biases (ENC < 35). Additional selection analysis revealed that no genes were under positive selection during the domestication of tree peony cultivars whereas four core photosynthesis-related genes (petA, psaA, psaB and rbcL) were under positive selection in herbaceous peony cultivars. This discovery might contribute to the wide adaption of these cultivars. Two types of molecular markers (SSR and SNP) were generated from the 63 plastomes. Even though SSR was more diverse than SNP, it had a weaker ability to delimit Paeonia species than SNP. The reconstruction of a phylogenetic backbone of Paeonia in East Asia revealed significant genetic divergence within the P. ostii groups. Evidence also indicated that the majority of P. suffruticosa cultivars had a maternal origin, from P. ostii. The results of this research also suggest that P. delavayi var. lutea, which likely resulted from hybridization with P. ludlowii, should be classified as a lineage within the broader P. delavayi group.ConclusionsOverall, this study’s research findings suggest that the Paeonia plastome is highly informative for phylogenetic and comparative genomic analyses, and could be useful in future research related to taxonomy, evolution, and domestication.

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.

Efficient control of cyanobacterial blooms with calcium peroxide: Threshold and mechanism

This study explored the feasibility and mechanism of cyanobacterial blooms control by calcium peroxide (CaO2). The obtained results demonstrated a strong inhibitory effect of CaO2 on cyanobacterial growth. The removal chlorophyll-a rate reached 31.4 %, while optimal/maximal quantum yield of PSII (Fv/Fm) decreased to 50 % after CaO2 treatment at a concentration of 100 mg L−1 for 96 h. Two main mechanisms were involved in the treatment of cyanobacterial bloom with CaO2, namely oxidative damage and cyanobacterial colony formation. It was found that CaO2 released reactive oxygen species (ROS), namely hydroxyl radicals (·OH), singlet oxygen (1O2), and superoxide radicals (·O2−), inhibiting the activity of antioxidant enzymes in cyanobacterial cells and resulting in intracellular oxidation imbalance. Cyanobacteria can resist oxidative damage by releasing extracellular polymeric substances (EPS). These EPS can combine with CaO2-derived Ca, forming large cyanobacterial aggregates and, consequently, accelerating cell sedimentation. In addition, CaO2 caused programmed cell death (PCD) of cyanobacteria and irreversible damage to the ultrastructure characteristic of the cyanobacterial cells. The apoptotic rate was greatly improved at 100 mg L−1 CaO2. On the other hand, the results obtained using qRT-PCR analysis confirmed the contribution of CaO2 to the down-regulation of photosynthesis-related genes (rbcL and psaB), the up-regulation of microcystins (mcyA and mcyD), the up-regulation of the oxidation system: peroxiredoxin (prx) through oxidative mechanisms. The present study proposes a novel treatment method for water-containing cyanobacterial blooms using CaO2.

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.

Phylogenetic relationship and comparative analysis of the main Bupleuri Radix species in China.

Bupleuri Radix (Chaihu) is a famous traditional Chinese medicine derived from Bupleurum, Apiaceae. The origin of cultivated Chaihu germplasm in China is unclear, which has led to unstable Chaihu quality. In this study, we reconstructed the phylogeny of the main Chaihu germplasm species in China and identified potential molecular markers to authenticate its origin. Three Bupleurum species (eight individuals), B. bicaule, B. chinense, and B. scorzonerifolium, were selected for genome skimming. Published genomes from B. falcatum and B. marginatum var. stenophyllum were used for comparative analysis. Sequences of the complete plastid genomes were conserved with 113 identical genes ranging from 155,540 to 155,866 bp in length. Phylogenetic reconstruction based on complete plastid genomes resolved intrageneric relationships of the five Bupleurum species with high support. Conflicts between the plastid and nuclear phylogenies were observed, which were mainly ascribed to introgressive hybridization. Comparative analysis showed that noncoding regions of the plastomes had most of the variable sequences. Eight regions (atpF-atpH, petN-psbM, rps16-psbK, petA-psbJ, ndhC-trnV/UAC and ycf1) had high divergence values in Bupleurum species and could be promising DNA barcodes for Chaihu authentication. A total of seven polymorphic cpSSRs and 438 polymorphic nSSRs were detected across the five Chaihu germplasms. Three photosynthesis-related genes were under positive selection, of which accD reflected the adaptation fingerprint of B. chinense to different ecological habitats. Our study provides valuable genetic information for phylogenetic investigation, germplasm authentication, and molecular breeding of Chaihu species.

Effects of 4-tert-butylpyrocatechol and tea polyphenol on growth, physiology and antioxidant responses in Microcystis aeruginosa

Global warming has increased the frequency of Microcystis aeruginosa blooms, leading to the deterioration of water quality and loss of biodiversity. Therefore, developing effective strategies for controlling M. aeruginosa blooms has become an important research topic. Plant extracts, 4‑tert-butylpyrocatechol (TBC) and tea polyphenol (TP) are commonly used for water purification and to increase fish immunity, which have great potential to inhibit cyanobacterial blooms. The inhibitory effects of TBC and TP on M. aeruginosa were investigated in terms of growth characteristics, cell membrane morphology, physiological, photosynthetic activities, and antioxidant enzymes activities. The results showed that TBC and TP inhibited the growth of M. aeruginosa by decreasing the chlorophyll fluorescence transients or increasing the antioxidant enzymes activities of M. aeruginosa. TBC damaged the cell morphology of M. aeruginosa, reduced extracellular polysaccharides and protein contents, and up-regulated the antioxidant activity-related gene (sod and gsh) expressions of M. aeruginosa. TP significantly decreased the photosynthetic pigment content, influenced the phycobiliprotein content, and strongly down-regulated the photosynthesis-related gene (psbA, psaB, and rbcL) relative expressions of M. aeruginosa. TBC caused significant oxidative stress, dysfunction of physiological metabolic processes, and damaged crucial biomacromolecules (e.g., lipids, proteins and polysaccharides), prompted the loss of cell integrity, ultimately leading to the death of M. aeruginosa. However, TP depressed photosynthetic activities and consequently inhibited the transfer of electrons, affected the electron transfer chain, decreased the photosynthetic efficiency, and eventually caused the death of M. aeruginosa cells. Our study showed the inhibitory effects and algicidal mechanisms of TBC and TP on M. aeruginosa, and provide a theoretical basis for restrain the overgrowth of M. aeruginosa.

The Genomic Variation and Differentially Expressed Genes on the 6P Chromosomes in Wheat-Agropyron cristatum Addition Lines 5113 and II-30-5 Confer Different Desirable Traits.

Wild relatives of wheat are essential gene pools for broadening the genetic basis of wheat. Chromosome rearrangements and genomic variation in alien chromosomes are widespread. Knowledge of the genetic variation between alien homologous chromosomes is valuable for discovering and utilizing alien genes. In this study, we found that 5113 and II-30-5, two wheat-A. cristatum 6P addition lines, exhibited considerable differences in heading date, grain number per spike, and grain weight. Genome resequencing and transcriptome analysis revealed significant differences in the 6P chromosomes of the two addition lines, including 143,511 single-nucleotide polymorphisms, 62,103 insertion/deletion polymorphisms, and 757 differentially expressed genes. Intriguingly, genomic variations were mainly distributed in the middle of the chromosome arms and the proximal centromere region. GO and KEGG analyses of the variant genes and differentially expressed genes showed the enrichment of genes involved in the circadian rhythm, carbon metabolism, carbon fixation, and lipid metabolism, suggesting that the differential genes on the 6P chromosome are closely related to the phenotypic differences. For example, the photosynthesis-related genes PsbA, PsbT, and YCF48 were upregulated in II-30-5 compared with 5113. ACS and FabG are related to carbon fixation and fatty acid biosynthesis, respectively, and both carried modification variations and were upregulated in 5113 relative to II-30-5. Therefore, this study provides important guidance for cloning desirable genes from alien homologous chromosomes and for their effective utilization in wheat improvement.