Arbuscular mycorrhizal fungi alter carbon metabolism and invertase genes expressions of Populus simonii × P. nigra under drought stress.

Arbuscular mycorrhizal fungi (AMF) play a crucial role in regulating the allocation of carbon between source and sink tissues in plants and in regulating their stress responses by changing the sucrose biosynthesis, transportation, and catabolism in plants. Invertase, a key enzyme for plant development, participates in the response of plants to drought stress by regulating sucrose metabolism. However, the detailed mechanisms by which INV genes respond to drought stress in mycorrhizal plants remain unclear. This study examined the sugar content, enzyme activity, and expression profiles of INV genes of Populus simonii × P. nigra (PsnINVs) under two inoculation treatments (inoculation or non-inoculation) and two water conditions (well-watered or drought stress). Results showed that under drought stress, AMF up-regulated the expressions of PsnA/NINV1, PsnA/NINV2, PsnA/NINV3, and PsnA/NINV5 in leaves, which may be related to the enhancement of photosynthetic capacity. Additionally, AMF up-regulated the expressions of PsnA/NINV6, PsnA/NINV10, and PsnA/NINV12 in leaves, which may be related to enhancing osmotic regulation ability and drought tolerance.

Improving photosynthetic efficiency of rice via over-expressing a ferredoxin-like protein gene from Methanothermobacter thermautotrophicus.

Ferredoxins (Fds) are crucial in various essential plant metabolic processes, including photosynthesis, fermentation and aerobic nitrogen fixation, due to their role in electron transport rate (ETR). However, the full scope of ferredoxin's function across prokaryotes and eukaryotic plants remains less understood. This study investigated the effect of MtFd from Methanothermobacter thermoautotrophicus on rice photosynthetic efficiency. We found that MtFd was localized in the chloroplasts of rice protoplasts. Transgenic analysis showed that MtFd significantly enhanced the photosynthetic capacity compared to the wild-type plants. This enhancement was evident through increased ETR, NADPH content and net photosynthetic rates, as well as decreased non-photochemical quenching (NPQ). Despite similar biomass to wild type plants, MtFd transgenic plants exhibited a marked increase in grain size and the 1000-grian weight. The elevated ETR and surplus free electrons in transgenic plants result in a considerable rise in cellular ROS content, which in turn enhances the enzymatic activity of the antioxidant system. In summary, our findings suggest that introducing the Fd protein from M. thermoautotrophicus into transgenic rice improves photosynthetic efficiency by accelerating ETR, which triggers the cellular oxidative stress response.

Chlorophyll and Carotenoid Metabolism Varies with Growth Temperatures among Tea Genotypes with Different Leaf Colors in Camellia sinensis.

The phenotype of albino tea plants (ATPs) is significantly influenced by temperature regimes and light conditions, which alter certain components of the tea leaves leading to corresponding phenotypic changes. However, the regulatory mechanism of temperature-dependent changes in photosynthetic pigment contents and the resultant leaf colors remain unclear. Here, we examined the chloroplast microstructure, shoot phenotype, photosynthetic pigment content, and the expression of pigment synthesis-related genes in three tea genotypes with different leaf colors under different temperature conditions. The electron microscopy results revealed that all varieties experienced the most severe chloroplast damage at 15 °C, particularly in albino cultivar Baiye 1 (BY), where chloroplast basal lamellae were loosely arranged, and some chloroplasts were even empty. In contrast, the chloroplast basal lamellae at 35 °C and 25 °C were neatly arranged and well-developed, outperforming those observed at 20 °C and 15 °C. Chlorophyll and carotenoid measurements revealed a significant reduction in chlorophyll content under low temperature treatment, peaking at ambient temperature followed by high temperatures. Interestingly, BY showed remarkable tolerance to high temperatures, maintaining relatively high chlorophyll content, indicating its sensitivity primarily to low temperatures. Furthermore, the trends in gene expression related to chlorophyll and carotenoid metabolism were largely consistent with the pigment content. Correlation analysis identified key genes responsible for temperature-induced changes in these pigments, suggesting that changes in their expression likely contribute to temperature-dependent leaf color variations.

Genetic analysis of stay green related traits in maize with major gene plus polygenes mixed model.

Maize is one of the main food crops in the world, and cultivating high-yield and high-quality maize varieties is of great significance in addressing food security issues. Leaves are crucial photosynthetic organs in maize, and leaf senescence can result in the degradation of chlorophyll. This, in turn, impacts photosynthetic activity and the accumulation of photosynthetic products. Delaying leaf senescence and increasing carbon assimilation can enhance grain yield and biomass production. The stay green of maize is an important trait closely related to yield, feed quality and resistance. Therefore, this study employed multi-generation joint analysis of major genes and a polygene model to investigate the genetic inheritance of stay green-related traits. Four populations (P1, P2, F1 and F2) were obtained by crossing T01 (stay green) × Xin3 (non-stay green) and T01 (stay green) × Mo17 (non-stay green) under two environments. Six stay green-related traits, including visual stay green (VSG), number of green leaves (GLNM), SPAD value of ear leaf at anthesis (SPADS), SPAD value of ear leaf at maturity (SPADM), absolute green leaf area (GLAD), grain yield per plant (GYP), displayed continuous variations with kurtosis and skewness values of absolute value less than 1 and distribution close to normal. They were characterized by typical inheritance of quantitative traits, with these traits demonstrating the transgressive segregation. The correlation analysis among the traits revealed that five stay green traits have a positive impact on yield. VSG, GLNM and SPADM in the two populations were regulated by the two major genes of additive effects plus additive-dominance polygene model with a major gene heritability varying from 89.03 to 95.95% in the F2 generation. GLAD in TMF2 was controlled by two major genes of equal-additive dominance effects with high heritability (93.47%). However, in TXF2, GLAD was regulated by two major genes of additive-dominance interaction effects plus additive-dominance polygene model. These results provide important genetic information for breeding, which could guide the improvement of stay green-related traits. They also lay a foundation for quantitative trait loci mapping of the stay stay-green traits in maize.

Multifaceted natural drought response mechanisms in three elite date palm cultivars uncovered by expressed sequence tags analysis.

This study extends our prior research on drought responses in three date palm cultivars (Khalas, Reziz, and Sheshi) under controlled conditions. Here, we investigated their drought stress adaptive strategies under ambient environment. Under natural field drought conditions, three date palm cultivars experienced significantly (p ≤ 0.05) varying regulations in their physiological attributes. Specifically, chlorophyll content, leaf RWC, photosynthesis, stomatal conductance, and transpiration reduced significantly, while intercellular CO2 concentration and water use efficiency increased. Through suppression subtraction hybridization (SSH), a rich repertoire (1026) of drought-responsive expressed sequence tags (ESTs) were identified: 300 in Khalas, 343 in Reziz, and 383 in Sheshi. Functional analysis of ESTs, including gene annotation and KEGG pathways elucidation, unveiled that these cultivars withstand drought by leveraging indigenous and multifaceted pathways. While some pathways aligned with previously reported drought resilience mechanism observed under controlled conditions, several new indigenous pathways were noted, pinpointing cultivar-specific adaptations. ESTs identified in three date palm cultivars were enriched through GSEA analysis. Khalas exhibited enrichment in cellular and metabolic processes, catalytic activity, and metal ion binding. Reziz showed enrichment in biological regulation, metabolic processes, signaling, and nuclear functions. Conversely, Sheshi displayed enrichment in organelle, photosynthetic, and ribosomal components. Notably, ca. 50% of the ESTs were unique and novel, underlining the complexity of their adaptive genetic toolkit. Overall, Khalas displayed superior drought tolerance, followed by Reziz and Sheshi, highlighting cultivar-specific variability in adaptation. Conclusively, date palm cultivars exhibited diverse genetic and physiological strategies to cope with drought, demonstrating greater complexity in their resilience compared to controlled settings.

Photosynthetic characteristics and genetic mapping of a yellow-green leaf mutant jym165 in soybean.

BACKGROUND: Leaves are important sites for photosynthesis and can convert inorganic substances into organic matter. Photosynthetic performance is an important factor affecting crop yield. Leaf colour is closely related to photosynthesis, and leaf colour mutants are considered an ideal material for studying photosynthesis. RESULTS: We obtained a yellow-green leaf mutant jym165, using ethyl methane sulfonate (EMS) mutagenesis. Physiological and biochemical analyses indicated that the contents of chlorophyll a, chlorophyll b, carotenoids, and total chlorophyll in the jym165 mutant decreased significantly compared with those in Jiyu47 (JY47). The abnormal chloroplast development of jym165 led to a decrease in net photosynthetic rate and starch content compared with that of JY47. However, quality traits analysis showed that the sum of oil and protein contents in jym165 was higher than that in JY47. In addition, the regional yield (seed spacing: 5 cm) of jym165 increased by 2.42% compared with that of JY47 under high planting density. Comparative transcriptome analysis showed that the yellow-green leaf phenotype was closely related to photosynthesis and starch and sugar metabolism pathways. Genetic analysis suggests that the yellow-green leaf phenotype is controlled by a single recessive nuclear gene. Using Mutmap sequencing, the candidate regions related of leaf colour was narrowed to 3.44 Mb on Chr 10. CONCLUSIONS: Abnormal chloroplast development in yellow-green mutants leads to a decrease in the photosynthetic pigment content and net photosynthetic rate, which affects the soybean photosynthesis pathway and starch and sugar metabolism pathways. Moreover, it has the potentiality to increase soybean yield under dense planting conditions. This study provides a useful reference for studying the molecular mechanisms underlying photosynthesis in soybean.

Ectopic expression of potato ARP1 encoding auxin-repressed protein confers salinity stress tolerance in Arabidopsis thaliana.

Salinity stress is one of the most detrimental factors affecting crop production worldwide. Genetic engineering offers a promising approach for improving agronomic traits and enhancing stress tolerance. In a previous work, several potential candidate genes were identified in potato using large-scale functional yeast screening. In this work, we characterized one of the identified genes, an auxin-repressed protein 1 (ARP1), in transgenic Arabidopsis plants. ARP1 transgenic lines were subjected to salinity stress and compared with wild-type (WT) plants. Compared to WT plants, transgenic ARP1 lines showed significant improvements in morphological parameters, such as plant height, leaves per plant, root length, and fresh weight. Additionally, biochemical and physiological analyses revealed that the transgenic ARP1 lines exhibited improved stomatal conductance, reduced electrolyte leakage, increased proline and chlorophyll accumulation, significantly enhanced malondialdehyde accumulation, and antioxidant enzyme activity. Additionally, spectral analysis revealed that transgenic ARP1 lines had increased photosynthetic capacity compared to WT plants, as indicated by various biochemical parameters and pigment indicators. Transgenic ARP1 lines also showed improved photosystem (PSII) efficiency compared to WT plants, as demonstrated by detailed chlorophyll fluorescence analyses. Moreover, both ARP1 lines showed significantly higher expression levels of SOD, CAT, and APX than the WT plants under salt stress. The highest increase in relative expression was observed with SOD (3-fold increase) as compared to their respective WT in both ARP1 lines. We conclude that potato ARP1 is a promising candidate gene for the future development of salt-tolerant crops.

YELLOW LEAF AND DWARF 7, Encoding a Novel Ankyrin Domain-Containing Protein, Affects Chloroplast Development in Rice.

Background: The proper development of grana and stroma within chloroplasts is critical for plant vitality and crop yield in rice and other cereals. While the molecular mechanisms underpinning these processes are known, the genetic networks governing them require further exploration. Methods and Results: In this study, we characterize a novel rice mutant termed yellow leaf and dwarf 7 (yld7), which presents with yellow, lesion-like leaves and a dwarf growth habit. The yld7 mutant shows reduced photosynthetic activity, lower chlorophyll content, and abnormal chloroplast structure. Transmission electron microscopy (TEM) analysis revealed defective grana stacking in yld7 chloroplasts. Additionally, yld7 plants accumulate high levels of hydrogen peroxide (H2O2) and exhibit an up-regulation of senescence-associated genes, leading to accelerated cell death. Map-based cloning identified a C-to-T mutation in the LOC_Os07g33660 gene, encoding the YLD7 protein, which is a novel ankyrin domain-containing protein localized to the chloroplast. Immunoblot analysis of four LHCI proteins indicated that the YLD7 protein plays an important role in the normal biogenesis of chloroplast stroma and grana, directly affecting leaf senescence and overall plant stature. Conclusions: This study emphasizes the significance of YLD7 in the intricate molecular mechanisms that regulate the structural integrity of chloroplasts and the senescence of leaves, thus providing valuable implications for the enhancement of rice breeding strategies and cultivation.

Multi-Omics Revealed Regulatory Mechanisms Underlying the Flowering of Ferula sinkiangensis across Three Dimensions.

Backgroud/Objectives: Ferula spp. is an essential crop in Central Asia with pronounced economic benefits governed by its flowering process. However, the mechanisms of the flowering phenotype remain unclear. Methods: In this study, using F. sinkiangensis as a model plant, we integrated transcriptome, proteome, and metabolome analyses to compare the multilayer differences in leaves and roots of plants with flowering and unflowering phenotypes. Results: We found that several variations in the transcriptome, proteome, and metabolome were closely associated with flowering. The Photosynthesis and Phenylpropanoid biosynthesis pathways in plants with the flowering phenotype were more active. Additionally, three flowering genes, named FL2-FL4, were upregulated in the leaves of flowering plants. Notably, six transcription factors were potentially responsible for regulating the expression of FL2-FL4 in the leaves to mediate flowering process of F. sinkiangensis. Moreover, genes relevant to Photosynthesis and Phenylpropanoid biosynthesis were also involved in regulating the expression of FL2-FL4 in flowering plants. Conclusions: The active regulation network together with Photosynthesis and Phenylpropanoid biosynthesis were essential for inducing the expression of flowering-related genes in leaves to promote the flowering process of F. sinkiangensis.

Conjunctive BSA-Seq and BSR-Seq to Map the Genes of Yellow Leaf Mutations in Hot Peppers (Capsicum annuum L.).

Yellow leaf mutations have been widely used to study the chloroplast structures, the pigment synthesis, the photosynthesis mechanisms and the chlorophyll biosynthesis pathways across various species. For this study, a spontaneous mutant with the yellow leaf color named 96-140YBM was employed to explore the primary genetic elements that lead to the variations in the leaf color of hot peppers. To identify the pathways and genes associated with yellow leaf phenotypes, we applied sequencing-based Bulked Segregant Analysis (BSA-Seq) combined with BSR-Seq. We identified 4167 differentially expressed genes (DEGs) in the mutant pool compared with the wild-type pool. The results indicated that DEGs were involved in zeatin biosynthesis, plant hormone signal transduction, signal transduction mechanisms, post-translational modification and protein turnover. A total of 437 candidates were identified by the BSA-Seq, while the BSR-Seq pinpointed four candidate regions in chromosomes 8 and 9, containing 222 candidate genes. Additionally, the combination of BSA-Seq and BSR-Seq showed that there were 113 overlapping candidate genes between the two methods, among which 8 common candidates have been previously reported to be related to the development of chloroplasts, the photomorphogenesis and chlorophyll formation of plant chloroplasts and chlorophyll biogenesis. qRT-PCR analysis of the 8 common candidates showed higher expression levels in the mutant pool compared with the wild-type pool. Among the overlapping candidates, the DEG analysis showed that the CaKAS2 and CaMPH2 genes were down-regulated in the mutant pool compared to the wild type, suggesting that these genes may be key contributors to the yellow leaf phenotype of 96-140YBM. This research will deepen our understanding of the genetic basis of leaf color formation and provide valuable information for the breeding of hot peppers with diverse leaf colors.

Physiological and Transcriptome Analyses Reveal the Effects of Fertilization on the Yield of Winter Wheat and on the Photosynthetic Performance of Leaves during the Flowering Period.

Fertilization significantly affects the growth and development of wheat. However, the precise mechanisms underlying gene regulation during flowering in response to fertilization deficiency remain elusive. In this study, fertilization (F) and non-fertilization (CK) ) treatments were set up to reveal examine the effect of fertilization on the photosynthetic capacity of winter wheat during the flowering period through physiological, biochemical, and transcriptome analyses. Upon analyzing analysing their yield, leaf photosynthetic system exchange parameters during flowering, antioxidant enzyme activity, and endogenous hormone parameters, we found that the F treatment resulted in higher net photosynthetic rates during flowering periods than the CK treatment. The superoxide dismutase (SOD) (83.92%), peroxidase (POD) (150.75%), and catalase (CAT) (22.74%) activities of leaves in treated with F during the flowering period were notably elevated compared to those of CK-treated leaves. Abscisic acid (ABA) (1.86%) and gibberellin acid (GA3) (33.69%) levels were reduced, whereas Auxin auxin (IAA) (98.27%) content was increasedwas increased under F treatment compared to those the results under the CK treatment. The chlorophyll a (32.53%), chlorophyll b (56%), total chlorophyll (37.96%), and carotenoid contents (29.80%) under F treatment were also increased compared to CK., exceeded exceeding those obtained under the CK treatment. Furthermore, transcriptional differences between the F and CK conditions were analyzed, and key genes were screened and validated by using q-PCR. Transcriptome analysis identified 2281 differentially expressed genes (DEGs), with enriched pathways related to photosynthesis and light harvesting. DEGs were subjected to cluster simulation, which revealed that 53 DEGS, both up- and down-regulated, responded to the F treatment. qRT-PCR-based validation confirmed the differential expression of genes associated with carbohydrate transport and metabolism, lipid transport, and signal transduction. This study revealed distinctive transcriptional patterns and crucial gene regulation networks in wheat during flowering under fertilization, providing transcriptomic guidance for the precise regulation of wheat breeding.

Silicon Modifies Photosynthesis Efficiency and hsp Gene Expression in European Beech (Fagus sylvatica) Seedlings Exposed to Drought Stress.

Background: Climate change is leading to severe and long-term droughts in European forest ecosystems. can have profound effects on various physiological processes, including photosynthesis, gene expression patterns, and nutrient uptake at the developmental stage of young trees. Objectives: Our study aimed to test the hypothesis that the application of silica (SiO2) influences photosynthetic efficiency and gene expression in 1- to 2-year-old Fagus sylvatica (L.) seedlings. Additionally, we aimed to assess whether silicon application positively influences the structural properties of leaves and roots. To determine whether the plant physiological responses are genotype-specific, seedlings of four geographically different provenances were subjected to a one-year evaluation under greenhouse conditions. Methods: We used the Kruskal-Wallis test followed by Wilcoxon's test to evaluate the differences in silicon content and ANOVA followed by Tukey's test to evaluate the physiological responses of seedlings depending on treatment and provenance. Results: Our results showed a significantly higher Si content in the roots compared with the leaves, regardless of provenance and treatment. The most significant differences in photosynthetic performance were found in trees exposed to Si treatment, but the physiological responses were generally nuanced and provenance-dependent. Expression of hsp70 and hsp90 was also increased in leaf tissues of all provenances. These results provide practical insights that Si can improve the overall health and resilience of beech seedlings in nursery and forest ecosystems, with possible differences in the beneficial role of silicon application arising from the large differences in wild populations of forest tree species.

Genome of Halimeda opuntia reveals differentiation of subgenomes and molecular bases of multinucleation and calcification in algae.

Algae mostly occur either as unicellular (microalgae) or multicellular (macroalgae) species, both being uninucleate. There are important exceptions, however, as some unicellular algae are multinucleate and macroscopic, some of which inhabit tropical seas and contribute to biocalcification and coral reef robustness. The evolutionary mechanisms and ecological significance of multinucleation and associated traits (e.g., rapid wound healing) are poorly understood. Here, we report the genome of Halimeda opuntia, a giant multinucleate unicellular chlorophyte characterized by interutricular calcification. We achieve a high-quality genome assembly that shows segregation into four subgenomes, with evidence for polyploidization concomitant with historical sea level and climate changes. We further find myosin VIII missing in H. opuntia and three other unicellular multinucleate chlorophytes, suggesting a potential mechanism that may underpin multinucleation. Genome analysis provides clues about how the unicellular alga could survive fragmentation and regenerate, as well as potential signatures for extracellular calcification and the coupling of calcification with photosynthesis. In addition, proteomic alkalinity shifts were found to potentially confer plasticity of H. opuntia to ocean acidification (OA). Our study provides crucial genetic information necessary for understanding multinucleation, cell regeneration, plasticity to OA, and different modes of calcification in algae and other organisms, which has important implications in reef conservation and bioengineering.

Investigating the cis-regulatory basis of C3 and C4 photosynthesis in grasses at single-cell resolution.

While considerable knowledge exists about the enzymes pivotal for C4 photosynthesis, much less is known about the cis-regulation important for specifying their expression in distinct cell types. Here, we use single-cell-indexed ATAC-seq to identify cell-type-specific accessible chromatin regions (ACRs) associated with C4 enzymes for five different grass species. This study spans four C4 species, covering three distinct photosynthetic subtypes: Zea mays and Sorghum bicolor (NADP-dependent malic enzyme), Panicum miliaceum (NAD-dependent malic enzyme), Urochloa fusca (phosphoenolpyruvate carboxykinase), along with the C3 outgroup Oryza sativa. We studied the cis-regulatory landscape of enzymes essential across all C4 species and those unique to C4 subtypes, measuring cell-type-specific biases for C4 enzymes using chromatin accessibility data. Integrating these data with phylogenetics revealed diverse co-option of gene family members between species, showcasing the various paths of C4 evolution. Besides promoter proximal ACRs, we found that, on average, C4 genes have two to three distal cell-type-specific ACRs, highlighting the complexity and divergent nature of C4 evolution. Examining the evolutionary history of these cell-type-specific ACRs revealed a spectrum of conserved and novel ACRs, even among closely related species, indicating ongoing evolution of cis-regulation at these C4 loci. This study illuminates the dynamic and complex nature of cis-regulatory elements evolution in C4 photosynthesis, particularly highlighting the intricate cis-regulatory evolution of key loci. Our findings offer a valuable resource for future investigations, potentially aiding in the optimization of C3 crop performance under changing climatic conditions.

A missense mutation in the barley Xan-h gene encoding the Mg-chelatase subunit I leads to a viable pale green line with reduced daily transpiration rate.

KEY MESSAGE: The barley mutant xan-h.chli-1 shows phenotypic features, such as reduced leaf chlorophyll content and daily transpiration rate, typical of wild barley accessions and landraces adapted to arid climatic conditions. The pale green trait, i.e. reduced chlorophyll content, has been shown to increase the efficiency of photosynthesis and biomass accumulation when photosynthetic microorganisms and tobacco plants are cultivated at high densities. Here, we assess the effects of reducing leaf chlorophyll content in barley by altering the chlorophyll biosynthesis pathway (CBP). To this end, we have isolated and characterised the pale green barley mutant xan-h.chli-1, which carries a missense mutation in the Xan-h gene for subunit I of Mg-chelatase (HvCHLI), the first enzyme in the CBP. Intriguingly, xan-h.chli-1 is the only known viable homozygous mutant at the Xan-h locus in barley. The Arg298Lys amino-acid substitution in the ATP-binding cleft causes a slight decrease in HvCHLI protein abundance and a marked reduction in Mg-chelatase activity. Under controlled growth conditions, mutant plants display reduced accumulation of antenna and photosystem core subunits, together with reduced photosystem II yield relative to wild-type under moderate illumination, and consistently higher than wild-type levels at high light intensities. Moreover, the reduced content of leaf chlorophyll is associated with a stable reduction in daily transpiration rate, and slight decreases in total biomass accumulation and water-use efficiency, reminiscent of phenotypic features of wild barley accessions and landraces that thrive under arid climatic conditions.

Leaf antioxidant activity in Colombian elite Hevea brasiliensis genotypes as a breeding strategy for water deficit tolerance under Amazonia conditions.

This study evaluated the foliar antioxidant activity in nine Hevea brasiliensis genotypes from the ECC-1 (Élite Caquetá Colombia) selection and IAN 873 cultivar (control) in trees in the growth stage in two large-scale clonal trials in response to different climatic (semi-humid warm and humid warm sites) and seasonal (dry and rainy periods) conditions in the Colombian Amazon. The results indicated that Reactive Oxygen Species (ROS) production increased under conditions of lower water availability (dry period), leading to lipid peroxidation, high defense of photosynthetic pigments, and development of better osmotic adjustment capacity in the ECC 64, IAN 873, ECC 90, and ECC 35 genotypes due to high concentrations of carotenoids (0.40 mg g-1), reducing sugars (65.83 µg mg-1), and malondialdehyde (MDA) (2.44 nmol ml-1). In contrast, during the rainy period, a post-stress action was observed due to high contents of proline and total sugars (39.43 µg g-1 and 173.03 µg g-1, respectively). At the site level, with high Photosynthetically Active Radiation (PAR) values (1143 moles photons m-2 s-1), temperature (32.11°C), and lower precipitation (135 mm), higher antioxidant activity (chlorophylls a, b and total, carotenoids, and proline) was recorded at the humid warm site, demonstrating that the ECC 90, ECC 64, and ECC 66 genotypes are tolerant to water deficit compared to IAN 873. The ECC 64 genotype, independent of seasonal changes and site conditions, presented the highest contents in Chl a, total Chl, reducing sugars, total sugars, and MDA, showing a tendency to adapt to fluctuating conditions. This study showed that water fluctuations do not cause the same metabolic responses, these vary within the same species, depending on their developmental stage and the climatic and seasonal variations characteristic of the Colombian Amazon.

Metabolomic and transcriptomic basis of photoperiodic response regulation in broomcorn millet (Panicum miliaceum L.).

To elucidate the mechanisms underlying photoperiodic responses, we investigated the genomic and metabolomic responses of two broomcorn millet (Panicum miliaceum L.) genotypes. For this purpose, light-insensitive (D32) and light-sensitive (M51) genotypes were exposed to a 16 h photoperiod (long-day (LD) conditions) and an 8 h photoperiod (short-day (SD) conditions), and various transcriptomic and metabolomic changes were investigated. A total of 1664, 2564, 13,017, and 15548 DEGs were identified in the SD-D, LD-D, LD-M, and SD-M groups, respectively. Furthermore, 112 common DEGs were identified as well. Interestingly, most DEGs in the different groups were associated with photosynthesis and phenylpropanoid and carotenoid biosynthesis. In addition, 822 metabolites were identified under different treatments. The main metabolites, including L-malic and fumaric acids, were identified in the negative mode, whereas brucine and loperamide were identified in the positive mode. KEGG analysis revealed that the metabolites in the different groups were enriched in the same metabolic pathway of the TCA cycle. Furthermore, in negative mode, the metabolites of M51 were mainly D-glucose, whereas those of D32 were mainly L-malic and fumaric acids. One photoperiod candidate gene (C2845_PM11G01290), annotated as ATP6B, significantly increased the levels of L-malic and fumaric acids. In conclusion, our study provides a theoretical basis for understanding the molecular mechanisms of photoperiodic response regulation and can be used as a reference for marker development and resource identification in Panicum miliaceum L..

Machine learning reveals the transcriptional regulatory network and circadian dynamics of Synechococcus elongatus PCC 7942.

Synechococcus elongatus is an important cyanobacterium that serves as a versatile and robust model for studying circadian biology and photosynthetic metabolism. Its transcriptional regulatory network (TRN) is of fundamental interest, as it orchestrates the cell's adaptation to the environment, including its response to sunlight. Despite the previous characterization of constituent parts of the S. elongatus TRN, a comprehensive layout of its topology remains to be established. Here, we decomposed a compendium of 300 high-quality RNA sequencing datasets of the model strain PCC 7942 using independent component analysis. We obtained 57 independently modulated gene sets, or iModulons, that explain 67% of the variance in the transcriptional response and 1) accurately reflect the activity of known transcriptional regulations, 2) capture functional components of photosynthesis, 3) provide hypotheses for regulon structures and functional annotations of poorly characterized genes, and 4) describe the transcriptional shifts under dynamic light conditions. This transcriptome-wide analysis of S. elongatus provides a quantitative reconstruction of the TRN and presents a knowledge base that can guide future investigations. Our systems-level analysis also provides a global TRN structure for S. elongatus PCC 7942.

Comparative physiological and transcriptomic analyses reveal genotype specific response to drought stress in Siberian wildrye (Elymus sibiricus).

Siberian wildrye (Elymus sibiricus) is a xero-mesophytic forage grass with high nutritional quality and stress tolerance. Among its numerous germplasm resources, some possess superior drought resistance. In this study, we firstly investigated the physiological differences between the leaves of drought-tolerant (DT) and drought-sensitive (DS) genotypes under different field water contents (FWC) in soil culture. The results showed that, under drought stress, DT maintained a lower leaf water potential for water absorption, sustained higher photosynthetic efficiency, and reduced oxidative damage in leaves by efficiently maintaining the ascorbic acid-glutathione (ASA-GSH) cycle to scavenge reactive oxygen species (ROS) compared to DS. Secondly, using RNA sequencing (RNA-seq), we analyzed the gene expression profiles of DT and DS leaves under osmotic stress of hydroponics induced by PEG-6000. Through differential analysis, we identified 1226 candidate unigenes, from which we subsequently screened out 115/212 differentially expressed genes (DEGs) that were more quickly induced/reduced in DT than in DS under osmotic stress. Among them, Unigene0005863 (EsSnRK2), Unigene0053902 (EsLRK10) and Unigene0031985 (EsCIPK5) may be involved in stomatal closure induced by abscisic acid (ABA) signaling pathway. Unigene0047636 (EsCER1) may positively regulates the synthesis of very-long-chain (VLC) alkanes in cuticular wax biosynthesis, influencing plant responses to abiotic stresses. Finally, the contents of wax and cutin were measured by GC-MS under osmotic stress of hydroponics induced by PEG-6000. Corresponding to RNA-seq, contents of wax monomers, especially alkanes and alcohols, showed significant induction by osmotic stress in DT but not in DS. It is suggested that limiting stomatal and cuticle transpiration under drought stress to maintain higher photosynthetic efficiency and water use efficiency (WUE) is one of the critical mechanisms that confer stronger drought resistance to DT. This study provides some insights into the molecular mechanisms underlying drought tolerance in E. sibiricus. The identified genes may provide a foundation for the selection and breeding of drought-tolerant crops.

The CsPPR gene with RNA-editing function involved in leaf color asymmetry of the reciprocal hybrids derived from Cucumis sativus and C. hystrix.

MAIN CONCLUSION: The leaf color asymmetry found in the reciprocal hybrids C. hystrix × C. sativus (HC) and C. sativus × C. hystrix (CH) could be influenced by the CsPPR gene (CsaV3_1G038250.1). Most angiosperm organelles are maternally inherited; thus, the reciprocal hybrids usually exhibit asymmetric phenotypes that are associated with the maternal parent. However, there are two sets of organelle genomes in the plant cytoplasm, and the mechanism of reciprocal differences are more complex and largely unknown, because the chloroplast genes are involved besides mitochondrial genes. Cucumis spp. contains the species, i.e., cucumber and melon, which chloroplasts and mitochondria are maternally inherited and paternally inherited, respectively, serving as good materials for the study of reciprocal differences. In this study, leaf color asymmetry was observed in the reciprocal hybrids (HC and CH) derived from C. sativus (2n = 14, CC) and C. hystrix (2n = 24, HH), where the leaves of HC were found to have reduced chlorophyll content, abnormal chloroplast structure and lower photosynthetic capacity. Transcriptomic analysis revealed that the chloroplast development-related genes were differentially expressed in leaf color asymmetry. Genetic analysis showed that leaf color asymmetry was caused by the maternal chloroplast genome. Comparative analysis of chloroplast genomes revealed that there was no mutation in the chloroplast genome during interspecific hybridization. Moreover, a PPR gene (CsaV3_1G038250.1) with RNA-editing function was found to be involved in the regulation of leaf color asymmetry. These findings provide new insights into the regulatory mechanisms of asymmetric phenotypes in plant reciprocal crosses.