Research on lncRNA Related to Drought Resistance of Shanlan Upland Rice

Background Drought has become the major abiotic stress that causes losses in rice yields and consequently is one of the main environmental factors threatening food security. Long non-coding RNA (lncRNA) is known to play an important role in plant response to drought stress, while the mechanisms of competing endogenous RNA (ceRNA) in drought resistance in upland rice have been rarely reported. Results In our study, a total of 191 lncRNAs, 2115 mRNAs and 32 miRNAs (microRNAs) were found by strand-specific sequencing and small RNA sequencing to be differentially expressed in drought-stressed rice. Functional analysis of results indicate that they play important roles in hormone signal transduction, chlorophyll synthesis, protein synthesis and other pathways. Construction of a ceRNA network revealed that MSTRG.28732.3 may interact with miR171 in the chlorophyll biosynthesis pathway and affect the ability of plants to withstand drought stress by regulating Os02g0662700, Os02g0663100 and Os06g0105350. The accuracy of the regulatory network was verified by qRT-PCR. Conclusion Our results provide a theoretical basis for future studies on the potential function of lncRNA in plant drought resistance, and they provide new genetic resources for drought-resistant rice breeding.

Utilization of a Sugarcane100K Single Nucleotide Polymorphisms Microarray-Derived High-Density Genetic Map in Quantitative Trait Loci Mapping and Function Role Prediction of Genes Related to Chlorophyll Content in Sugarcane

Chlorophyll is the most important pigment for plant photosynthesis that plays an important role in crop growth and production. In this study, the chlorophyll content trait was explored to improve sugarcane yield. Two hundred and eighty-five F1 progenies from the cross YT93-159 × ROC22 with significantly different chlorophyll contents were included as test materials. The chlorophyll content of the +1 leaves during elongation phase was measured using a SPAD-502 meter through a three-crop cycle (plant cane, first ratoon, and second ratoon). Linkage analysis was conducted on a high-density genetic map constructed based on the sugarcane 100K SNP chip. In addition, Fv/Fm, plant height, stalk diameter, brix data were collected on plant cane during the elongation and maturation phases. The results showed that the +1 leaf SPAD values, which can be used as an important reference to evaluate the growth potential of sugarcane, were significantly and positively correlated with the Fv/Fm during elongation phase, as well as with plant height, stalk diameter, and brix during maturity phase (P < 0.01). The broad sense heritability (H2) of the chlorophyll content trait was 0.66 for plant cane crop, 0.67 for first ratoon crop, and 0.73 for second ratoon crop, respectively, indicating that this trait was mainly controlled by genetic factors. Thirty-one quantitative trait loci (QTL) were detected by QTL mapping. Among them, a major QTL, qCC-R1, could account for 12.95% of phenotypic variation explained (PVE), and the other 30 minor QTLs explained 2.37–7.99% PVE. Twenty candidate genes related to chlorophyll content were identified in the QTLs plus a 200-Kb extension region within either sides, of which four were homologous genes involved in the chlorophyll synthesis process and the remaining 16 played a certain role in chlorophyll catabolic pathway, chloroplast organization, or photosynthesis. These results provide a theoretical reference for analyzing the genetic mechanism of chlorophyll synthesis and subsequent improvement of photosynthetic characteristics in sugarcane.

GUN4 Affects the Circadian Clock and Seedlings Adaptation to Changing Light Conditions

The chloroplast is a key organelle for photosynthesis and perceiving environmental information. GENOME UNCOUPLED 4 (GUN4) has been shown to be required for the regulation of both chlorophyll synthesis, reactive oxygen species (ROS) homeostasis and plastid retrograde signaling. In this study, we found that growth of the gun4 mutant was significantly improved under medium strong light (200 μmol photons m−2s−1) compared to normal light (100 μmol photons m−2s−1), in marked contrast to wild-type (WT). Further analysis revealed that GUN4 interacts with SIGNAL RECOGNITION PARTICLE 54 KDA SUBUNIT (SRP43) and SRP54. RNA-seq analysis indicated that the expression of genes for light signaling and the circadian clock is altered in gun4 compared with (WT). qPCR analysis confirmed that the expression of the clock genes CLOCK-RELATED 1 (CCA1), LATE ELONGATION HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION 1 (TOC1) and PSEUDO RESPONSE REGULATOR 7 (PRR7) is significantly changed in the gun4 and srp54 mutants under normal and medium strong light conditions. These results suggest that GUN4 may coordinate the adaptation of plants to changing light conditions by regulating the biological clock, although it is not clear whether the effect is direct or indirect.

iTRAQ-Based Quantitative Proteomics Analysis Reveals the Mechanism of Golden-Yellow Leaf Mutant in Hybrid Paper Mulberry

Plant growth and development relies on the conversion of light energy into chemical energy, which takes place in the leaves. Chlorophyll mutant variations are important for studying certain physiological processes, including chlorophyll metabolism, chloroplast biogenesis, and photosynthesis. To uncover the mechanisms of the golden-yellow phenotype of the hybrid paper mulberry plant, this study used physiological, cytological, and iTRAQ-based proteomic analyses to compare the green and golden-yellow leaves of hybrid paper mulberry. Physiological results showed that the mutants of hybrid paper mulberry showed golden-yellow leaves, reduced chlorophyll, and carotenoid content, and increased flavonoid content compared with wild-type plants. Cytological observations revealed defective chloroplasts in the mesophyll cells of the mutants. Results demonstrated that 4766 proteins were identified from the hybrid paper mulberry leaves, of which 168 proteins displayed differential accumulations between the green and mutant leaves. The differentially accumulated proteins were primarily involved in chlorophyll synthesis, carotenoid metabolism, and photosynthesis. In addition, differentially accumulated proteins are associated with ribosome pathways and could enable plants to adapt to environmental conditions by regulating the proteome to reduce the impact of chlorophyll reduction on growth and survival. Altogether, this study provides a better understanding of the formation mechanism of the golden-yellow leaf phenotype by combining proteomic approaches.

Identification and Characterization of an Early Leaf Senescence Gene ELS1 in Soybean

Early leaf senescence phenotype in soybean could be helpful to shorten the maturation period and prevent green stem disorder. From a high-density mutation library, we identified two early leaf senescence soybean mutant lines, els1-1 (early leaf senescence 1) and els1-2. The chlorophyll contents of both els1-1 and els1-2 were low in pre-senescent leaves. They degraded rapidly in senescent leaves, revealing that ELS1 is involved in chlorophyll biosynthesis during leaf development and chlorophyll degradation during leaf senescence. The causal mutations in els1 were identified by next-generation sequencing-based bulked segregant analysis. ELS1 encodes the ortholog of the Arabidopsis CaaX-like protease BCM1, which is localized in chloroplasts. Soybean ELS1 was highly expressed in green tissue, especially in mature leaves. The accumulation of photosystem I core proteins and light-harvesting proteins in els1 was low even in pre-senescent leaves, and their degradation was accelerated during leaf senescence. These results suggest that soybean ELS1 is involved in both chlorophyll synthesis and degradation, consistent with the findings in Arabidopsis BCM1. The gene els1, characterized by early leaf senescence and subsequent early maturation, does not affect the flowering time. Hence, the early leaf senescence trait regulated by els1 helps shorten the harvesting period because of early maturation characteristics. The els1-1 allele with weakly impaired function of ELS1 has only a small effect on agricultural traits and could contribute to practical breeding.

Mechanism Underlying the Shading-Induced Chlorophyll Accumulation in Tea Leaves

Besides aroma and taste, the color of dry tea leaves, tea infusion, and infused tea leaves is also an important index for tea quality. Shading can significantly increase the chlorophyll content of tea leaves, leading to enhanced tea leaf coloration. However, the underlying regulatory mechanism remains unclear. In this study, we revealed that the expressions of chlorophyll synthesis genes were significantly induced by shading, specially, the gene encoding protochlorophyllide oxidoreductase (CsPOR). Indoor control experiment showed that decreased light intensity could significantly induce the expression of CsPOR, and thus cause the increase of chlorophyll content. Subsequently, we explored the light signaling pathway transcription factors regulating chlorophyll synthesis, including CsPIFs and CsHY5. Through expression level and subcellular localization analysis, we found that CsPIF3-2, CsPIF7-1, and CsHY5 may be candidate transcriptional regulators. Transcriptional activation experiments proved that CsHY5 inhibits CsPORL-2 transcription. In summary, we concluded that shading might promote the expression of CsPORL-2 by inhibiting the expression of CsHY5, leading to high accumulation of chlorophyll in tea leaves. The results of this study provide insights into the mechanism regulating the improvements to tea plant quality caused by shading.

Adaptation of Temperate Seagrass to Arctic Light Relies on Seasonal Acclimatization of Carbon Capture and Metabolism

Due to rising global surface temperatures, Arctic habitats are becoming thermally suitable for temperate species. Whether a temperate species can immigrate into an ice-free Arctic depends on its ability to tolerate extreme seasonal fluctuations in daylength. Thus, understanding adaptations to polar light conditions can improve the realism of models predicting poleward range expansions in response to climate change. Plant adaptations to polar light have rarely been studied and remain unknown in seagrasses. If these ecosystem engineers can migrate polewards, seagrasses will enrich biodiversity, and carbon capture potential in shallow coastal regions of the Arctic. Eelgrass (Zostera marina) is the most widely distributed seagrass in the northern hemisphere. As the only seagrass species growing as far north as 70°N, it is the most likely candidate to first immigrate into an ice-free Arctic. Here, we describe seasonal (and diurnal) changes in photosynthetic characteristics, and in genome-wide gene expression patterns under strong annual fluctuations of daylength. We compared PAM measurements and RNA-seq data between two populations at the longest and shortest day of the year: (1) a Mediterranean population exposed to moderate annual fluctuations of 10–14 h daylength and (2) an Arctic population exposed to high annual fluctuations of 0–24 h daylength. Most of the gene expression specificities of the Arctic population were found in functions of the organelles (chloroplast and mitochondrion). In winter, Arctic eelgrass conserves energy by repressing respiration and reducing photosynthetic energy fluxes. Although light-reactions, and genes involved in carbon capture and carbon storage were upregulated in summer, enzymes involved in CO2 fixation and chlorophyll-synthesis were upregulated in winter, suggesting that winter metabolism relies not only on stored energy resources but also on active use of dim light conditions. Eelgrass is unable to use excessive amounts of light during summer and demonstrates a significant reduction in photosynthetic performance under long daylengths, possibly to prevent photoinhibition constrains. Our study identified key mechanisms that allow eelgrass to survive under Arctic light conditions and paves the way for experimental research to predict whether and up to which latitude eelgrass can potentially migrate polewards in response to climate change.

ZjSEP3 modulates flowering time by regulating the LHY promoter

Background SEPALLATA3 (SEP3), which is conserved across various plant species, plays essential and various roles in flower and fruit development. However, the regulatory network of the role of SEP3 in flowering time at the molecular level remained unclear. Results Here, we investigated that SEP3 in Ziziphus jujuba Mill. (ZjSEP3) was expressed in four floral organs and exhibited strong transcriptional activation activity. ZjSEP3 transgenic Arabidopsis showed an early-flowering phenotype and altered the expression of some genes related to flowering. Among them, the expression of LATE ELONGATED HYPOCOTYL (AtLHY), the key gene of circadian rhythms, was significantly suppressed. Yeast one-hybrid (Y1H) and electrophoretic mobility shift assays (EMSAs) further verified that ZjSEP3 inhibited the transcription of AtLHY by binding to the CArG-boxes in its promoter. Moreover, ZjSEP3 also could bind to the ZjLHY promoter and the conserved binding regions of ZjSEP3 were found in the LHY promoter of various plant species. The ectopic regulatory pathway of ZjSEP3-AtLHY was further supported by the ability of 35S::AtLHY to rescue the early-flowering phenotype in ZjSEP3 transgenic plants. In ZjSEP3 transgenic plants, total chlorophyll content and the expression of genes involved in chlorophyll synthesis increased during vegetative stages, which should contribute to its early flowering and relate to the regulatory of AtLHY. Conclusion Overall, ZjSEP3-AtLHY pathway represents a novel regulatory mechanism that is involved in the regulation of flowering time.

Genotoxic Evaluation of Fe3O4 Nanoparticles in Different Three Barley (Hordeum vulgare L.) Genotypes to Explore the Stress-Resistant Molecules

Sustainable agricultural practices are still essential due to soil degradation and crop losses. Recently, the relationship between plants and nanoparticles (NPs) attracted scientists’ attention, especially for applications in agricultural production as nanonutrition. Therefore, the present research was carried out to investigate the effect of Fe3O4 NPs at low concentrations (0, 1, 10, and 20 mg/L) on three genotypes of barley (Hordeum vulgare L.) seedlings grown in hydroponic conditions. Significant increases in seedling growth, enhanced chlorophyll quality and quantity, and two miRNA expression levels were observed. Additionally, increased genotoxicity was observed in seedlings grown with NPs. Generally, Fe3O4 NPs at low concentrations could be successfully used as nanonutrition for increasing barley photosynthetic efficiency with consequently enhanced yield. These results are important for a better understanding of the potential impact of Fe3O4 NPs at low concentrations in agricultural crops and the potential of these NPs as nanonutrition for barley growth and yield enhancement. Future studies are needed to investigate the effect of these NPs on the expression of resistance-related genes and chlorophyll synthesis-related gene expression in treated barley seedlings.

Effects of Nanoplastics on the Dinoflagellate Amphidinium carterae Hulburt from the Perspectives of Algal Growth, Oxidative Stress and Hemolysin Production

Recently, the effects of nanoplastics (NPs) on aquatic organisms have attracted much attention; however, research on the toxicity of NPs to microalgae has been insufficient. In the present study, the effects of polystyrene nanoplastics (nano-PS, 50 nm) on growth inhibition, chlorophyll content, oxidative stress, and algal toxin production of the marine toxigenic dinoflagellate Amphidinium carterae Hulburt were investigated. Chlorophyll synthesis was promoted by nano-PS on day 2 but was inhibited on day 4; high concentrations of nano-PS (≥50 mg/L) significantly inhibited the growth of A. carterae. Moreover, despite the combined effect of superoxide dismutase (SOD) and glutathione (GSH), high reactive oxygen species (ROS) level and malondialdehyde (MDA) content were still induced by nano-PS (≥50 mg/L), indicating severe lipid peroxidation. In addition, the contents of extracellular and intracellular hemolytic toxins in nano-PS groups were significantly higher than those in control groups on days 2 and 8, except that those of extracellular hemolytic toxins in the 100 mg/L nano-PS group decreased on day 8 because of severe adsorption of hemolytic toxins to the nano-PS. Hence, the effects of nano-PS on A. carterae are closely linked to nano-PS concentration and surface properties and exposure time. These findings provide a deep understanding of the complex effects of NPs on toxigenic microalgae and present valuable data for assessing their environmental risks.