Comparative transcriptome profiling of low light tolerant and sensitive rice varieties induced by low light stress at active tillering stage

Physiological and Transcriptome Responses of Sweet Potato [Ipomoea batatas (L.) Lam] to Weak-Light Stress

In the relay intercropping system of maize/sweet potato, the growth of the sweet potatoes is seriously limited by weak light stress in the early stage due to shade from maize plants. However, it is not clear how the weak light affects sweet potatoes and causes tuberous root loss. By setting two light intensity levels (weak light = 30% transmittance of normal light), this study evaluated the responses of two sweet potato cultivars with different tolerances to weak light in a field-based experiment and examined the divergence of gene expression related to light and photosynthesis in a pot-based experiment. The results showed that under weak light, the anatomic structure of functional leaves changed, and the leaf thickness decreased by 39.98% and 17.32% for Yuhongxinshu-4 and Wanshu-7, respectively. The ratio of S/R increased, and root length, root superficial area, and root volume all decreased. The photosynthetic enzyme rubisco was weakened, and the net photosynthetic rate (Pn) declined as well. The level of gene expression in Wanshu-7 was higher than that of Yuhongxinshu-4. The KEGG analysis showed that differentially expressed genes from the two cultivars under weak-light stress used the same enrichment pathway, mainly via glutathione metabolism and flavonoid biosynthesis. After full light levels were restored, the differentially expressed genes were all enriched in pathways such as photosynthesis, photosynthetic pigment synthesis, and carbon metabolism. These findings indicated that weak light changed the plant morphology, photosynthetic physiology and gene expression levels of sweet potatoes, which eventually caused losses in the tuberous root yield. The more light-sensitive cultivar (Wanshu-7) had stronger reactions to weak light. This study provides a theoretical basis and strategy for breeding low-light-tolerant varieties and improving relay intercropping production in sweet potatoes.

Proteomic and metabolomic revealed the effect of shading treatment on cigar tobacco

Shading or low light conditions are essential cultivation techniques for cigar wrapper tobacco leaves production, yet their impact on protein and metabolic regulatory networks is not well understood. In this study, we integrated proteomic and metabolomic analyses to uncover the potential molecular mechanisms affecting cigar tobacco leaves under shading treatment. Our findings include: (1) Identification of 780 significantly differentially expressed proteins (DEPs) in the cigar wrapper tobacco leaves, comprising 560 up-regulated and 220 down-regulated proteins, predominantly located in the chloroplast, cytoplasm, and nucleus, collectively accounting for 50.01%. (2) Discovery of 254 significantly differentially expressed metabolites (DEMs), including 148 up-regulated and 106 down-regulated metabolites. (3) KEGG pathway enrichment analysis revealed that the mevalonate (MVA) pathway within 'Terpenoid backbone biosynthesis' was inhibited, leading to a down-regulation of 'Sesquiterpenoid and triterpenoid biosynthesis'. Conversely, the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway was enhanced, resulting in an up-regulation of 'Monoterpenoid biosynthesis', 'Diterpenoid biosynthesis', and 'Carotenoid biosynthesis', thereby promoting the synthesis of terpenoids such as carotenoids and chlorophylls. Simultaneously, the Calvin cycle in 'Carbon fixation in photosynthetic organisms' was amplified, increasing photosynthetic efficiency. These results suggest that under low light conditions, cigar tobacco optimizes photosynthetic efficiency by reconfiguring its energy metabolism and terpenoid biosynthesis. This study contributes valuable insights into protein and metabolic analyses, paving the way for future functional studies on plant responses to low light.

Transcriptome and functional analyses of phenotypic plasticity in sea grape Caulerpa okamurae

Caulerpa is a marine green macroalga distinguished by a large single cell with multiple nuclei. It also exhibits remarkable morphological intraspecies variations, in response to diverse environmental types. However, the molecular mechanisms underlying this phenotypic plasticity remain poorly understood. In this work, we compare the transcriptomes of Caulerpa okamurae Weber Bosse, 1897 displaying altered phenotypes of cultivation and natural phenotypes and investigate significantly regulated genes and their biological functions using differential expression analyses. We observe light-harvesting complex upregulation and cellular framework stability downregulation in altered phenotypes compared to the natural phenotypes. Intertidal macrophytes reduce light capture to avoid photodamage and regulate their morphology to protect against wave damage. In contrast, the lower light conditions and the cultivation environment augment light capture and increase a morphology prioritizing light trapping. Moreover, the addition of simulated wave-sweeping stimuli induces a return to the natural morphology under high-light conditions, showing how mechanical stress affects morphological organization in C. okamurae. We provide detailed gene expression patterns in C. okamurae under varying light intensities and water conditions, suggesting a distinct influence on its morphological traits.

Genome-wide identification and expression analysis of the cryptochromes reveal the CsCRY1 role under low-light-stress in cucumber

Introduction

Low-light-stress is a common meteorological disaster that can result in slender seedlings. The photoreceptors play a crucial role in perceiving and regulating plants' tolerance to low-light-stress. However, the low-light-stress tolerance of cucumber has not been effectively evaluated, and the functions of these photoreceptor genes in cucumber, particularly under low-light-stress conditions, are not clear.

Methods

Herein, we evaluated the growth characteristics of cucumber seedlings under various LED light treatment. The low-light-stress tolerant cucumber CR and intolerant cucumber CR were used as plant materials for gene expression analysis, and then the function of CsCRY1 was analyzed.

Results

The results revealed that light treatment below 40 μmol m-2 s-1 can quickly and effectively induce low-light-stress response. Then, cucumber CR exhibited remarkable tolerance to low-light-stress was screened. Moreover, a total of 11 photoreceptor genes were identified and evaluated. Among them, the cryptochrome 1 (CRY1) had the highest expression level and was only induced in the low-light sensitive cucumber CS. The transcript CsaV3_3G047490.1 is predicted to encode a previously unknown CsCRY1 protein, which lacks 70 amino acids at its C-terminus due to alternative 5' splice sites within the final intron of the CsCRY1 gene.

Discussion

CRY1 is a crucial photoreceptor that plays pivotal roles in regulating plants' tolerance to low-light stress. In this study, we discovered that alternative splicing of CsCRY1 generates multiple transcripts encoding distinct CsCRY1 protein variants, providing valuable insights for future exploration and utilization of CsCRY1 in cucumber.

Effects of Light Intensity on Growth and Quality of Lettuce and Spinach Cultivars in a Plant Factory

The decreased quality of leafy vegetables and tipburn caused by inappropriate light intensity are serious problems faced in plant factories, greatly reducing the economic benefits. The purpose of this study was to comprehensively understand the impact of light intensity on the growth and quality of different crops and to develop precise lighting schemes for specific cultivars. Two lettuce (Lactuca sativa L.) cultivars-Crunchy and Deangelia-and one spinach (Spinacia oleracea L.) cultivar-Shawen-were grown in a plant factory using a light-emitting diode (LED) under intensities of 300, 240, 180, and 120 μmol m-2 s-1, respectively. Cultivation in a solar greenhouse using only natural light (NL) served as the control. The plant height, number of leaves, and leaf width exhibited the highest values under a light intensity of 300 μmol m-2 s-1 for Crunchy. The plant width and leaf length of Deangelia exhibited the smallest values under a light intensity of 300 μmol m-2 s-1. The fresh weight of shoot and root, soluble sugar, soluble protein, and ascorbic acid contents in the three cultivars increased with the increasing light intensity. However, tipburn was observed in Crunchy under 300 μmol m-2 s-1 light intensity, and in Deangelia under both 300 and 240 μmol m-2 s-1 light intensities. Shawen spinach exhibited leaf curling under all four light intensities. The light intensities of 240 and 180 μmol m-2 s-1 were observed to be the most optimum for Crunchy and Deangelia (semi-heading lettuce variety), respectively, which would exhibit relative balance growth and morphogenesis. The lack of healthy leaves in Shawen spinach under all light intensities indicated the need to comprehensively optimize cultivation for Shawen in plant factories to achieve successful cultivation. The results indicated that light intensity is an important factor and should be optimized for specific crop species and cultivars to achieve healthy growth in plant factories.

Light intensity-mediated auxin homeostasis in spikelets links carbohydrate metabolism enzymes with grain filling rate in rice

Low light (LL) stress during the grain-filling stage acutely impairs the quality and quantity of starch accumulation in rice grains. Here, we observed that LL-induced poor starch biosynthesis is modulated by auxin homeostasis, which regulates the activities of major carbohydrate metabolism enzymes such as starch synthase (SS) and ADP-glucose pyrophosphorylase (AGPase) in rice. Further, during the grain-filling period under LL, the starch/sucrose ratio increased in leaves but significantly decreased in the developing spikelets. This suggests poor sucrose biosynthesis in leaves and starch in the grains of the rice under LL. A lower grain starch was found to be correlated with the depleted AGPase and SS activities in the developing rice grains under LL. Further, under LL, the endogenous auxin (IAA) level in the spikelets was found to be synchronized with the expression of a heteromeric G protein gene, RGB1. Interestingly, under LL, the expression of OsYUC11 was significantly downregulated, which subsequently resulted in reduced IAA in the developing rice spikelets, followed by poor activation of grain-filling enzymes. This resulted in lowered grain starch accumulation, grain weight, panicle number, spikelet fertility, and eventually grain yield, which was notably higher in the LL-susceptible (GR4, IR8) than in the LL-tolerant (Purnendu, Swarnaprabha) rice genotypes. Therefore, we hypothesize that depletion in auxin biosynthesis under LL stress is associated with the downregulation of RBG1, which discourages the expression and activities of grain-filling enzymes, resulting in lower starch production, panicle formation, and grain yield in rice.

Sequence Characteristics and Expression Analysis of the Gene Encoding Sedoheptulose-1,7-Bisphosphatase, an Important Calvin Cycle Enzyme in Upland Cotton (Gossypium hirsutum L.)

Sedoheptulose-1,7-bisphosphatase (SBPase, EC 3.1.3.37) is a key enzyme in the plant Calvin cycle and one of the main rate-limiting enzymes in the plant photosynthesis pathway. Many studies have demonstrated that the SBPase gene plays an important role in plant photosynthetic efficiency, yield, and stress responses; however, few studies have been conducted on the function and expression of the GhSBPase gene in upland cotton. In this study, our results showed that the coding sequence (CDS) of GhSBPase gene was 1182 bp, encoding a protein with 393 amino acids. The GhSBPase protein had adenosine monophosphate (AMP) binding site and a FIG (FBPase/IMPase/glpX) domain, and had six Cys residues and a CGGT(A/Q)C motif that were involved in redox regulation in plants. Evolutionarily, the GhSBPase protein clustered into the dicotyledon subgroup and was most closely related to the tomato SlSBPase protein. Western-blot analysis further indicated that the GhSBPase gene was indeed the gene encoding the SBPase protein in upland cotton. The GhSBPase protein was localized in chloroplast, which was consistent with its function as a key enzyme in photosynthesis. The GhSBPase gene was specifically highly expressed in leaves, and its expression level was significantly lower in a yellow-green leaf mutant than in the wild type. Moreover, the GhSBPase expression was in response to drought, salt, high- and low-temperature stress, and exhibits different expression patterns. The GhSBPase promoter had the cis-acting elements in response to abiotic stress, phytohormone, and light. In addition, the GhSBPase expression was positively correlated with the chlorophyll fluorescence parameters, suggesting that changes in the expression of the GhSBPase had potential applicability in breeding for enhanced cotton photosynthetic efficiency. These results will help to understand the function of the GhSBPase gene in photosynthesis and the adaptability of plants to external stress and provide important gene information for the high-yield breeding of crops in the future.

Changes in physio-biochemical parameters and expression of metallothioneins in Avena sativa L. in response to drought

Drought is one of the major threats to food security. Among several mechanisms involved in plant stress tolerance, one protein family-the plant metallothioneins (MTs)-shows great promise for enhancing drought resistance. Plant metallothioneins in oat (Avena sativa L.) have not yet been deeply analysed, and the literature lacks a comprehensive study of the whole family of plant MTs in response to drought. In this study, we showed that the number and nature of cis-elements linked with stress response in promoters of AsMTs1-3 differed depending on the MT type. Drought stress in oat plants caused an increase in the expression of AsMT2 and AsMT3 and a decrease in the expression of AsMT1 compared to well-watered plants. Moreover, the low values of relative water content, water use efficiency, net photosynthesis (P_N), transpiration (E), stomatal conductance (g_s), chlorophyll a, and carotenoid were accompanied by high levels of electrolyte leakage, internal CO₂ concentration (C_i) and abscisic acid content, and high activity of antioxidants enzymes in plants under drought stress. The present study puts forward the idea that AsMTs are crucial for oat response to drought stress not only by regulating antioxidant activity but also by changing the plant water regime and photosynthesis. Our results support the hypothesis that structural differences among types of plant MTs reflect their diversified physiological roles.

Integrative analysis of different low-light-tolerant cucumber lines in response to low-light stress

INTRODUCTION

Low light stress inhibits plant growth due to a line of physiological disruptions in plants, and is one of the major barriers to protected cucumber cultivation in northern China.

METHODS

To comprehensively understand the responses of cucumber seedlings to low-light stress, the low-light-tolerant line (M67) and The low-light-sensitive line (M14) were conducted for the analysis of photosynthetic phenotype, RNA sequencing (RNA-seq) and the expression level of photosynthesis-related genes in leaves under low-light stress and normal light condition (control).

RESULTS

The results showed that there was a sharp decrease in the photosynthate accumulation in the leaves of the sensitive line, M14, resulting in a large decrease in the photosynthetic rate (Pn) (with 31.99%) of leaves compared to that of the control, which may have been caused by damage to chloroplast ultrastructure or a decrease in chlorophyll (Chl) content. However, under the same low-light treatment, there was no large drop in the photosynthate accumulation and even no decrease in Pn and Chl content for the tolerant line, M67. Moreover, results of gene expression analysis showed that the expression level of genes CsPsbQ (the photosystem II oxygen-evolving enhancer protein 3 gene) and Csgamma (ATPase, F1 complex gene) in the M14 leaves decreased sharply (by 35.04% and 30.58%, respectively) compared with the levels in the M67 leaves, which decreased by 14.78% and 23.61%, respectively. The expression levels of genes involved in Chl synthesis and carbohydrate biosynthesis in the leaves of M14 decreased markedly after low-light treatment; in contrast, there were no sharp decreases or changes in leaves of M67.

DISCUSSION

Over all, the ability of cucumber to respond to low-light stress, as determined on the basis of the degree of damage in leaf structure and chloroplast ultrastructure, which corresponded to decreased gene expression levels and ATP phosphorylase activity, significantly differed between different low-light-tolerant lines, which was manifested as significant differences in photosynthetic capacity between them. Results of this study will be a reference for comprehensive insight into the physiological mechanism involved in the low-light tolerance of cucumber.

Identification of potential light deficiency response regulators in endangered species Magnolia sinostellata

Magnolia sinostellata is one of the endangered species in China and largely suffers light deficiency stress in the understory of forest. However, the weak light response molecular mechanism remains unclear. More importantly, hub genes in the molecular network have not been pinpointed. To explore potential regulators in the mechanism, weighted gene co-expression network analysis (WGCNA) was performed to analysis the trancriptome data of M. sinostellata leaves subjected to weak light with different time points. Gene co-expression analysis illustrated that module 1, 2 and 3 were closely associated with light deficiency treatment, which. Gene ontology and KEGG analyses showed that genes in module 1 mainly participated in amino and nucleotide metabolism, module 2 mostly involved in carbon fixation and module 3 mostly regulated photosynthesis related pathways, among which 6, 7 and 8 hub genes were identified, respectively. Hub genes isoform_107196 in module 1 and isoform_55976 in module 2 were unique to M. sinostellata. This study found that light deficiency inhibited photosynthesis and stress tolerance, while improved carbon metabolism and flowering related pathways in M. sinostellata, which can impact its accumulation reserves of growth and reproduction in the next season. In addition, key shade response regulators identified in this study have laid a firm foundation for further investigation of shade response molecular mechanism and protection of other shade sensitive plants.

Exploration of the genomic atlas of Dof transcription factor family across genus Oryza provides novel insights on rice breeding in changing climate

DNA-binding with one finger (Dof) transcription factors have been demonstrated to regulate various stresses and developmental processes in plants. Their identification and comparative evolutionary analyses in cultivated and wild species of genus oryza were yet to be explored. In this context, we report a comprehensive genomics atlas of DNA-binding with one finger (Dof) family genes in 13 diverse rice genomes (five cultivated and eight rice wild-relatives) through a genome-wide scanning approach. A galore of 238 Dof genes, identified across the genus Oryza, are categorized into seven distinct subgroups by comparative phylogenetic analysis with the model plant Arabidopsis. Conserved motifs and gene structure analyses unveiled the prevalence of species- and subgroups-specific structural and functional diversity that is expediating with the evolutionary period. Our results indicate that Dof genes might have undergone strong purifying selections and segmental duplications to expand their gene family members in corresponding Oryza genomes. We speculate that miR2927 potentially targets the Dof domain to regulate gene expression under different climatic conditions, which are supported by in-silico and wet-lab experiments-based expression profiles. In a nutshell, we report several superior haplotypes significantly associated with early flowering in a treasure trove of 3,010 sequenced rice accessions and have validated these haplotypes with two years of field evaluation-based flowering data of a representative subpanel. Finally, we have provided some insights on the resolution of Oryza species phylogeny discordance and divergence highlighting the mosaic evolutionary history of the genus Oryza. Overall, this study reports a complete genomic landscape of the Dof family in cultivated and wild Oryza species that could greatly facilitate in fast-track development of early maturing and climate-resilient rice cultivars through modern haplotype-led breeding.

The ÓMICAS alliance, an international research program on multi-omics for crop breeding optimization

The OMICAS alliance is part of the Colombian government's Scientific Ecosystem, established between 2017-2018 to promote world-class research, technological advancement and improved competency of higher education across the nation. Since the program's kick-off, OMICAS has focused on consolidating and validating a multi-scale, multi-institutional, multi-disciplinary strategy and infrastructure to advance discoveries in plant science and the development of new technological solutions for improving agricultural productivity and sustainability. The strategy and methods described in this article, involve the characterization of different crop models, using high-throughput, real-time phenotyping technologies as well as experimental tissue characterization at different levels of the omics hierarchy and under contrasting conditions, to elucidate epigenome-, genome-, proteome- and metabolome-phenome relationships. The massive data sets are used to derive in-silico models, methods and tools to discover complex underlying structure-function associations, which are then carried over to the production of new germplasm with improved agricultural traits. Here, we describe OMICAS' R&D trans-disciplinary multi-project architecture, explain the overall strategy and methods for crop-breeding, recent progress and results, and the overarching challenges that lay ahead in the field.

Identification of microRNAs That Provide a Low Light Stress Tolerance-Mediated Signaling Pathway during Vegetative Growth in Rice

Low light intensity affects several physiological parameters during the different growth stages in rice. Plants have various regulatory mechanisms to cope with stresses. One of them is the differential and temporal expression of genes, which is governed by post-transcriptional gene expression regulation through endogenous miRNAs. To decipher low light stress-responsive miRNAs in rice, miRNA expression profiling was carried out using next-generation sequencing of low-light-tolerant (Swarnaprabha) and -sensitive (IR8) rice genotypes through Illumina sequencing. Swarnaprabha and IR8 were subjected to 25% low light treatment for one day, three days, and five days at the active tillering stage. More than 43 million raw reads and 9 million clean reads were identified in Swarnaprabha, while more than 41 million raw reads and 8.5 million clean reads were identified in IR8 after NGS. Importantly, 513 new miRNAs in rice were identified, whose targets were mostly regulated by the genes involved in photosynthesis and metabolic pathways. Additionally, 114 known miRNAs were also identified. Five novel (osa-novmiR1, osa-novmiR2, osa-novmiR3, osa-novmiR4, and osa-novmiR5) and three known (osa-miR166c-3p, osa-miR2102-3p, and osa-miR530-3p) miRNAs were selected for their expression validation through miRNA-specific qRT-PCR. The expression analyses of most of the predicted targets of corresponding miRNAs show negative regulation. Hence, miRNAs modulated the expression of genes providing tolerance/susceptibility to low light stress. This information might be useful in the improvement of crop productivity under low light stress.

Transcriptome analysis reveals the accelerated expression of genes related to photosynthesis and chlorophyll biosynthesis contribution to shade-tolerant in Phoebe bournei

BACKGROUND

Phoebe bournei (P. bournei) is an important and endemic wood species in China. However, the plantation, nursing, and preservation of P. bournei are often affected by light. To investigate its physiological changes and molecular mechanism of low light tolerance, two-year-old P. bournei seedlings were subjected to different shading conditions. With the increase of light intensity in the shade, the leaf color of P. bournei seedlings became darkened, the aboveground/underground biomass significantly increased, the content of chlorophyll increased and the net photosynthetic rate significantly increased.

RESULTS

de novo transcriptome analysis showed that 724 and 3,248 genes were differentially expressed due to low light intensity at T1 (35% light exposure) and T2 (10% light exposure), respectively, when compared to the controls. Furthermore, the differentially expressed genes (DEGs) were implicated in photosynthesis, nitrogen metabolism, plant hormone signal transduction, biosynthesis of secondary metabolites, and protein processing in the endoplasmic reticulum by functional enrichment analysis. Moreover, the expression of HSP, CAB, HEMA1, GSA, DVR, MYB, bHLH, PORA, CAO, GLK, and photosystem I and II complex-related genes significantly increased after low light exposure at T2 and T1.

CONCLUSIONS

The present study suggests that the rapid growth of P. bournei seedlings under shading conditions may be the result of the accelerated expression of genes related to photosynthesis and chlorophyll biosynthesis, which enable plants to maintain a high photosynthesis rate even under low light conditions.

Integrated Expression Analysis of Small RNA, Degradome and Microarray Reveals Complex Regulatory Action of miRNA during Prolonged Shade in Swarnaprabha Rice

Prolonged shade during the reproductive stage can result in significant yield losses in rice. For this study, we elucidated the role of microRNAs in prolonged-shade tolerance (~20 days of shade) in a shade-tolerant rice variety, Swarnaprabha (SP), in its reproductive stage using small RNA and degradome sequencing with expression analysis using microarray and qRT-PCR. This study demonstrates that miRNA (miR) regulation for shade-tolerance predominately comprises the deactivation of the miR itself, leading to the upregulation of their targets. Up- and downregulated differentially expressed miRs (DEms) presented drastic differences in the category of targets based on the function and pathway in which they are involved. Moreover, neutrally regulated and uniquely expressed miRs also contributed to the shade-tolerance response by altering the differential expression of their targets, probably due to their differential binding affinities. The upregulated DEms mostly targeted the cell wall, membrane, cytoskeleton, and cellulose synthesis-related transcripts, and the downregulated DEms targeted the transcripts of photosynthesis, carbon and sugar metabolism, energy metabolism, and amino acid and protein metabolism. We identified 16 miRNAs with 21 target pairs, whose actions may significantly contribute to the shade-tolerance phenotype and sustainable yield of SP. The most notable among these were found to be miR5493-OsSLAC and miR5144-OsLOG1 for enhanced panicle size, miR5493-OsBRITTLE1-1 for grain formation, miR6245-OsCsIF9 for decreased stem mechanical strength, miR5487-OsGns9 and miR168b-OsCP1 for better pollen development, and miR172b-OsbHLH153 for hyponasty under shade.

The role of phytochrome-mediated gibberellic acid signaling in the modulation of seed germination under low light stress in rice (O. sativa L.)

Seed germination plays cardinal roles in seedling establishment and their successive growth. However, seed germination is retarded by far-red (FR) enrichment under low light stress, and the inhibitory signalling mechanism remains ambiguous. Our results indicated that low light treatment, both in the open and growth chamber conditions, inhibits rice seed germination by decreasing the gibberellin (GA) contents. To explore the mechanism of GA-deficiency under low light stress, differential expression profiling of GA-anabolic, -catabolic, ABA -anabolic, -catabolic, and SLR1 was investigated, revealing that expression of ABA- anabolic, GA-catabolic genes and SLR1 was upregulated with a simultaneous downregulation of ABA-catabolic and GA-anabolic genes under low light treatment. These results suggested that FR-induced GA inadequacy is resulted by upregulation of SLR1 and GA-catabolism genes consequently increase DELLA that further subsided GA-responses in the germinating rice seeds. Moreover, we provided evidence that FR-induced GA inadequacy demotes rice seed germination by decreasing amylase activity, eventually decreasing the carbohydrate solubilization in the germinating seeds. Finally, we suggest that under low light stress, due to a retarded conversion of phytochrome A to their bioactive form, the ABA-catabolic genes were eventually upregulated with a simultaneous downregulation of GA-anabolic genes. Consequently, a lower GA pool fails to leverage the GA-dependent DELLA degradation, further shutting down the expected GA responses that reduce germination efficiency under FR-enriched light.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01167-7.

Light Deficiency Inhibits Growth by Affecting Photosynthesis Efficiency as well as JA and Ethylene Signaling in Endangered Plant Magnolia sinostellata

The endangered plant Magnolia sinostellata largely grows in the understory of forest and suffers light deficiency stress. It is generally recognized that the interaction between plant development and growth environment is intricate; however, the underlying molecular regulatory pathways by which light deficiency induced growth inhibition remain obscure. To understand the physiological and molecular mechanisms of plant response to shading caused light deficiency, we performed photosynthesis efficiency analysis and comparative transcriptome analysis in M. sinostellata leaves, which were subjected to shading treatments of different durations. Most of the parameters relevant to the photosynthesis systems were altered as the result of light deficiency treatment, which was also confirmed by the transcriptome analysis. Gene Ontology and KEGG pathway enrichment analyses illustrated that most of differential expression genes (DEGs) were enriched in photosynthesis-related pathways. Light deficiency may have accelerated leaf abscission by impacting the photosynthesis efficiency and hormone signaling. Further, shading could repress the expression of stress responsive transcription factors and R-genes, which confer disease resistance. This study provides valuable insight into light deficiency-induced molecular regulatory pathways in M. sinostellata and offers a theoretical basis for conservation and cultivation improvements of Magnolia and other endangered woody plants.

Low Light/Darkness as Stressors of Multifactor-Induced Senescence in Rice Plants

Leaf senescence, as an integral part of the final development stage for plants, primarily remobilizes nutrients from the sources to the sinks in response to different stressors. The premature senescence of leaves is a critical challenge that causes significant economic losses in terms of crop yields. Although low light causes losses of up to 50% and affects rice yield and quality, its regulatory mechanisms remain poorly elucidated. Darkness-mediated premature leaf senescence is a well-studied stressor. It initiates the expression of senescence-associated genes (SAGs), which have been implicated in chlorophyll breakdown and degradation. The molecular and biochemical regulatory mechanisms of premature leaf senescence show significant levels of redundant biomass in complex pathways. Thus, clarifying the regulatory mechanisms of low-light/dark-induced senescence may be conducive to developing strategies for rice crop improvement. This review describes the recent molecular regulatory mechanisms associated with low-light response and dark-induced senescence (DIS), and their effects on plastid signaling and photosynthesis-mediated processes, chloroplast and protein degradation, as well as hormonal and transcriptional regulation in rice.

Light and water treatment during the early grain filling stage regulates yield and aroma formation in aromatic rice

The effect of light and water on aromatic rice remain largely unclear. A pot experiment was conducted to investigate the influences of light-water treatments (CK: natural light and well-watered conditions, WS: natural light and water-stressed conditions, LL: low light and well-watered conditions, LL-WS: low light and water-stressed treatment) on yield and 2-acetyl-1-pyrroline (2AP) formation in aromatic rice. Compared with CK, the light-water treatments decreased grain yield (10.32–39.19%) due to reductions in the filled grain percentage and total dry weight, in the regulation of biomass distribution, and in the attributes of gas exchange and antioxidant response parameters. The 2AP content in grains increased in the LL treatment (5.08–16.32%) but decreased in the WS treatment compared with that in CK. The changes in 2AP were associated with changes in 2AP formation-related traits and element content. Low light and water stress led to yield declines in aromatic rice, but low light alleviated the decrease in 2AP content caused by water stress.

Spatial Variation of Leaf Chlorophyll in Northern Hemisphere Grasslands

Chlorophyll is the molecular basis for the function of photosystems and is also a promising tool for ecological prediction. However, the large-scale patterns of chlorophyll variation in grasslands remain poorly understood. We performed consistent measurements of chlorophyll a, b, a+b, and the a:b ratio (chlorophyll a/b) for 421 species across northern hemisphere grassland transects, recorded their distributions, variations, and influencing factors, and examined their relationships with leaf nitrogen. The results showed that the distributional ranges were 0.52-28.33 (mean 5.49) mg·g^-1 dry weight, 0.15-12.11 (mean 1.83) mg·g^-1 dry weight, 0.67-39.29 (mean 7.32) mg·g^-1 dry weight, and 1.28-7.84 (mean 3.02) for chlorophyll a, b, a+b, and a/b, respectively. The chlorophyll averages differed among regions (higher in the Loess Plateau and the Mongolian Plateau than in the Tibetan Plateau), grassland types (desert grasslands > meadow > typical grasslands), life forms, life spans, and taxonomies. In the entire northern hemisphere grassland, chlorophyll concentrations and chlorophyll a/b were negatively correlated to photosynthetically active radiation and the soil N:P ratio, and positively correlated to the mean annual temperatures. These results implied that chlorophyll in grasslands was shaped by the layered structure of grasses, distinct plateau environments, and phylogeny. The allocation patterns of leaf nitrogen to chlorophyll differed among regions and grassland types, showing that caution is required if simply relating single leaf N or chlorophyll to productivity separately. These findings enhance our understanding of chlorophyll in natural grasslands on a large scale, as well as providing information for ecological predictive models.

Proteomic Analysis of Rice Subjected to Low Light Stress and Overexpression of OsGAPB Increases the Stress Tolerance

BACKGROUND

Light provides the energy for photosynthesis and determines plant morphogenesis and development. Low light compromises photosynthetic efficiency and leads to crop yield loss. It remains unknown how rice responds to low light stress at a proteomic level.

RESULTS

In this study, the quantitative proteomic analysis with isobaric tags for relative and absolute quantitation (iTRAQ) was used and 1221 differentially expressed proteins (DEPs) were identified from wild type rice plants grown in control or low light condition (17% light intensity of control), respectively. Bioinformatic analysis of DEPs indicated low light remarkably affects the abundance of chloroplastic proteins. Specifically, the proteins involved in carbon fixation (Calvin cycle), electron transport, and ATPase complex are severely downregulated under low light. Furthermore, overexpression of the downregulated gene encoding rice β subunit of glyceraldehyde-3-phosphate dehydrogenase (OsGAPB), an enzyme in Calvin cycle, significantly increased the CO₂ assimilation rate, chlorophyll content and fresh weight under low light conditions but have no obvious effect on rice growth and development under control light.

CONCLUSION

Our results revealed that low light stress on vegetative stage of rice inhibits photosynthesis possibly by decreasing the photosynthetic proteins and OsGAPB gene is a good candidate for manipulating rice tolerance to low light stress.

Comparative transcriptome analysis reveals the molecular regulation underlying the adaptive mechanism of cherry (Cerasus pseudocerasus Lindl.) to shelter covering

BACKGROUND

Rain-shelter covering is widely applied during cherry fruit development in subtropical monsoon climates with the aim of decreasing the dropping and cracking of fruit caused by excessive rainfall. Under rain-shelter covering, the characteristics of the leaves and fruit of the cherry plant may adapt to the changes in the microclimate. However, the molecular mechanism underlying such adaptation remains unclear, although clarifying it may be helpful for improving the yield and quality of cherry under rain-shelter covering.

RESULTS

To better understand the regulation and adaptive mechanism of cherry under rain-shelter covering, 38,621 and 3584 differentially expressed genes were identified with a combination of Illumina HiSeq and single-molecule real-time sequencing in leaves and fruits, respectively, at three developmental stages. Among these, key genes, such as those encoding photosynthetic-antenna proteins (Lhca and Lhcb) and photosynthetic electron transporters (PsbP, PsbR, PsbY, and PetF), were up-regulated following the application of rain-shelter covering, leading to increased efficiency of light utilization. The mRNA levels of genes involved in carbon fixation, namely, rbcL and rbcS, were clearly increased compared with those under shelter-free conditions, resulting in improved CO₂ utilization. Furthermore, the transcription levels of genes involved in chlorophyll (hemA, hemN, and chlH) and carotenoid synthesis (crtB, PDS, crtISO, and lcyB) in the sheltered leaves peaked earlier than those in the unsheltered leaves, thereby promoting organic matter accumulation in leaves. Remarkably, the expression levels of key genes involved in the metabolic pathways of phenylpropanoid (PAL, C4H, and 4CL) and flavonoid (CHS, CHI, F3'H, DFR, and ANS) in the sheltered fruits were also up-regulated earlier than of those in the unsheltered fruits, conducive to an increase in anthocyanin content in the fruits.

CONCLUSIONS

According to the physiological indicators and transcriptional expression levels of the related genes, the adaptive regulation mechanism of cherry plants was systematically revealed. These findings can help understand the effect of rain-shelter covering on Chinese cherry cultivation in rainy regions.