Genome-Wide Identification and Analysis of Genes, Conserved between japonica and indica Rice Cultivars, that Respond to Low-Temperature Stress at the Vegetative Growth Stage

The basic helix-loop-helix transcription factor gene, OsbHLH38, plays a key role in controlling rice salt tolerance

The plant hormone abscisic acid (ABA) is crucial for plant seed germination and abiotic stress tolerance. However, the association between ABA sensitivity and plant abiotic stress tolerance remains largely unknown. In this study, 436 rice accessions were assessed for their sensitivity to ABA during seed germination. The considerable diversity in ABA sensitivity among rice germplasm accessions was primarily reflected by the differentiation between the Xian (indica) and Geng (japonica) subspecies and between the upland-Geng and lowland-Geng ecotypes. The upland-Geng accessions were most sensitive to ABA. Genome-wide association analyses identified four major quantitative trait loci containing 21 candidate genes associated with ABA sensitivity of which a basic helix-loop-helix transcription factor gene, OsbHLH38, was the most important for ABA sensitivity. Comprehensive functional analyses using knockout and overexpression transgenic lines revealed that OsbHLH38 expression was responsive to multiple abiotic stresses. Overexpression of OsbHLH38 increased seedling salt tolerance, while knockout of OsbHLH38 increased sensitivity to salt stress. A salt-responsive transcription factor, OsDREB2A, interacted with OsbHLH38 and was directly regulated by OsbHLH38. Moreover, OsbHLH38 affected rice abiotic stress tolerance by mediating the expression of a large set of transporter genes of phytohormones, transcription factor genes, and many downstream genes with diverse functions, including photosynthesis, redox homeostasis, and abiotic stress responsiveness. These results demonstrated that OsbHLH38 is a key regulator in plant abiotic stress tolerance.

Metabolomics-based exploration the response mechanisms of Saussurea involucrata leaves under different levels of low temperature stress

BACKGROUND

Saussurea involucrata (Sik.) is alpine plant that have developed special adaptive mechanisms to resist adverse environmental conditions such as low temperature chilling during long-term adaptation and evolution. Exploring the changes of its metabolites under different temperature stresses is helpful to gain insight into its cold stress tolerance.

METHODS

Ultra-performance liquid chromatography and tandem mass spectrometry were used to analyze the metabolites in the leaves of Sik. under low different temperature stress conditions.

RESULTS

A total of 753 metabolites were identified, and 360 different metabolites were identified according to the Kyoto Encyclopedia of Genes and Genomes (KEGG) involved in the biosynthesis of secondary metabolites and amino acids and sugars. Sucrose and trehalose synthesis, glycolysis, tricarboxylic acid cycle, pentose phosphate pathway, glutamic acid-mediated proline biosynthesis, purine metabolism, amino acid metabolism, phenylpropane synthesis pathway metabolites all respond to low temperature stress. Under cold stress conditions, carbohydrates in Sik. leaves accumulate first than under freezing conditions, and the lower the temperature under freezing conditions, the less amino acids accumulate, while the phenolic substances increase. The expression of various substances in LPE and LPC increased more than 10-fold after low temperature stress compared with the control, but the content of LPE and LPC substances decreased after cold adaptation. In addition, purines and phenolics decreased and amino acids accumulated significantly under freezing conditions.

CONCLUSION

The metabolic network of Sik. leaves under different low temperature stress conditions was proposed, which provided a reference for further exploration of the metabolic mechanism related to low temperature stress tolerance of Sik.

Genome-wide identification and expression analysis of DREB genes in alfalfa (Medicago sativa) in response to cold stress

Dehydration-responsive element-binding proteins (DREBs) belong to members of the AP2/ERF transcription factor superfamily, which has been reported to involve various abiotic-stress responses and tolerance in plants. However, research on the DREB-family is still limited in alfalfa (Medicago sativa L.), a forage legume cultivated worldwide. The recent genome-sequence release of the alfalfa cultivar "XinJiangDaYe" allowed us to identify 172 DREBs by a multi-step homolog search. The phylogenetic analysis indicated that such MsDREBs could be classified into 5 groups, namely A-1 (56 members), A-2 (39), A-3 (3), A-4 (61) and 13 (A-5 (13), thus adding substantial new members to the DREB-family in alfalfa. Furthermore, a comprehensive survey in silico of conserved motif, gene structure, molecular weight, and isoelectric point (pI) as well as gene expression was conducted. The resulting data showed that, for cold-stress response, 33 differentially expressed MsDREBs were identified with a threshold of Log2-fold > 1, and most of which were transcriptionally upregulated within 48 h during a cold treatment(s). Moreover, the expression profiling of MsDREBs from two ecotypes of alfalfa subspecies i.e. M. sativa ssp. falcata (F56, from a colder region of Central Asia) and M. sativa ssp. sativa (B47, from Near East) revealed that most of the cold-stress responsive MsDREBs exhibited a significantly lower expression in F56, leading to a proposal of the existence of a distinct mechanism(s) for cold tolerance regulated by DREB-related action, which would have been evolved in alfalfa with a genotypic specificity. Additionally, by examining the transcriptome of a freezing-tolerance species (M. sativa cv. Zhaodong), eight DREBs were found to be implicated in a long-term freezing-stress adaptation with a great potential. Taken together, the current genome-wide identification in alfalfa points to the importance of some MsDREBs in the cold-stress response, providing some promising molecular targets to be functionally characterized for the improvement of cold tolerance in crops including alfalfa.

Methylation and Expression of Rice NLR Genes after Low Temperature Stress

Nucleotide-binding leucine-rich repeat receptors (NLRs) are included in most plant disease resistance proteins. Some NLR proteins have been revealed to be induced by the invasion of plant pathogens. DNA methylation is required for adaption to adversity and proper regulation of gene expression in plants. Low temperature stress (LTS) is a restriction factor in rice growth, development and production. Here, we report the methylation and expression of NLR genes in two rice cultivars, i.e., 9311 (an indica rice cultivar sensitive to LTS), and P427 (a japonica cultivar, tolerant to LTS), after LTS. We found that the rice NLR genes were heavily methylated within CG sites at room temperature and low temperature in 9311 and P427, and many rice NLR genes showed DNA methylation alteration after LTS. A great number of rice NLR genes were observed to be responsive to LTS at the transcriptional level. Our observation suggests that the alteration of expression of rice NLR genes was similar but their change in DNA methylation was dynamic between the two rice cultivars after LTS. We identified that more P427 NLR genes reacted to LTS than those of 9311 at the methylation and transcriptional level. The results in this study will be useful for further understanding the transcriptional regulation and potential functions of rice NLR genes.

Identification and Functional Analysis of the Caffeic Acid O-Methyltransferase (COMT) Gene Family in Rice (Oryza sativa L.)

Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.

Transcriptome Profiling of Maize (Zea mays L.) Leaves Reveals Key Cold-Responsive Genes, Transcription Factors, and Metabolic Pathways Regulating Cold Stress Tolerance at the Seedling Stage

Cold tolerance is a complex trait that requires a critical perspective to understand its underpinning mechanism. To unravel the molecular framework underlying maize (Zea mays L.) cold stress tolerance, we conducted a comparative transcriptome profiling of 24 cold-tolerant and 22 cold-sensitive inbred lines affected by cold stress at the seedling stage. Using the RNA-seq method, we identified 2237 differentially expressed genes (DEGs), namely 1656 and 581 annotated and unannotated DEGs, respectively. Further analysis of the 1656 annotated DEGs mined out two critical sets of cold-responsive DEGs, namely 779 and 877 DEGs, which were significantly enhanced in the tolerant and sensitive lines, respectively. Functional analysis of the 1656 DEGs highlighted the enrichment of signaling, carotenoid, lipid metabolism, transcription factors (TFs), peroxisome, and amino acid metabolism. A total of 147 TFs belonging to 32 families, including MYB, ERF, NAC, WRKY, bHLH, MIKC MADS, and C₂H₂, were strongly altered by cold stress. Moreover, the tolerant lines’ 779 enhanced DEGs were predominantly associated with carotenoid, ABC transporter, glutathione, lipid metabolism, and amino acid metabolism. In comparison, the cold-sensitive lines’ 877 enhanced DEGs were significantly enriched for MAPK signaling, peroxisome, ribosome, and carbon metabolism pathways. The biggest proportion of the unannotated DEGs was implicated in the roles of long non-coding RNAs (lncRNAs). Taken together, this study provides valuable insights that offer a deeper understanding of the molecular mechanisms underlying maize response to cold stress at the seedling stage, thus opening up possibilities for a breeding program of maize tolerance to cold stress.

Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

Background: As Oryza sativa ssp. indica and Oryza sativa ssp. japonica are the two major subspecies of Asian cultivated rice, the adaptative evolution of these varieties in divergent environments is an important topic in both theoretical and practical studies. However, the cell type-specific differentiation between indica and japonica rice varieties in response to divergent habitat environments, which facilitates an understanding of the genetic basis underlying differentiation and environmental adaptation between rice subspecies at the cellular level, is little known.

Methods: We analyzed a published single-cell RNA sequencing dataset to explore the differentially expressed genes between indica and japonica rice varieties in each cell type. To estimate the relationship between cell type-specific differentiation and environmental adaptation, we focused on genes in the WRKY, NAC, and BZIP transcription factor families, which are closely related to abiotic stress responses. In addition, we integrated five bulk RNA sequencing datasets obtained under conditions of abiotic stress, including cold, drought and salinity, in this study. Furthermore, we analyzed quiescent center cells in rice root tips based on orthologous markers in Arabidopsis.

Results: We found differentially expressed genes between indica and japonica rice varieties with cell type-specific patterns, which were enriched in the pathways related to root development and stress reposes. Some of these genes were members of the WRKY, NAC, and BZIP transcription factor families and were differentially expressed under cold, drought or salinity stress. In addition, LOC_Os01g16810, LOC_Os01g18670, LOC_Os04g52960, and LOC_Os08g09350 may be potential markers of quiescent center cells in rice root tips.

Conclusion: These results identified cell type-specific differentially expressed genes between indica-japonica rice varieties that were related to various environmental stresses and provided putative markers of quiescent center cells. This study provides new clues for understanding the development and physiology of plants during the process of adaptative divergence, in addition to identifying potential target genes for the improvement of stress tolerance in rice breeding applications.

Systematic Analysis of Cold Stress Response and Diurnal Rhythm Using Transcriptome Data in Rice Reveals the Molecular Networks Related to Various Biological Processes

Rice (Oryza sativa L.), a staple crop plant that is a major source of calories for approximately 50% of the human population, exhibits various physiological responses against temperature stress. These responses are known mechanisms of flexible adaptation through crosstalk with the intrinsic circadian clock. However, the molecular regulatory network underlining this crosstalk remains poorly understood. Therefore, we performed systematic transcriptome data analyses to identify the genes involved in both cold stress responses and diurnal rhythmic patterns. Here, we first identified cold-regulated genes and then identified diurnal rhythmic genes from those (119 cold-upregulated and 346 cold-downregulated genes). We defined cold-responsive diurnal rhythmic genes as CD genes. We further analyzed the functional features of these CD genes through Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses and performed a literature search to identify functionally characterized CD genes. Subsequently, we found that light-harvesting complex proteins involved in photosynthesis strongly associate with the crosstalk. Furthermore, we constructed a protein-protein interaction network encompassing four hub genes and analyzed the roles of the Stay-Green (SGR) gene in regulating crosstalk with sgr mutants. We predict that these findings will provide new insights in understanding the environmental stress response of crop plants against climate change.

Fast Track to Discover Novel Promoters in Rice

Promoters are key components for the application of biotechnological techniques in crop plants. Reporter genes such as GUS or GFP have been used to test the activity of promoters for diverse applications. A huge number of T-DNAs carrying promoterless GUS near their right borders have been inserted into the rice genome, and 105,739 flanking sequence tags from rice lines with this T-DNA insertion have been identified, establishing potential promoter trap lines for 20,899 out of 55,986 genes in the rice genome. Anatomical meta-expression data and information on abiotic stress related to these promoter trap lines enable us to quickly identify new promoters associated with various expression patterns. In the present report, we introduce a strategy to identify new promoters in a very short period of time using a combination of meta-expression analysis and promoter trap lines.

Overexpression of Rice Expansin7 (Osexpa7) Confers Enhanced Tolerance to Salt Stress in Rice

Expansins are key regulators of cell-wall extension and are also involved in the abiotic stress response. In this study, we evaluated the function of OsEXPA7 involved in salt stress tolerance. Phenotypic analysis showed that OsEXPA7 overexpression remarkably enhanced tolerance to salt stress. OsEXPA7 was highly expressed in the shoot apical meristem, root, and the leaf sheath. Promoter activity of OsEXPA7:GUS was mainly observed in vascular tissues of roots and leaves. Morphological analysis revealed structural alterations in the root and leaf vasculature of OsEXPA7 overexpressing (OX) lines. OsEXPA7 overexpression resulted in decreased sodium ion (Na⁺) and accumulated potassium ion (K⁺) in the leaves and roots. Under salt stress, higher antioxidant activity was also observed in the OsEXPA7-OX lines, as indicated by lower reactive oxygen species (ROS) accumulation and increased antioxidant activity, when compared with the wild-type (WT) plants. In addition, transcriptional analysis using RNA-seq and RT-PCR revealed that genes involved in cation exchange, auxin signaling, cell-wall modification, and transcription were differentially expressed between the OX and WT lines. Notably, salt overly sensitive 1, which is a sodium transporter, was highly upregulated in the OX lines. These results suggest that OsEXPA7 plays an important role in increasing salt stress tolerance by coordinating sodium transport, ROS scavenging, and cell-wall loosening.

Transcriptomic data-driven discovery of global regulatory features of rice seeds developing under heat stress

Plants respond to abiotic stressors through a suite of strategies including differential regulation of stress-responsive genes. Hence, characterizing the influences of the relevant global regulators or on stress-related transcription factors is critical to understand plant stress response. Rice seed development is highly sensitive to elevated temperatures. To elucidate the extent and directional hierarchy of gene regulation in rice seeds under heat stress, we developed and implemented a robust multi-level optimization-based algorithm called Minimal Regulatory Network identifier (MiReN). MiReN could predict the minimal regulatory relationship between a gene and its potential regulators from our temporal transcriptomic dataset. MiReN predictions for global regulators including stress-responsive gene Slender Rice 1 (SLR1) and disease resistance gene XA21 were validated with published literature. It also predicted novel regulatory influences of other major regulators such as Kinesin-like proteins KIN12C and STD1, and WD repeat-containing protein WD40. Out of the 228 stress-responsive transcription factors identified, we predicted de novo regulatory influences on three major groups (MADS-box M-type, MYB, and bZIP) and investigated their physiological impacts during stress. Overall, MiReN results can facilitate new experimental studies to enhance our understanding of global regulatory mechanisms triggered during heat stress, which can potentially accelerate the development of stress-tolerant cultivars.

Transcriptomic Analysis of Dark-Induced Senescence in Bermudagrass (Cynodon dactylon)

Leaf senescence induced by prolonged light deficiency is inevitable whenever turfgrass is cultivated in forests, and this negatively influences the survival and aesthetic quality of the turfgrass. However, the mechanism underlying dark-induced senescence in turfgrass remained obscure. In this study, RNA sequencing was performed to analyze how genes were regulated in response to dark-induced leaf senescence in bermudagrass. A total of 159,207 unigenes were obtained with a mean length of 948 bp. The differential expression analysis showed that a total of 59,062 genes, including 52,382 up-regulated genes and 6680 down-regulated genes were found to be differentially expressed between control leaves and senescent leaves induced by darkness. Subsequent bioinformatics analysis showed that these differentially expressed genes (DEGs) were mainly related to plant hormone (ethylene, abscisic acid, jasmonic acid, auxin, cytokinin, gibberellin, and brassinosteroid) signal transduction, N-glycan biosynthesis, and protein processing in the endoplasmic reticulum. In addition, transcription factors, such as WRKY, NAC, HSF, and bHLH families were also responsive to dark-induced leaf senescence in bermudagrass. Finally, qRT-PCR analysis of six randomly selected DEGs validated the accuracy of sequencing results. Taken together, our results provide basic information of how genes respond to darkness, and contribute to the understanding of comprehensive mechanisms of dark-induced leaf senescence in turfgrass.

Integration of Abscisic Acid Signaling with Other Signaling Pathways in Plant Stress Responses and Development

Plants are immobile and, to overcome harsh environmental conditions such as drought, salt, and cold, they have evolved complex signaling pathways. Abscisic acid (ABA), an isoprenoid phytohormone, is a critical signaling mediator that regulates diverse biological processes in various organisms. Significant progress has been made in the determination and characterization of key ABA-mediated molecular factors involved in different stress responses, including stomatal closure and developmental processes, such as seed germination and bud dormancy. Since ABA signaling is a complex signaling network that integrates with other signaling pathways, the dissection of its intricate regulatory network is necessary to understand the function of essential regulatory genes involved in ABA signaling. In the present review, we focus on two aspects of ABA signaling. First, we examine the perception of the stress signal (abiotic and biotic) and the response network of ABA signaling components that transduce the signal to the downstream pathway to respond to stress tolerance, regulation of stomata, and ABA signaling component ubiquitination. Second, ABA signaling in plant development processes, such as lateral root growth regulation, seed germination, and flowering time regulation is investigated. Examining such diverse signal integration dynamics could enhance our understanding of the underlying genetic, biochemical, and molecular mechanisms of ABA signaling networks in plants.

A Gene Regulatory Network Controlled by BpERF2 and BpMYB102 in Birch under Drought Conditions

Gene expression profiles are powerful tools for investigating mechanisms of plant stress tolerance. Betula platyphylla (birch) is a widely distributed tree, but its drought-tolerance mechanism has been little studied. Using RNA-Seq, we identified 2917 birch genes involved in its response to drought stress. These drought-responsive genes include the late embryogenesis abundant (LEA) family, heat shock protein (HSP) family, water shortage-related and ROS-scavenging proteins, and many transcription factors (TFs). Among the drought-induced TFs, the ethylene responsive factor (ERF) and myeloblastosis oncogene (MYB) families were the most abundant. BpERF2 and BpMYB102, which were strongly induced by drought and had high transcription levels, were selected to study their regulatory networks. BpERF2 and BpMYB102 both played roles in enhancing drought tolerance in birch. Chromatin immunoprecipitation combined with qRT-PCR indicated that BpERF2 regulated genes such as those in the LEA and HSP families, while BpMYB102 regulated genes such as Pathogenesis-related Protein 1 (PRP1) and 4-Coumarate:Coenzyme A Ligase 10 (4CL10). Multiple genes were regulated by both BpERF2 and BpMYB102. We further characterized the function of some of these genes, and the genes that encode Root Primordium Defective 1 (RPD1), PRP1, 4CL10, LEA1, SOD5, and HSPs were found to be involved in drought tolerance. Therefore, our results suggest that BpERF2 and BpMYB102 serve as transcription factors that regulate a series of drought-tolerance genes in B. platyphylla to improve drought tolerance.

Transcriptome analysis of Oryza sativa in responses to different concentrations of thiocyanate

Effective concentrations of potassium thiocyanate (KSCN) to rice seedlings were experimentally determined using relative growth rate as a sensitive endpoint. Agilent 44-K rice microarray was used to profile the molecular responses of rice seedlings exposed to thiocyanate ion (SCN^-) at three different effective concentrations (EC₁₀, EC₂₀, and EC₅₀). A total of 18,498 known genes were collected from SCN-treated rice microarray analysis. Out of all, 1603, 1882, and 5085 differentially expressed genes (DEGs) were observed at EC₁₀, EC₂₀, and EC₅₀ concentrations, respectively. More upregulated/downregulated DEGs were detected in shoots than in roots after SCN^- exposure. Gene functions and pathway enrichment analysis of DEGs indicated that different effective concentrations of SCN^- resulted in multiple enriched GO categories and KEGG pathways and outcomes were quite tissue-specific. Different regulations and adaptations of gene expression in molecular function (MF), biological process (BP), and cellular components (CC) were observed in rice tissues at different effective concentrations of SCN^-, suggesting their different responsive and adaptive strategies. Information collected here presents a detailed description of SCN-induced alternations of gene expression in rice seedlings and provide valuable information for further searching specific genes participating in transportation, phytotoxic responses, and detoxification of SCN^- in rice seedlings.

Genome-Wide Identification of Cyclophilin Gene Family in Cotton and Expression Analysis of the Fibre Development in Gossypium barbadense

Cyclophilins (CYPs) are a member of the immunophilin superfamily (in addition to FKBPs and parvulins) and play a significant role in peptidyl-prolyl cis-trans isomerase (PPIase) activity. Previous studies have shown that CYPs have important functions in plants, but no genome-wide analysis of the cotton CYP gene family has been reported, and the specific biological function of this gene is still elusive. Based on the release of the cotton genome sequence, we identified 75, 78, 40 and 38 CYP gene sequences from G. barbadense, G. hirsutum, G. arboreum, and G. raimondii, respectively; 221 CYP genes were unequally located on chromosomes. Phylogenetic analysis showed that 231 CYP genes clustered into three major groups and eight subgroups. Collinearity analysis showed that segmental duplications played a significant role in the expansion of CYP members in cotton. There were light-responsiveness, abiotic-stress and hormone-response elements upstream of most of the CYPs. In addition, the motif composition analysis revealed that 49 cyclophilin proteins had extra domains, including TPR (tetratricopeptide repeat), coiled coil, U-box, RRM (RNA recognition motif), WD40 (RNA recognition motif) and zinc finger domains, along with the cyclophilin-like domain (CLD). The expression patterns based on qRT-PCR showed that six CYP expression levels showed greater differences between Xinhai21 (long fibres, G. barbadense) and Ashmon (short fibres, G. barbadense) at 10 and 20 days postanthesis (DPA). These results signified that CYP genes are involved in the elongation stage of cotton fibre development. This study provides a valuable resource for further investigations of CYP gene functions and molecular mechanisms in cotton.

Quantitative Proteomic Analysis of the Response to Cold Stress in Jojoba, a Tropical Woody Crop

Jojoba (Simmondsia chinensis) is a semi-arid, oil-producing industrial crop that have been widely cultivated in tropical arid region. Low temperature is one of the major environmental stress that impair jojoba's growth, development and yield and limit introduction of jojoba in the vast temperate arid areas. To get insight into the molecular mechanisms of the cold stress response of jojoba, a combined physiological and quantitative proteomic analysis was conducted. Under cold stress, the photosynthesis was repressed, the level of malondialdehyde (MDA), relative electrolyte leakage (REL), soluble sugars, superoxide dismutase (SOD) and phenylalanine ammonia-lyase (PAL) were increased in jojoba leaves. Of the 2821 proteins whose abundance were determined, a total of 109 differentially accumulated proteins (DAPs) were found and quantitative real time PCR (qRT-PCR) analysis of the coding genes for 7 randomly selected DAPs were performed for validation. The identified DAPs were involved in various physiological processes. Functional classification analysis revealed that photosynthesis, adjustment of cytoskeleton and cell wall, lipid metabolism and transport, reactive oxygen species (ROS) scavenging and carbohydrate metabolism were closely associated with the cold stress response. Some cold-induced proteins, such as cold-regulated 47 (COR47), staurosporin and temperature sensitive 3-like a (STT3a), phytyl ester synthase 1 (PES1) and copper/zinc superoxide dismutase 1, might play important roles in cold acclimation in jojoba seedlings. Our work provided important data to understand the plant response to the cold stress in tropical woody crops.

Physiological Analysis and Transcriptome Profiling of Inverted Cuttings of Populus yunnanensis Reveal That Cell Wall Metabolism Plays a Crucial Role in Responding to Inversion

Inverted cuttings of Populus yunnanensis remain alive by rooting from the original morphological apex and sprouting from the base, but the lateral branches exhibit less vigorous growth than those of the upright plant. In this study, we examined the changes in hormone contents, oxidase activities, and transcriptome profiles between upright and inverted cuttings of P. yunnanensis. The results showed that the indole-3-acetic acid (IAA) and gibberellic acid (GA₃) contents were significantly lower in inverted cuttings than in upright cuttings only in the late growth period (September and October), while the abscisic acid (ABA) level was always similar between the two direction types. The biosynthesis of these hormones was surprisingly unrelated to the inversion of P. yunnanensis during the vegetative growth stage (July and August). Increased levels of peroxidases (PODs) encoded by 13 differentially expressed genes (DEGs) served as lignification promoters that protected plants against oxidative stress. Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis showed that most DEGs (107) were related to carbohydrate metabolism. Furthermore, altered activities of uridine diphosphate (UDP)-sugar pyrophosphorylase (USP, 15 DEGs) for nucleotide sugars, pectin methylesterase (PME, 7 DEGs) for pectin, and POD (13 DEGs) for lignin were important factors in the response of the trees to inversion, and these enzymes are all involved cell wall metabolism.

Comparative Genomic and Transcriptomic Analyses of Family-1 UDP Glycosyltransferase in Prunus Mume

Glycosylation mediated by Family-1 UDP-glycosyltransferases (UGTs) plays crucial roles in plant growth and adaptation to various stress conditions. Prunus mume is an ideal crop for analyzing flowering for its early spring flowering characteristics. Revealing the genomic and transcriptomic portfolio of the UGT family in P. mume, a species in which UGTs have not yet been investigated, is therefore important. In this study, 130 putative UGT genes were identified and phylogenetically clustered into 14 groups. These PmUGTs were distributed unevenly across eight chromosomes and 32 tandem duplication and 8 segmental duplication pairs were revealed. A highly conserved intron insertion event was revealed on the basis of intron/exon patterns within PmUGTs. According to RNA-seq data, these PmUGTs were specifically expressed in different tissues and during the bud dormancy process. In addition, we confirmed the differential expression of some representative genes in response to abscisic acid treatment. Our results will provide important information on the UGT family in P. mume that should aid further characterization of their biological roles in response to environmental stress.

Hitting the Wall-Sensing and Signaling Pathways Involved in Plant Cell Wall Remodeling in Response to Abiotic Stress

Plant cells are surrounded by highly dynamic cell walls that play important roles regulating aspects of plant development. Recent advances in visualization and measurement of cell wall properties have enabled accumulation of new data about wall architecture and biomechanics. This has resulted in greater understanding of the dynamics of cell wall deposition and remodeling. The cell wall is the first line of defense against different adverse abiotic and biotic environmental influences. Different abiotic stress conditions such as salinity, drought, and frost trigger production of Reactive Oxygen Species (ROS) which act as important signaling molecules in stress activated cellular responses. Detection of ROS by still-elusive receptors triggers numerous signaling events that result in production of different protective compounds or even cell death, but most notably in stress-induced cell wall remodeling. This is mediated by different plant hormones, of which the most studied are jasmonic acid and brassinosteroids. In this review we highlight key factors involved in sensing, signal transduction, and response(s) to abiotic stress and how these mechanisms are related to cell wall-associated stress acclimatization. ROS, plant hormones, cell wall remodeling enzymes and different wall mechanosensors act coordinately during abiotic stress, resulting in abiotic stress wall acclimatization, enabling plants to survive adverse environmental conditions.

Screening and Evaluation of Saline–Alkaline Tolerant Germplasm of Rice (Oryza sativa L.) in Soda Saline–Alkali Soil

The improvement and development of saline–alkali land is of great significance for promoting food production and sustainable development. It is necessary to study the mechanism of saline–alkaline tolerance and breed saline–alkaline tolerant crops to improve the utilization of saline–alkali land. For this study, we conducted a three-year pot experiment to screen the saline–alkaline tolerant germplasm of 72 rice genotypes from hundreds of elite cultivars during the whole growth period using a certain proportion of soda saline–alkali soil. The selected salt-tolerant variety was combined with a salt-sensitive variety to analyze the saline–alkaline tolerance mechanism by using the saline–alkaline soil leachate. We eliminated 36 genotypes with low seedling survival rates under salt–alkali stress, and the salt-tolerant Jiudao-66 (D68) variety had a higher survival rate than most varieties. The membership degree of Jiudao-66, according to the salt tolerance index of multiple agronomic traits, is higher than that of 34 varieties, with a higher survival rate except when compared to D36. The survival rate and these salt tolerance indexes of Jiudao-66 were significantly higher than those of Kitaake (salt-sensitive). Under the stress of leachate, the content of proline and soluble sugars in the shoots of Jiudao-66 were higher than that of Kitaake, and the total antioxidant capacity was stronger than that of Kitaake. However, the content of malondialdehyde was lower than that of Kitaake. Additionally, the Na+/K+ ratios in shoots and roots were not significantly differently between Kitaake and Jiudao-66. The results showed that Jiudao-66, as a salt-tolerant variety, is more tolerant to salt and alkali in a near-natural state due to its stronger tolerance of osmotic stress, and it can accumulate more proline and soluble sugars under stress. At the same time, Jiudao-66 also has a stronger antioxidant capacity. Its ion regulation ability has no obvious advantage.

Transcriptome Analysis of JA Signal Transduction, Transcription Factors, and Monoterpene Biosynthesis Pathway in Response to Methyl Jasmonate Elicitation in Mentha canadensis L

Mentha canadensis L. has important economic value for its abundance in essential oils. Menthol is the main component of M. canadensis essential oils, which is certainly the best-known monoterpene for its simple structure and wide applications. However, the regulation of menthol biosynthesis remains elusive in M. canadensis. In this study, transcriptome sequencing of M. canadensis with MeJA treatment was applied to illustrate the transcriptional regulation of plant secondary metabolites, especially menthol biosynthesis. Six sequencing libraries were constructed including three replicates for both control check (CK) and methyl jasmonate (MeJA) treatment and at least 8 Gb clean bases was produced for each library. After assembly, a total of 81,843 unigenes were obtained with an average length of 724 bp. Functional annotation indicated that 64.55% of unigenes could be annotated in at least one database. Additionally, 4430 differentially expressed genes (DEGs) with 2383 up-regulated and 2047 down-regulated transcripts were identified under MeJA treatment. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment indicated that "Monoterpenoid biosynthesis" was one of the most significantly enriched pathways in metabolism. Subsequently, DEGs involved in JA signal transduction, transcription factors, and monoterpene biosynthesis were analyzed. 9 orthologous genes involved in menthol biosynthesis were also identified. This is the first report of a transcriptome study of M. canadensis and will facilitate the studies of monoterpene biosynthesis in the genus Mentha.

Genome-Wide Characterization of DNA Demethylase Genes and Their Association with Salt Response in Pyrus

DNA methylation plays important roles in genome protection and the regulation of gene expression and it is associated with plants’ responses to environments. DNA demethylases are very important proteins in DNA methylation regulation. In this study, we performed genome-wide and deep analysis of putative demethylases (DMEs) in pear. Seven DME genes were found in the pear genome and were defined as PbDME1–7 based on their domain organization. Results were supported by the gene structural characteristics and phylogenetic analysis. The gene structure of the DME genes were relatively complex and the DME7 proteins didn’t contain the Perm_CXXC domain. The DME genes experienced a whole genome duplication event (WGD) that occurred in the ancestor genome of pear and apple before their divergence based on the Ks values. Expression results showed that high salinity stress could influence the expression level of DMEs and salt-responsive genes in Pyrus betulaefolia. Furthermore, the methylation levels of salt-responsive genes changed under salt stress treatment. Results suggested important roles of PbDME genes in response to salt stress and are useful for better understanding the complex functions of this DME genes, which will facilitate epigenetic studies in pear trees salt tolerance.

Classification and Genome-Wide Analysis of Chitin-Binding Proteins Gene Family in Pepper (Capsicum annuum L.) and Transcriptional Regulation to Phytophthora capsici, Abiotic Stresses and Hormonal Applications

Chitin-binding proteins are pathogenesis-related gene family, which play a key role in the defense response of plants. However, thus far, little is known about the chitin-binding family genes in pepper (Capsicum annuum L.). In current study, 16 putative chitin genes (CaChi) were retrieved from the latest pepper genome database, and were classified into four distinct classes (I, III, IV and VI) based on their sequence structure and domain architectures. Furthermore, the structure of gene, genome location, gene duplication and phylogenetic relationship were examined to clarify a comprehensive background of the CaChi genes in pepper. The tissue-specific expression analysis of the CaChi showed the highest transcript levels in seed followed by stem, flower, leaf and root, whereas the lowest transcript levels were noted in red-fruit. Phytophthora capsici post inoculation, most of the CaChi (CaChiI3, CaChiIII1, CaChiIII2, CaChiIII4, CaChiIII6, CaChiIII7, CaChiIV1, CaChiVI1 and CaChiVI2) were induced by both strains (PC and HX-9). Under abiotic and exogenous hormonal treatments, the CaChiIII2, CaChiIII7, CaChiVI1 and CaChiVI2 were upregulated by abiotic stress, while CaChiI1, CaChiIII7, CaChiIV1 and CaChiIV2 responded to hormonal treatments. Furthermore, CaChiIV1-silenced plants display weakened defense by reducing (60%) root activity and increase susceptibility to NaCl stress. Gene ontology (GO) enrichment analysis revealed that CaChi genes primarily contribute in response to biotic, abiotic stresses and metabolic/catabolic process within the biological process category. These results exposed that CaChi genes are involved in defense response and signal transduction, suggesting their vital roles in growth regulation as well as response to stresses in pepper plant. In conclusion, these finding provide basic insights for functional validation of the CaChi genes in different biotic and abiotic stresses.