Linkage of cold acclimation and disease resistance through plant-pathogen interaction pathway in Vitis amurensis grapevine

Identification of genetic loci and candidate genes underlying freezing tolerance in wheat seedlings

KEY MESSAGE

Ten stable loci for freezing tolerance (FT) in wheat were detected by genome-wide association analysis. The putative candidate gene TaRPM1-7BL underlying the major locus QFT.ahau-7B.2 was identified and validated. Frost damage restricts wheat growth, development, and geographical distribution. However, the genetic mechanism of freezing tolerance (FT) remains unclear. Here, we evaluated FT phenotypes of 245 wheat varieties and lines, and genotyped them using a Wheat 90 K array. The association analysis showed that ten stable loci were significantly associated with FT (P < 1 × 10-4), and explained 6.45-26.33% of the phenotypic variation. In particular, the major locus QFT.ahau-7B.2 was consistently related to all nine sets of FT phenotypic data. Based on five cleaved amplified polymorphic sequence (CAPS) markers closely linked to QFT.ahau-7B.2, we narrowed down the target region to the 570.67-571.16 Mb interval (0.49 Mb) on chromosome 7B, in which four candidate genes were annotated. Of these, only TaRPM1-7BL exhibited consistent differential expression after low temperature treatment between freezing-tolerant and freezing-sensitive varieties. The results of cloning and whole-exome capture sequencing indicated that there were two main haplotypes for TaRPM1-7BL, including freezing-tolerant Hap1 and freezing-sensitive Hap2. Based on the representative SNP (+1956, A/G), leading to an amino acid change in the NBS domain, a CAPS marker (CAPS-TaRPM1-7BL) was developed and validated in 431 wheat varieties (including the above 245 materials) and 318 F2 lines derived from the cross of 'Annong 9267' (freezing-tolerant) × 'Yumai 9' (freezing-sensitive). Subsequently, the TaRPM1-7BL gene was silenced in 'Yumai 9' by virus-induced gene silencing (VIGS), and these silenced wheat seedlings exhibited enhanced FT phenotypes, suggesting that TaRPM1-7BL negatively regulates FT. These findings are valuable for understanding the complex genetic basis of FT in wheat.

Constitutive expression of nucleotide-binding and leucine-rich repeat gene AtRPS2 enhanced drought and salt tolerance in rice

Drought and salt are major abiotic stresses that severely restricts plant growth and development, leading to serious losses in agricultural production. Therefore, improving crop tolerance to drought and salt stresses is an urgent issue. A previous study showed that overexpression of Arabidopsis NLR gene AtRPS2 conferred broad-spectrum disease resistance in rice. In this study, we demonstrated that constitutive expression of AtRPS2 increased abscisic acid (ABA) sensitivity during seedling stage, the shoot length of transgenic plants were shorter than wild type plants. Exogenous application of ABA markedly induced the expression of stress-related genes and promoted stomatal close in transgenic plants. Overexpression of AtRPS2 also enhanced drought and salt tolerance in rice, transgenic plants exhibited higher survival rates under drought and salt conditions than wild type plants. The activities of catalase (CAT) and superoxide dismutase (SOD) were higher in AtRPS2 transgenic rice than wild type plants. In addition, the expression of stress-related genes and ABA-responsive genes were significantly upregulated in AtRPS2 transgenic plants than wild type plants under drought and salt treatments. Besides, exogenous application of ABA could facilitate drought and salt tolerance in AtRPS2 transgenic plants. Taken together, this study indicated that AtRPS2 could improve drought and salt tolerance in rice, and this phenomenon is likely to be regulated through ABA signaling pathways.

The RNA-binding protein MdHYL1 modulates cold tolerance and disease resistance in apple

Apple (Malus domestica) trees often experience various abiotic and biotic stresses. However, due to the long juvenile period of apple and its high degree of genetic heterozygosity, only limited progress has been made in developing cold-hardy and disease-resistant cultivars through traditional approaches. Numerous studies reveal that biotechnology is a feasible approach to improve stress tolerance in woody perennial plants. HYPONASTIC LEAVES1 (HYL1), a double-stranded RNA-binding protein, is a key regulator involved in apple drought stress response. However, whether HYL1 participates in apple cold response and pathogen resistance remains unknown. In this study, we revealed that MdHYL1 plays a positive role in cold tolerance and pathogen resistance in apple. MdHYL1 acted upstream to positively regulate freezing tolerance and Alternaria alternata resistance by positively modulating transcripts of MdMYB88 and MdMYB124 in response to cold stress or A. alternata infection. In addition, MdHYL1 regulated the biogenesis of several miRNAs responsive to cold and A. alternata infection in apple. Furthermore, we identified Mdm-miRNA156 (Mdm-miR156) as a negative regulator of cold tolerance and Mdm-miRNA172 (Mdm-miR172) as a positive regulator of cold tolerance, and that Mdm-miRNA160 (Mdm-miR160) decreased plant resistance to infection by A. alternata. In summary, we highlight the molecular role of MdHYL1 regarding cold tolerance and A. alternata infection resistance, thereby providing candidate genes for breeding apple with freezing tolerance and A. alternata resistance using biotechnology.

Chemical profile and analysis of biosynthetic pathways and genes of volatile terpenes in Pityopsis ruthii, a rare and endangered flowering plant

It is critical to gather biological information about rare and endangered plants to incorporate into conservation efforts. The secondary metabolism of Pityopsis ruthii, an endangered flowering plant that only occurs along limited sections of two rivers (Ocoee and Hiwassee) in Tennessee, USA was studied. Our long-term goal is to understand the mechanisms behind P. ruthii's adaptation to restricted areas in Tennessee. Here, we profiled the secondary metabolites, specifically in flowers, with a focus on terpenes, aiming to uncover the genomic and molecular basis of terpene biosynthesis in P. ruthii flowers using transcriptomic and biochemical approaches. By comparative profiling of the nonpolar portion of metabolites from various tissues, P. ruthii flowers were rich in terpenes, which included 4 monoterpenes and 10 sesquiterpenes. These terpenes were emitted from flowers as volatiles with monoterpenes and sesquiterpenes accounting for almost 68% and 32% of total emission of terpenes, respectively. These findings suggested that floral terpenes play important roles for the biology and adaptation of P. ruthii to its limited range. To investigate the biosynthesis of floral terpenes, transcriptome data for flowers were produced and analyzed. Genes involved in the terpene biosynthetic pathway were identified and their relative expressions determined. Using this approach, 67 putative terpene synthase (TPS) contigs were detected. TPSs in general are critical for terpene biosynthesis. Seven full-length TPS genes encoding putative monoterpene and sesquiterpene synthases were cloned and functionally characterized. Three catalyzed the biosynthesis of sesquiterpenes and four catalyzed the biosynthesis of monoterpenes. In conclusion, P. ruthii plants employ multiple TPS genes for the biosynthesis of a mixture of floral monoterpenes and sesquiterpenes, which probably play roles in chemical defense and attracting insect pollinators alike.

Transcriptomics Reveals the Effect of Short-Term Freezing on the Signal Transduction and Metabolism of Grapevine

Low temperature is an important factor limiting plant growth. Most cultivars of Vitis vinifera L. are sensitive to low temperatures and are at risk of freezing injury or even plant death during winter. In this study, we analyzed the transcriptome of branches of dormant cv. Cabernet Sauvignon exposed to several low-temperature conditions to identify differentially expressed genes and determine their function based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)enrichment analyses. Our results indicated that exposure to subzero low temperatures resulted in damage to plant cell membranes and extravasation of intracellular electrolytes, and that this damage increased with decreasing temperature or increasing duration. The number of differential genes increased as the duration of stress increased, but most of the common differentially expressed genes reached their highest expression at 6 h of stress, indicating that 6 h may be a turning point for vines to tolerate extreme low temperatures. Several pathways play key roles in the response of Cabernet Sauvignon to low-temperature injury, namely: (1) the role of calcium/calmodulin-mediated signaling; (2) carbohydrate metabolism, including the hydrolysis of cell wall pectin and cellulose, decomposition of sucrose, synthesis of raffinose, and inhibition of glycolytic processes; (3) the synthesis of unsaturated fatty acids and metabolism of linolenic acid; and (4) the synthesis of secondary metabolites, especially flavonoids. In addition, pathogenesis-related protein may also play a role in plant cold resistance, but the mechanism is not yet clear. This study reveals possible pathways for the freezing response and leads to new insights into the molecular basis of the tolerance to low temperature in grapevine.

Advances in understanding cold tolerance in grapevine

Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely low temperatures, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.

Annotation of Siberian Larch (Larix sibirica Ledeb.) Nuclear Genome—One of the Most Cold-Resistant Tree Species in the Only Deciduous GENUS in Pinaceae

The recent release of the nuclear, chloroplast and mitochondrial genome assemblies of Siberian larch (Larix sibirica Ledeb.), one of the most cold-resistant tree species in the only deciduous genus of Pinaceae, with seasonal senescence and a rot-resistant valuable timber widely used in construction, greatly contributed to the development of genomic resources for the larch genus. Here, we present an extensive repeatome analysis and the first annotation of the draft nuclear Siberian larch genome assembly. About 66% of the larch genome consists of highly repetitive elements (REs), with the likely wave of retrotransposons insertions into the larch genome estimated to occur 4–5 MYA. In total, 39,370 gene models were predicted, with 87% of them having homology to the Arabidopsis-annotated proteins and 78% having at least one GO term assignment. The current state of the genome annotations allows for the exploration of the gymnosperm and angiosperm species for relative gene abundance in different functional categories. Comparative analysis of functional gene categories across different angiosperm and gymnosperm species finds that the Siberian larch genome has an overabundance of genes associated with programmed cell death (PCD), autophagy, stress hormone biosynthesis and regulatory pathways; genes that may play important roles in seasonal senescence and stress response to extreme cold in larch. Despite being incomplete, the draft assemblies and annotations of the conifer genomes are at a point of development where they now represent a valuable source for further genomic, genetic and population studies.

Transcriptomic and Metabolomic Analyses Reveal Key Metabolites, Pathways and Candidate Genes in Sophora davidii (Franch.) Skeels Seedlings Under Drought Stress

Soil aridification and desertification are particularly prominent in China's karst areas, severely limiting crop yields and vegetation restoration. Therefore, it is very important to identify naturally drought-tolerant plant species. Sophora davidii (Franch.) Skeels is resistant to drought and soil infertility, is deeply rooted and is an excellent plant material for soil and water conservation. We studied the transcriptomic and metabolomic changes in S. davidii in response to drought stress (CK, control; LD, mild drought stress; MD, moderate drought stress; and SD, severe drought stress). Sophora davidii grew normally under LD and MD stress but was inhibited under SD stress; the malondialdehyde (MDA), hydrogen peroxide (H₂O₂), soluble sugar, proline, chlorophyll a, chlorophyll b and carotenoid contents and ascorbate peroxidase (APX) activity significantly increased, while the superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activities and soluble protein content significantly decreased. In the LD/CK, MD/CK and SD/CK comparison groups, there were 318, 734 and 1779 DEGs, respectively, and 100, 168 and 281 differentially accumulated metabolites, respectively. Combined analysis of the transcriptomic and metabolomic data revealed the metabolic regulation of S. davidii in response to drought stress. First, key candidate genes such as PRR7, PRR5, GI, ELF3, PsbQ, PsaK, INV, AMY, E2.4.1.13, E3.2.1.2, NCED, PP2C, PYL, ABF, WRKY33, P5CS, PRODH, AOC3, HPD, GPX, GST, CAT and SOD1 may govern the drought resistance of S. davidii. Second, three metabolites (oxidised glutathione, abscisic acid and phenylalanine) were found to be related to drought tolerance. Third, several key candidate genes and metabolites involved in 10 metabolic pathways were identified, indicating that these metabolic pathways play an important role in the response to drought in S. davidii and possibly other plant species.

The Brachypodium distachyon cold-acclimated plasma membrane proteome is primed for stress resistance

In order to survive subzero temperatures, some plants undergo cold acclimation (CA) where low, nonfreezing temperatures, and/or shortened day lengths allow cold-hardening and survival during subsequent freeze events. Central to this response is the plasma membrane (PM), where low temperature is perceived and cellular homeostasis must be preserved by maintaining membrane integrity. Here, we present the first PM proteome of cold-acclimated Brachypodium distachyon, a model species for the study of monocot crops. A time-course experiment investigated CA-induced changes in the proteome following two-phase partitioning PM enrichment and label-free quantification by nano-liquid chromatography-mass spectrophotometry. Two days of CA were sufficient for membrane protection as well as an initial increase in sugar levels and coincided with a significant change in the abundance of 154 proteins. Prolonged CA resulted in further increases in soluble sugars and abundance changes in more than 680 proteins, suggesting both a necessary early response to low-temperature treatment, as well as a sustained CA response elicited over several days. A meta-analysis revealed that the identified PM proteins have known roles in low-temperature tolerance, metabolism, transport, and pathogen defense as well as drought, osmotic stress, and salt resistance suggesting crosstalk between stress responses, such that CA may prime plants for other abiotic and biotic stresses. The PM proteins identified here present keys to an understanding of cold tolerance in monocot crops and the hope of addressing economic losses associated with modern climate-mediated increases in frost events.

De novo transcriptome assembly and comparative transcriptomic analysis provide molecular insights into low temperature stress response of Canarium album

A de novo transcriptome analysis was performed in C. album, a temperature sensitive fruit tree in China, after treatment with varied temperatures. A total number of 168,385 transcripts were assembled, comprising of 109,439 unigenes, of which 70,530 were successfully annotated. Compared with control check group (CK), which was treated under 25 °C, the chilling stress (4 °C) treated group (CT), showed about 2810 up-regulated and 2567 down-regulated genes. Whereas, group treated under freezing (- 3 °C) stress (FT) showed an up-regulation and a down-regulation of 1748 and 1459 genes, respectively. GO classification analysis revealed that DEGs related to metabolic processes, single-organism metabolic process, and catalytic activity are significantly enriched in both CT and FT conditions. KEGG pathway enrichment analysis for both CT and FT treatments showed an enrichment of genes encoding or related to glycine/serine and threonine metabolism, alpha-linolenic acid metabolism, carotenoid biosynthesis, photosynthesis-antenna proteins, and circadian rhythm. However, genes related to photosynthesis, carbon fixation in photosynthetic organisms, glutathione metabolism, pyruvate metabolism, nicotinate and nicotinamide metabolism were specifically enriched in CT condition. Nevertheless, FT treatment induced genes related to plant-pathogen interaction, linoleic acid metabolism, plant hormone signal transduction and pentose phosphate pathway. Many of the genes involved in plant hormone signal transduction showed significantly different expression in both FT and CT conditions. However, the change was more evident in FT. Here we present the first of the reports for a de novo transcriptomic analysis in C. album, suggesting that the plant shows differential responses in chilling and freezing temperatures, where the hormone signaling and transduction contribute greatly to FT responses. Our study thus paves way for future research regarding functions of these potentially identified genes.

The Endophytic Fungus Piriformospora indica Reprograms Banana to Cold Resistance

Banana (Musa spp.), one of the most important fruits worldwide, is generally cold sensitive. In this study, by using the cold-sensitive banana variety Tianbaojiao (Musa acuminate) as the study material, we investigated the effects of Piriformospora indica on banana cold resistance. Seedlings with and without fungus colonization were subjected to 4 °C cold treatment. The changes in plant phenotypes, some physiological and biochemical parameters, chlorophyll fluorescence parameters, and the expression of eight cold-responsive genes in banana leaves before and after cold treatment were measured. Results demonstrated that P. indica colonization reduced the contents of malondialdehyde (MDA) and hydrogen peroxide (H₂O₂) but increased the activities of superoxide dismutase (SOD) and catalase (CAT) and the contents of soluble sugar (SS) and proline. Noteworthily, the CAT activity and SS content in the leaves of P. indica-colonized banana were significant (p < 0.05). After 24 h cold treatment, the decline in maximum photochemistry efficiency of photosystem II (F_v/F_m), photochemical quenching coefficient (qP), efficient quantum yield [Y(II)], and photosynthetic electron transport rate (ETR) in the leaves of P. indica-colonized banana was found to be lower than in the non-inoculated controls (p < 0.05). Moreover, although the difference was not significant, P. indica colonization increased the photochemical conversion efficiency and electron transport rate and alleviated the damage to the photosynthetic reaction center of banana leaves under cold treatment to some extent. Additionally, the expression of the most cold-responsive genes in banana leaves was significantly induced by P. indica during cold stress (p < 0.05). It was concluded that P. indica confers banana with enhanced cold resistance by stimulating antioxidant capacity, SS accumulation, and the expression of cold-responsive genes in leaves. The results obtained from this study are helpful for understanding the P. indica-induced cold resistance in banana.

Transcriptome Analysis and Cell Morphology of Vitis rupestris Cells to Botryosphaeria Dieback Pathogen Diplodia seriata

Diplodia seriata, one of the major causal agents of Botryosphaeria dieback, spreads worldwide, causing cankers, leaf spots and fruit black rot in grapevine. Vitis rupestris is an American wild grapevine widely used for resistance and rootstock breeding and was found to be highly resistant to Botryosphaeria dieback. The defense responses of V. rupestris to D. seriata 98.1 were analyzed by RNA-seq in this study. There were 1365 differentially expressed genes (DEGs) annotated with Gene Ontology (GO) and enriched by the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The DEGs could be allocated to the flavonoid biosynthesis pathway and the plant–pathogen interaction pathway. Among them, 53 DEGs were transcription factors (TFs). The expression levels of 12 genes were further verified by real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). The aggregation of proteins on the plasma membrane, formation variations in the cytoskeleton and plasmodesmata and hormone regulations revealed a declined physiological status in V. rupestris suspension cells after incubation with the culture filtrates of D. seriata 98.1. This study provides insights into the molecular mechanisms in grapevine cells’ response to D. seriata 98.1, which will be valuable for the control of Botryosphaeria dieback.

Integrated RNA-Seq Analysis and Meta-QTLs Mapping Provide Insights into Cold Stress Response in Rice Seedling Roots

Rice (Oryza sativa L.) is a widely cultivated food crop around the world, especially in Asia. However, rice seedlings often suffer from cold stress, which affects their growth and yield. Here, RNA-seq analysis and Meta-QTLs mapping were performed to understand the molecular mechanisms underlying cold tolerance in the roots of 14-day-old seedlings of rice (RPY geng, cold-tolerant genotype). A total of 4779 of the differentially expressed genes (DEGs) were identified, including 2457 up-regulated and 2322 down-regulated DEGs. The GO, COG, KEEG, and Mapman enrichment results of DEGs revealed that DEGs are mainly involved in carbohydrate transport and metabolism, signal transduction mechanisms (plant hormone signal transduction), biosynthesis, transport and catabolism of secondary metabolites (phenylpropanoid biosynthesis), defense mechanisms, and large enzyme families mechanisms. Notably, the AP2/ERF-ERF, NAC, WRKY, MYB, C2H2, and bHLH transcription factors participated in rice’s cold–stress response and tolerance. On the other hand, we mapped the identified DEGs to 44 published cold–stress-related genes and 41 cold-tolerant Meta-QTLs regions. Of them, 12 DEGs were the published cold–stress-related genes and 418 DEGs fell into the cold-tolerant Meta-QTLs regions. In this study, the identified DEGs and the putative molecular regulatory network can provide insights for understanding the mechanism of cold stress tolerance in rice. In addition, DEGs in KEGG term-enriched terms or cold-tolerant Meta-QTLs will help to secure key candidate genes for further functional studies on the molecular mechanism of cold stress response in rice.

Comprehensive Evaluation and Analysis of the Mechanism of Cold Tolerance Based on the Transcriptome of Weedy Rice Seedlings

In this study, the cold-tolerance capacity of 133 varieties of weedy rice was evaluated based on the comprehensive evaluation index D, with Kongyu 131 used as a cold-tolerant control. A total of 39.8% of the 133 varieties were considered 'strong', indicating that weedy rice populations indeed have relatively strong cold-tolerance capacity as a whole, and the robust cold-tolerant varieties WR29 and WR157 were identified. Regression analysis showed that the metrics including the nitrogen recovery index, superoxide dismutase (SOD) content and malondialdehyde (MDA) content correlated significantly (P < 0.05) with cold tolerance and could be used as indicators of cold tolerance. On the basis of a transcriptome analysis of WR157, a robust cold-tolerant variety identified in this study, a total of 4645 putative DEGs were identified in treated groups compared to the control groups, with 2123 upregulated DEGs and 2522 downregulated DEGs. All upregulated DEGs were enriched on 1388 terms, all downregulated DEGs were enriched on 1566 terms; 911 of the 2123 upregulated DEGs fell into 98 KEGG categories and 1103 of the 2522 downregulated DEGs were in 115 categories. Further analysis showed that GO:0019740 and GO:0006808 are involved in nitrogen utilization; GO:0009269 and GO:0009414 are related to the stress response; and GO:0016491 and GO:0016614 are related to oxidoreductase activity. BACKGROUND: Weedy rice (Oryza) is a related pest species of cultivated rice (Oryza sativa L.) that has strong abiotic stress resistance; however, the comprehensive mechanism governing its cold tolerance is poorly understood. CONCLUSION: Our comprehensive evaluation based on five morphological indices and nine physiological indicators revealed outstanding levels of cold-tolerance capacity among weedy rice varieties from different regions and revealed some terms related to cold tolerance via transcriptome analysis. Our results underscored the reliable evaluation methods for additional cold tolerance studies and revealed several genes related to cold tolerance, which will help researchers breed cultivated rice varieties to increase their cold-tolerance capacity. These traits have the ability to increase seedling survival rate and growth, as well as future yields.

De novo transcriptomic profiling of the clonal Leymus chinensis response to long-term overgrazing-induced memory

Sheepgrass (Leymus chinensis) is one of the dominant grass species present on typical steppes of the Inner Mongolia Plateau. However, L. chinensis has developed a dwarfing phenotype in response to the stressful habitat in grasslands that are severely degraded due to heavy grazing. The lack of transcriptomic and genomic information has prohibited the understanding of the transgenerational effect on physiological alterations in clonal L. chinensis at the molecular level in response to livestock grazing. To solve this problem, transcriptomic information from the leaves of clonal L. chinensis obtained from overgrazed (GR) and non-grazed (NG) grasslands was studied using a paired-end Illumina HiSeq 2500 sequencing platform. First, despite the influence of grazing being absent during the growth of clonal offspring in our hydroponic experiment, compared with those from the NG group, clonal L. chinensis from the GR group exhibited significant dwarf-type morphological traits. A total of 116,356 unigenes were subsequently generated and assembled de novo, of which 55,541 could be annotated to homologous matches in the NCBI non-redundant (Nr), Swiss-Prot, Clusters of Orthologous Groups (COG), gene ontology (GO), or Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The expression of 3,341 unigenes significantly differed between the GR group and the NG group with an absolute value of Log₂ ratio ≥ 1. The altered expression of genes involved in defence and immune responses, pathogenic resistance and cell development indicates that livestock grazing induces a transgenerational effect on the growth inhibition of clonal L. chinensis. The results of the present study will provide important large-scale transcriptomic information on L. chinensis. Furthermore, the results facilitated our investigation of grazing-induced transgenerational effects on both the morphological and physiological characteristics of L. chinensis at the molecular levels.

Segmental and Tandem Duplications Driving the Recent NBS-LRR Gene Expansion in the Asparagus Genome

Garden asparagus is an important horticultural plant worldwide. It is, however, susceptible to a variety of diseases, which can affect the potential yield, spear quality, and lifespan of production fields. Screening studies have identified resistant germplasm. The genetic resistance is usually complex, and the genes underlying that resistance are still unknown. Most often, disease resistance is determined by resistance genes (R). The most predominant R-genes contain nucleotide binding site and leucine-rich repeat (NBS-LRR) domains. Using bioinformatics and data mining approaches, we identified and characterized 68 NBS predicted proteins encoded by 49 different loci in the asparagus genome. The NBS-encoding genes were grouped into seven distinct classes based on their domain architecture. The NBS genes are unevenly distributed through the genome and nearly 50% of the genes are present in clusters. Chromosome 6 is significantly NBS-enriched and one single cluster hosts 10% of the genes. Phylogenetic analysis points to their diversification into three families during their evolution. Recent duplications are likely to have dominated the NBS expansion with both tandem genes and duplication events across multiple chromosomes. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. The total number of cis-regulatory elements as well as their relative positions within the NBS promoters suggests a complex transcriptional network regulating defense responses. Our study provides a strong groundwork for the isolation of candidate R-genes in garden asparagus.

An Overview of Biomembrane Functions in Plant Responses to High-Temperature Stress

Biological membranes are highly ordered structures consisting of mosaics of lipids and proteins. Elevated temperatures can directly and effectively change the properties of these membranes, including their fluidity and permeability, through a holistic effect that involves changes in the lipid composition and/or interactions between lipids and specific membrane proteins. Ultimately, high temperatures can alter microdomain remodeling and instantaneously relay ambient cues to downstream signaling pathways. Thus, dynamic membrane regulation not only helps cells perceive temperature changes but also participates in intracellular responses and determines a cell's fate. Moreover, due to the specific distribution of extra- and endomembrane elements, the plasma membrane (PM) and membranous organelles are individually responsible for distinct developmental events during plant adaptation to heat stress. This review describes recent studies that focused on the roles of various components that can alter the physical state of the plasma and thylakoid membranes as well as the crucial signaling pathways initiated through the membrane system, encompassing both endomembranes and membranous organelles in the context of heat stress responses.

Grapevine immune signaling network in response to drought stress as revealed by transcriptomic analysis

Drought is a ubiquitous abiotic factor that severely impedes growth and development of horticulture crops. The challenge postured by global climate change is the evolution of drought-tolerant cultivars that could cope with concurrent stress. Hence, in this study, biochemical, physiological and transcriptome analysis were investigated in drought-treated grapevine leaves. The results revealed that photosynthetic activity and reducing sugars were significantly diminished which were positively correlated with low stomatal conductance and CO₂ exchange in drought-stressed leaves. Further, the activities of superoxide dismutase, peroxidase, and catalase were significantly actuated in the drought-responsive grapevine leaves. Similarly, the levels of abscisic acid and jasmonic acid were also significantly increased in the drought-stressed leaves. In transcriptome analysis, 12,451 differentially-expressed genes (DEGs) were annotated, out of which 8021 DEGs were up-regulated and 4430 DEGs were down-regulated in response to drought stress. In addition, the genes encoding pathogen-associated molecular pattern (PAMP) triggered immunity (PTI), including calcium signals, protein phosphatase 2C, calcineurin B-like proteins, MAPKs, and phosphorylation (FLS2 and MEKK1) cascades were up-regulated in response to drought stress. Several genes related to plant-pathogen interaction pathway (RPM1, PBS1, RPS5, RIN4, MIN7, PR1, and WRKYs) were also found up-regulated in response to drought stress. Overall the results of present study showed the dynamic interaction of DEG in grapevine physiology which provides the premise for selection of defense-related genes against drought stress for subsequent grapevine breeding programs.

Effect of the Winter Wheat Cheyenne 5A Substituted Chromosome on Dynamics of Abscisic Acid and Cytokinins in Freezing-Sensitive Chinese Spring Genetic Background

The effect of short- and long-term cold treatment on the abscisic acid (ABA) and cytokinin (CK) metabolism, and their main biosynthesis- and signaling-related genes were investigated in freezing-sensitive and freezing-tolerant wheat genotypes. Varieties Cheyenne and Chinese Spring substituted with the 5A Cheyenne chromosome, which represented freezing-tolerant genotypes, were compared with the freezing-sensitive Chinese Spring. Hormone levels and gene expression data indicated that the short- and long-term cold treatments are associated with specific regulation of the accumulation of cold-protective proteins and phytohormone levels, as well as the expression profiles of the hormone-related genes. The significant differences were observed between the genotypes, and between their leaf and crown tissues, too. The level of dehydrins, including WCS120 protein, and expression of WCS120 gene were considerably higher in the freezing-tolerant genotypes after 21 days of cold treatment. Expression of Cor14b and CBF14, cold-responsive regulator genes, was increased by cold treatment in all genotypes, to higher extent in freezing-tolerant genotypes. Cluster analysis revealed that the tolerant genotypes had a similar response to cold treatment, regarding expression of the ABA and CK metabolic genes, as well as hormone levels in leaves. As far as hormone levels in crowns are concerned, however, the strongly freezing-tolerant Cheyenne variety clustered separately from the Chinese Spring and the substitution line, which were more similar to each other after both 1 and 21 days of cold treatment than to Cheyenne. Based on these results we concluded that the 5A chromosome of wheat might have both a direct and an indirect impact on the phytohormone-dependent cold-induced freezing tolerance. Based on the gene expression data, novel genetic markers could be developed, which may be used to determine the freezing tolerance level in a wide range of wheat varieties.

Fructans As DAMPs or MAMPs: Evolutionary Prospects, Cross-Tolerance, and Multistress Resistance Potential

This perspective paper proposes that endogenous apoplastic fructans in fructan accumulating plants, released after stress-mediated cellular leakage, or increased by exogenous application, can act as damage-associated molecular patterns (DAMPs), priming plant innate immunity through ancient receptors and defense pathways that most probably evolved to react on microbial fructans acting as microbe-associated molecular patterns (MAMPs). The proposed model is placed in an evolutionary perspective. How this type of DAMP signaling may contribute to cross-tolerance and multistress resistance effects in plants is discussed. Besides apoplastic ATP, NAD and fructans, apoplastic polyamines, secondary metabolites, and melatonin may be considered potential players in DAMP-mediated stress signaling. It is proposed that mixtures of DAMP priming formulations hold great promise as natural and sustainable alternatives for toxic agrochemicals.

Overexpression of Muscadinia rotundifolia CBF2 gene enhances biotic and abiotic stress tolerance in Arabidopsis

C-repeat-binding factor dehydration-responsive element-binding factor 1C (CBF2/DREB1C) gene encodes a small family of transcriptional activator that has been described as playing an important role in freezing tolerance and cold acclimation of plants. We here report that CBF2 gene also plays an important role in the early response to the pathogen infection of grapevine downy mildew disease. The expression level of CBF2 increased dramatically and reached a peak at 7 h after infection in immune grapevine Muscadinia rotundifolia 'Noble', which was much faster than moderate resistant Vitis amurensis 'PI1288' and susceptible Vitis vinifera 'Cabernet Sauvignon'. Muscadinia rotundifolia MrCBF2 exhibited amino acid domains characteristic of Vitis CBF2 proteins with unique features including rich serine repeats and slight differences in NLS, DSAWRL, and AP2 domains. The MrCBF2 gene was introduced to Arabidopsis 'COL0' which are susceptible to downy mildew pathogen. The transgenic lines showed an increased resistance to downy mildew disease and more accumulation of SA as well as higher expression of pathogenesis-related (PR) genes (AtPR1, AtPR4, and AtPR5) as a consequence of MrCBF2 overexpression. Besides, constitutive expression of MrCBF2 enhanced phytohormone abscisic acid (ABA)-independent drought tolerance of transgenic plants. Freezing tolerance of transgenic lines was also enhanced accompanied with an increase in the expression of the cold-regulated genes AtCOR, AtCOR15A, AtKIN1, AtRD29A, and AtSuSy. In addition, the development of MrCBF2-overexpressing plants was seen to be altered and resulted in growth retardation, dwarfism, late flowering, and prone rosette leaves, which may be because of an increase in the gene expression of partial DELLA proteins and DDF1.

Caspases in plants: metacaspase gene family in plant stress responses

Programmed cell death (PCD) is an ordered cell suicide that removes unwanted or damaged cells, playing a role in defense to environmental stresses and pathogen invasion. PCD is component of the life cycle of plants, occurring throughout development from embryogenesis to the death. Metacaspases are cysteine proteases present in plants, fungi, and protists. In certain plant-pathogen interactions, the PCD seems to be mediated by metacaspases. We adopted a comparative genomic approach to identify genes coding for the metacaspases in Viridiplantae. We observed that the metacaspase was divided into types I and II, based on their protein structure. The type I has a metacaspase domain at the C-terminus region, presenting or not a zinc finger motif in the N-terminus region and a prodomain rich in proline. Metacaspase type II does not feature the prodomain and the zinc finger, but has a linker between caspase-like catalytic domains of 20 kDa (p20) and 10 kDa (p10). A high conservation was observed in the zinc finger domain (type I proteins) and in p20 and p10 subunits (types I and II proteins). The phylogeny showed that the metacaspases are divided into three principal groups: type I with and without zinc finger domain and type II metacaspases. The algae and moss are presented as outgroup, suggesting that these three classes of metacaspases originated in the early stages of Viridiplantae, being the absence of the zinc finger domain the ancient condition. The study of metacaspase can clarify their assignment and involvement in plant PCD mechanisms.