LncRNA33732-respiratory burst oxidase module associated with WRKY1 in tomato- Phytophthora infestans interactions

Over Time Changes in the Transcriptomic Profiles of Tomato Plants with or Without Mi-1 Gene During Their Incompatible or Compatible Interactions with the Whitefly Bemisia tabaci

Understanding the resistance mechanisms of plants against pests contributes to the sustainable deployment of plant resistance in Integrated Pest Management (IPM) programmes. The Mi-1 gene in tomato is the only one described with the capacity to provide resistance to different types of harmful organisms such as plant parasitic nematodes and pest insects, including the whitefly Bemisia tabaci MED (Mediterranean species). In this work, gene expression in the interaction of B. tabaci with susceptible tomato plants lacking the Mi-1 gene (cv. Moneymaker, compatible interaction), and with resistant plants carrying the Mi-1 gene (cv. Motelle, incompatible interaction) was studied using the oligonucleotide microarray technique. Both interactions were studied 2 and 12 days post infestation (dpi) of plants with adult insects. At 2 dpi, 159 overexpressed and 189 repressed transcripts were detected in the incompatible interaction, while these figures were 32 and 47 in the compatible one. Transcriptional reprogramming was more intense at 12 dpi but, as at 2 dpi, the number of transcripts overexpressed and repressed was higher in the incompatible (595 and 437, respectively) than in the compatible (71 and 52, respectively) interaction. According to the Mapman classification, these transcripts corresponded mainly to genes in the protein and RNA categories, some of which are involved in the defence response (signalling, respiratory burst, regulation of transcription, PRs, HSPs, cell wall or hormone signalling). These results provide a wealth of information about possible genes related to the resistance provided by the Mi-1 gene to B. tabaci, and whose role deserves further investigation.

Genome-Wide Identification and Expression Profile Analysis of the NADPH Oxidase Gene Family in Avena sativa L

The plant respiratory burst oxidase homologs (RBOHs) are crucial enzymes responsible for the production of reactive oxygen species (ROS) in plants, playing a pivotal role in regulating various aspects of plant growth, development, and stress responses. While RBOH family members have been identified across a wide range of plant species, the functions and characteristics of the RBOH gene family in oats remain poorly understood. In this study, 35 members of the RBOH gene family in the oat genome were identified using bioinformatics approaches. Conserved motif and gene structure analyses revealed that most AsRBOH genes contain Motif4 and Motif5. Phylogenetic tree analysis demonstrated that the AsRBOHs can be classified into five distinct subfamilies. Synteny analysis indicated that AsRBOHs share the highest number of syntenic gene pairs with wheat. Additionally, cis-regulatory element analysis identified several elements associated with drought and hypoxia-specific responses in AsRBOHs. Expression analysis using qRT-PCR showed that 28 AsRBOH genes were upregulated under drought stress, while 18 were downregulated under salt stress. Notably, the genes 7DG1382190 and 7AG1225850 were found to be involved in both drought and salt stress responses. In conclusion, these findings provide a valuable foundation for future functional studies of the AsRBOH gene family in oats, offering insights that could contribute to the improvement and innovation of oat varieties and germplasm.

Transcriptome Analysis of Onobrychis viciifolia During Seed Germination Reveals GA3-Inducible Genes Associated with Phenylpropanoid and Hormone Pathways

Sainfoin (Onobrychis viciifolia) is a type of leguminous plant with high feeding value. It contains a high concentration of tannins at all growth stages, which can precipitate soluble proteins and form a large number of persistent foams in the rumen, so that ruminant livestock will not develop dilatation disease during green feeding and grazing. The germination rate of O. viciifolia seeds is very low under natural conditions. The preliminary experiment showed that 600 mg/L GA3 treatment significantly improved the germination rate and seed vitality of sainfoin seeds. In comparison to CK, GA3 significantly decreased the relative content of endogenous inhibitors, with the most notable reduction observed in 4-nitroso-N-phenyl-benzenamine. Therefore, we selected the dry seed stage (GZ), imbibition stage (XZ), split stage (LK), and radicle emergence stage (MF) of four different germination stages treated with GA3 for transcriptome analysis. RNA-seq identified 1392, 2534 and 4284 differentially expressed genes (DEGs) in GZ vs. XZ, XZ vs. LK, and LK vs. MF, respectively. During seed germination, DEGs are mainly enriched in hormone signaling and phenylalanine biosynthesis pathways, and up-down-regulation of these DEGs may alter hormone and secondary metabolite levels to promote germination. The results of weighted gene co-expression network construction (WGCNA) also indicate that plant hormone signal transduction and phenylpropanoid biosynthesis play a dominant role in GA3-induced seed germination. In conclusion, the combined analysis of transcriptomic and physiological indicators provided new insights into seed germination and a theoretical basis for further study of candidate genes.

The Tomato lncRNA47258-miR319b-TCP Module in Biocontrol Bacteria Sneb821 Induced Plants Resistance to Meloidogyne incognita

Long non-coding RNAs (lncRNAs) represent a class of non-coding RNAs. In the study of Pseudomonas putida Sneb821-induced tomato resistance to Meloidogyne incognita, reverse transcription polymerase chain reaction (RT-PCR) was employed to validate 12 lncRNAs in tomato. Among them, the lncRNA47258/miR319b/TCP molecular regulatory module was likely implicated in the process of Sneb821-induced tomato resistance against M. incognita. Through the application of tomato hairy root and virus-induced gene silencing (VIGS) technologies for the investigation of lncRNA47258, it was determined that lncRNA47258 could target the TCP (Solyc07g062681.1) gene and modulate the metabolic pathway of tomato jasmonic acid-related indices, thereby impeding the infection of M. incognita. Moreover, the overexpression of the target gene TCP (Solyc07g062681.1) using tomato hairy root technology demonstrated that it could regulate the jasmonic acid synthesis pathway in tomato, consequently obstructing the infection and suppressing the development of M. incognita. Collectively, lncRNA47258/miR319b/TCP (Solyc07g062681.1) was preliminarily verified to be involved in the Sneb821-induced resistance process against M. incognita in tomato.

Mechanisms of Chinese Hickory Resistance to Dry Rot Disease by Botryosphaeria dothidea: A Comprehensive Analysis from Gene Expression to Non-Coding RNAs

Chinese hickory (Carya cathayensis) is an important tree species for agriculture, but dry rot disease, caused by Botryosphaeria dothidea, threatens its viability. To study the interactions between the tree and the pathogen, transcriptomic sequencing was conducted on infected and healthy tissues from field-grown hickory. Differential gene expression analysis identified key defense pathways and genes activated during infection. The study also explored the roles of non-coding RNAs, such as lncRNAs and circRNAs, in the tree's defense. The results showed that during the early and mid stages of infection, the tree defends itself through mechanisms like enhanced lignin synthesis and increased peroxidase activity. Non-coding RNAs contribute to disease resistance by reinforcing the cell wall, increasing oxidase activity, and promoting the synthesis of antibiotic-related secondary metabolites. Additionally, gene expression patterns at these stages differ significantly from those at the late stage of infection, when most disease resistance pathways are suppressed, and genes like PR1 and WRKY2 show a decline. These findings offer valuable insights into the pathogenesis of Chinese hickory dry rot disease and potential strategies for improving resistance.

Combination of PAMP-induced peptide signaling and its regulator SpWRKY65 boosts tomato resistance to Phytophthora infestans

Late blight, caused by Phytophthora infestans (P. infestans), seriously compromises tomato growth and yield. PAMP-induced peptides (PIPs) are secreted peptides that act as endogenous elicitors, triggering plant immune responses. Our previous research indicated that the exogenous application of PIP1 from Solanum pimpinelifolium L3708, named SpPIP1, enhances tomato resistance to P. infestans. However, little is known about the roles of additional family members in tomato resistance to P. infestans. In addition, there remains a significant gap in understanding the receptors of SpPIPs and the transcription factors (TFs) that regulate SpPIPs signaling in tomato defense, and the combination of SpPIPs signaling and TFs in defending against pathogens is rarely studied. This study demonstrates that the exogenous application of SpPIP-LIKE1 (SpPIPL1) also strengthens tomato resistance by affecting the phenylpropanoid biosynthesis pathway. Both SpPIP1 and SpPIPL1 trigger plant defense responses in a manner dependent on RLK7L. Tomato plants overexpressing the precursors of SpPIP1 and SpPIPL1 (SpprePIP1 and SpprePIPL1) exhibited enhanced expression of pathogenesis-related genes, elevated H2O2 and ABA levels, and increased lignin accumulation. Notably, SpWRKY65 was identified as a transcriptional activator of SpprePIP1 and SpprePIPL1. Disease resistance assays and gene expression analyses revealed that overexpression of SpWRKY65 (OEWRKY65) confers tomato resistance to P. infestans, while wrky65 knockout led to the opposite effect. Intriguingly, transgenic tomato studies showed that either spraying OEWRKY65 with SpPIPs or co-overexpressing SpprePIP1 and SpWRKY65 further augmented tomato resistance, underscoring the potential of gene stacking in enhancing disease resistance. In summary, this study offers new perspectives on controlling late blight and developing tomato varieties with improved resistance. The results emphasize the potential of exogenous SpPIPs application as an eco-friendly strategy for crop protection, laying a theoretical foundation for advancing crop breeding.

LTR retrotransposon-derived novel lncRNA2 enhances cold tolerance in Moso bamboo by modulating antioxidant activity and photosynthetic efficiency

In Moso bamboo, the mechanism of long terminal repeat (LTR) retrotransposon-derived long non-coding RNA (TElncRNA) in response to cold stress remains unclear. In this study, several Pe-TElncRNAs were identified from Moso bamboo transcriptome data. qRT-PCR analysis showed that the expression of a novel Pe-TElncRNA2 in Moso bamboo seedlings reached its highest level at 8 hours of cold treatment at 4 °C and was significantly higher in the stems compared to the leaves, roots, and buds. Furthermore, cellular localization analysis revealed that Pe-TElncRNA2 expression was significantly higher in the cytoplasm than in the nucleus. Pe-TElncRNA2 overexpression in Moso bamboo protoplasts showed that Pe-TElncRNA2 positively regulated the expression of FZR2, NOT3, ABCG44 and AGD6 genes. Further validation of this lncRNA in Arabidopsis thaliana enhanced antioxidant activities, as evidenced by increased superoxide dismutase (SOD) activity and proline content, as well as maximum photochemical efficiency PS II in dark-adapted leaves (F v/F m), in the transgenic plants compared to the wild-type controls. Conversely, malondialdehyde (MDA) content, a lipid peroxidation marker (a marker of oxidative stress), was significantly reduced in the transgenic plants. Notably, the expression levels of both Pe-TElncRNA2 and the genes that were regulated by this lncRNA were upregulated in the transgenic plants after two days of cold stress treatment. These findings elucidate the critical role of LTR retrotransposon-derived lncRNAs in mediating cold stress responses in Moso bamboo.

Transcription factor KUA1 positively regulates tomato resistance against Phytophthora infestans by fine-tuning reactive oxygen species accumulation

Tomato is a horticultural crop of global significance. However, the pathogen Phytophthora infestans causing the late blight disease imposes a severe threat to tomato production and quality. Many transcription factors (TFs) are known to be involved in responses to plant pathogens, however, the key TFs in tomato resistant to P. infestans remain to be explored. Here, we identified six TFs related to tomato responses to P. infestans infection. In particular, we found overexpression of SlKUA1 could significantly improve tomato resistance to P. infestans; moreover, reactive oxygen species (ROS) accumulation was significantly increased in OE-SlKUA1 compared with WT after P. infestans infection along with higher expression of SlRBOHD. Surprisingly, we found that SlKUA1 could not bind to the promoter of SlRBOHD. Further experiments revealed that SlKUA1 inhibited the expression of SlPrx1 by binding to its promoter region, thereby decreasing POD enzyme abundance and causing compromised ROS scavenge. Meanwhile, we identified that SlKUA1 also binds to the promoter region of two plant immune-related genes, SlMAPK7 and SlRLP4, promoting their expression and enhancing tomato disease resistance. Together, our results have unraveled that SlKUA1 can boost tomato resistance against P. infestans through quantitatively regulating ROS accumulation and related immune gene expression, thus, providing promising new targets for breeding late blight resistance tomatoes.

Genome-wide identification of high-affinity nitrate transporter 2 (NRT2) gene family under phytohormones and abiotic stresses in alfalfa (Medicago sativa)

The high-affinity nitrate transporter 2 (NRT2) protein plays an important role in nitrate uptake and transport in plants. In this study, the NRT2s gene family were systematically analyzed in alfalfa. We identified three MsNRT2 genes from the genomic database. They were named MsNRT2.1-2.3 based on their chromosomal location. The phylogenetic tree revealed that NRT2 proteins were categorized into two main subgroups, which were further confirmed by their gene structure and conserved motifs. Three MsNRT2 genes distributed on 2 chromosomes. Furthermore, we studied the expression patterns of MsNRT2 genes in six tissues based on RNA-sequencing data from the Short Read Archive (SRA) database of NCBI, and the results showed that MsNRT2 genes were widely expressed in six tissues. After leaves and roots were treated with drought, salt, abscisic acid (ABA) and salicylic acid (SA) for 0-48 h, and we used quantitative RT-PCR to analyze the expression levels of MsNRT2 genes and the results showed that most of the MsNRT2 genes responded to these stresses. However, there are specific genes that play a role under specific treatment conditions. This result provides a basis for further research on the target genes. In summary, MsNRT2s play an irreplaceable role in the growth, development and stress response of alfalfa, and this study provides valuable information and theoretical basis for future research on MsNRT2 function.

Correlation Between Effector Gene Expression Targeted by lncRNAs in the Oomycete Fish Pathogen, Saprolegnia parasitica

Saprolegniasis caused by Saprolegnia parasitica leads to significant economic losses in the aquaculture industry worldwide. Effector proteins secreted by pathogens are key molecules involved in their pathogenicity and long non-coding lncRNAs (lncRNAs) act as regulators in these processes. However, little is known about the lncRNAs and effector proteins in S. parasitica. Here, we first identified 1027 lncRNAs during the developmental stages and infection process of S. parasitica. Compared with mRNAs, these lncRNAs had shorter sequences and exon lengths and lower expression levels. In addition, their sequence conservation among other oomycete species was also low. The S. parasitica lncRNAs were characterized according to developmental stage and infection time point. We also identified effector proteins using a computational pipeline. In total, 131 S. parasitica effector proteins were identified and classified into 34 families. The 47 genes encoding effector genes were neighbors of 39 lncRNAs, and there was a correlation between the transcription level of lncRNAs and their neighboring genes. Gain- and loss-of-function experiments revealed that lncRNA8375.2 promoted the expression of a neighboring effector gene, SpCAP. Our results provide new data on S. parasitica lncRNAs and effector proteins, and provide insights into the lncRNA-effector module involved in S. parasitica.

Functions of membrane proteins in regulating fruit ripening and stress responses of horticultural crops

Fruit ripening is accompanied by the development of fruit quality traits; however, this process also increases the fruit's susceptibility to various environmental stresses, including pathogen attacks and other stress factors. Therefore, modulating the fruit ripening process and defense responses is crucial for maintaining fruit quality and extending shelf life. Membrane proteins play intricate roles in mediating signal transduction, ion transport, and many other important biological processes, thus attracting extensive research interest. This review mainly focuses on the functions of membrane proteins in regulating fruit ripening and defense responses against biotic and abiotic factors, addresses their potential as targets for improving fruit quality and resistance to environmental challenges, and further highlights some open questions to be addressed.

Genome-wide analysis of long non-coding RNAs involved in the fruit development process of Cucumis melo Baogua

Melon (Cucumis melo L.) is a horticultural crop that is planted globally. Cucumis melo L. cv. Baogua is a typical melon that is suitable for studying fruit development because of its ability to adapt to different climatic conditions. Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs longer than 200 nucleotides, which play important roles in a wide range of biological processes by regulating gene expression. In this study, the transcriptome of the Baogua melon was sequenced at three stages of the process of fruit development (14 days, 21 days, and 28 days) to study the role of lncRNAs in fruit development. The cis and trans lncRNAs were subsequently predicted and identified to determine their target genes. Notably, 1716 high-confidence lncRNAs were obtained in the three groups. A subsequent differential expression analysis of the lncRNAs between the three groups revealed 388 differentially expressed lncRNAs. A total of 11 genes were analyzed further to validate the transcriptome sequencing results. Interestingly, the MELO3C001376.2 and MSTRG.571.2 genes were found to be significantly (P < 0.05) downregulated in the fruits. This study provides a basis to better understand the functions and regulatory mechanisms of lncRNAs during the development of melon fruit.

From environmental responses to adaptation: the roles of plant lncRNAs

As sessile organisms, plants are continuously exposed to heterogeneous and changing environments and constantly need to adapt their growth strategies. They have evolved complex mechanisms to recognize various stress factors, activate appropriate signaling pathways, and respond accordingly by reprogramming the expression of multiple genes at the transcriptional, post-transcriptional, and even epigenome levels to tolerate stressful conditions such as drought, high temperature, nutrient deficiency, and pathogenic interactions. Apart from protein-coding genes, long non-coding RNAs (lncRNAs) have emerged as key players in plant adaptation to environmental stresses. They are transcripts larger than 200 nucleotides without protein-coding potential. Still, they appear to regulate a wide range of processes, including epigenetic modifications and chromatin reorganization, as well as transcriptional and post-transcriptional modulation of gene expression, allowing plant adaptation to various environmental stresses. LncRNAs can positively or negatively modulate stress responses, affecting processes such as hormone signaling, temperature tolerance, and nutrient deficiency adaptation. Moreover, they also seem to play a role in stress memory, wherein prior exposure to mild stress enhances plant ability to adapt to subsequent stressful conditions. In this review, we summarize the contribution of lncRNAs in plant adaptation to biotic and abiotic stresses, as well as stress memory. The complex evolutionary conservation of lncRNAs is also discussed and provides insights into future research directions in this field.

Genome-wide characterization of post-transcriptional processes related to wood formation in Dalbergia odorifera

BACKGROUND

Alternative polyadenylation (APA), alternative splicing (AS), and long non-coding RNAs (lncRNAs) play regulatory roles in post-transcriptional processes in plants. However, little is known about their involvement in xylem development in Dalbergia odorifera, a valuable rosewood species with medicinal and commercial significance. We addressed this by conducting Isoform Sequencing (Iso-Seq) using PacBio's SMRT technology and combined it with RNA-seq analysis (RNA sequencing on Illumina platform) after collecting xylem samples from the transition zone and the sapwood of D. odorifera.

RESULTS

We identified 14,938 full-length transcripts, including 9,830 novel isoforms, which has updated the D. odorifera genome annotation. Our analysis has revealed that 4,164 genes undergo APA, whereas 3,084 genes encounter AS. We have also annotated 118 lncRNAs. Furthermore, RNA-seq analysis identified 170 differential alternative splicing (DAS) events, 344 genes with differential APA site usage (DE-APA), and 6 differentially expressed lncRNAs in the transition zone when compared to the sapwood. AS, APA, and lncRNAs are differentially regulated during xylem development. Differentially expressed APA genes were enriched for terpenoid and flavonoid metabolism, indicating their role in the heartwood formation. Additionally, DE-APA genes were associated with cell wall biosynthesis and terpenoid metabolism, implying an APA's role in wood formation. A DAS gene (involved in chalcone accumulation) with a significantly greater inclusion of the last exon in the transition zone than in the sapwood was identified. We also found that differentially expressed lncRNAs targeted the genes related to terpene synthesis.

CONCLUSIONS

This study enhances our understanding of the molecular regulatory mechanisms underlying wood formation in D. odorifera, and provides valuable genetic resources and insights for its molecular-assisted breeding.

Emerging roles and mechanisms of lncRNAs in fruit and vegetables

With the development of genome sequencing technologies, many long non-coding RNAs (lncRNAs) have been identified in fruit and vegetables. lncRNAs are primarily transcribed and spliced by RNA polymerase II (Pol II) or plant-specific Pol IV/V, and exhibit limited evolutionary conservation. lncRNAs intricately regulate various aspects of fruit and vegetables, including pigment accumulation, reproductive tissue development, fruit ripening, and responses to biotic and abiotic stresses, through diverse mechanisms such as gene expression modulation, interaction with hormones and transcription factors, microRNA regulation, and involvement in alternative splicing. This review presents a comprehensive overview of lncRNA classification, basic characteristics, and, most importantly, recent advances in understanding their functions and regulatory mechanisms.

Abscisic-acid-responsive StlncRNA13558 induces StPRL expression to increase potato resistance to Phytophthora infestans infection

Late blight, caused by Phytophthora infestans, is one of the most serious diseases affecting potatoes (Solanum tuberosum L.). Long non-coding RNAs (lncRNAs) are transcripts with a length of more than 200 nucleotides that have no protein-coding potential. Few studies have been conducted on lncRNAs related to plant immune regulation in plants, and the molecular mechanisms involved in this regulation require further investigation. We identified and screened an lncRNA that specifically responds to P. infestans infection, namely, StlncRNA13558. P. infestans infection activates the abscisic acid (ABA) pathway, and ABA induces StlncRNA13558 to enhance potato resistance to P. infestans. StlncRNA13558 positively regulates the expression of its co-expressed PR-related gene StPRL. StPRL promotes the accumulation of reactive oxygen species and transmits a resistance response by affecting the salicylic acid hormone pathway, thereby enhancing potato resistance to P. infestans. In summary, we identified the potato late blight resistance lncRNA StlncRNA13558 and revealed its upstream and downstream regulatory relationship of StlncRNA13558. These results improve our understanding of plant-pathogen interactions' immune mechanism and elucidate the response mechanism of lncRNA-target genes regulating potato resistance to P. infestans infection.

Plant non-coding RNAs: The new frontier for the regulation of plant development and adaptation to stress

Most plant transcriptomes constitute functional non-coding RNAs (ncRNAs) that lack the ability to encode proteins. In recent years, more research has demonstrated that ncRNAs play important regulatory roles in almost all plant biological processes by modulating gene expression. Thus, it is important to study the biogenesis and function of ncRNAs, particularly in plant growth and development and stress tolerance. In this review, we systematically explore the process of formation and regulatory mechanisms of ncRNAs, particularly those of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs). Additionally, we provide a comprehensive overview of the recent advancements in ncRNAs research, including their regulation of plant growth and development (seed germination, root growth, leaf morphogenesis, floral development, and fruit and seed development) and responses to abiotic and biotic stress (drought, heat, cold, salinity, pathogens and insects). We also discuss research challenges and provide recommendations to advance the understanding of the roles of ncRNAs in agronomic applications.

The lncRNA20718-miR6022-RLPs module regulates tomato resistance to Phytophthora infestans

KEY MESSAGE

Sl-lncRNA20718 acts as an eTM of Sl-miR6022 regulating its expression thereby affecting SlRLP6/10 expression. SlRLP6/10 regulate PRs expression, ROS accumulation, and JA/ET content thereby affecting tomato resistance to P. infestans. Tomato (Solanum lycopersicum) is an important horticultural and cash crop whose yield and quality can be severely affected by Phytophthora infestans (P. infestans). Long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) are widely involved in plant defense responses against pathogens. The involvement of Sl-lncRNA20718 and Sl-miR6022 in tomato resistance to P. infestans as well as the targeting of Sl-miR6022 to receptor-like protein genes (RLPs) were predicted in our previous study. However, uncertainty exists regarding their potential interaction as well as the molecular processes regulating tomato resistance. Here, we found that Sl-lncRNA20718 and Sl-miR6022 are positive and negative regulators of tomato resistance to P. infestans by gain- and loss-of-function experiments, respectively. Overexpression of Sl-lncRNA20718 decreased the expression of Sl-miR6022, induced the expression of PRs, reduced the diameter of lesions (DOLs), thereby enhanced disease resistance. A six-point mutation in the binding region of Sl-lncRNA20718 to Sl-miR6022 disabled the interaction, indicating that Sl-lncRNA20718 acts as an endogenous target mimic (eTM) of Sl-miR6022. We demonstrated that Sl-miR6022 cleaves SlRLP6/10. Overexpression of Sl-miR6022 decreases the expression levels of SlRLP6/10, induces the accumulation of reactive oxygen species (ROS) and reduces the content of JA and ET, thus inhibiting tomato resistance to P. infestans. In conclusion, our study provides detailed information on the lncRNA20718-miR6022-RLPs module regulating tomato resistance to P. infestans by affecting the expression of disease resistance-related genes, the accumulation of ROS and the phytohormone levels, providing a new reference for tomato disease resistance breeding.

Transcriptional landscape of pathogen-responsive lncRNAs in tomato unveils the role of hydrolase encoding genes in response to Botrytis cinerea invasion

LncRNAs have gained increasing attention owing to their important regulatory roles on growth and stress responses of plants. However, the mechanisms underlying the functions of lncRNAs in fruit-pathogen interaction are still largely unknown. In this study, a total of 273 lncRNAs responding to Botrytis cinerea infection were identified in tomato fruit, among which a higher percentage of antisense lncRNAs were targeted to the genes enriched in hydrolase activity. To ascertain the roles of these lncRNAs, seven hydrolase-related transcripts were transiently knocked-down by virus-induced gene silencing. Silencing of lncRNACXE20 reduced the expression level of a carboxylesterase gene, further enhancing the resistance of tomato to B. cinerea. In contrast, silencing of lncRNACHI, lncRNAMMP, lncRNASBT1.9 and lncRNAPME1.9 impaired the resistance to B. cinerea, respectively. Further RT-qPCR assay and enzymatic activity detection displayed that the attenuated resistance of lncRNAMMP and lncRNASBT1.9-silenced plants was associated with the inhibition on the expression of JA-related genes, while the decreased resistance of lncRNACHI-silenced plants resulted in reduced chitinase activity. Collectively, these results may provide references for deciphering the mechanisms underlying specific lncRNAs to interfere with B. cinerea infection by regulating the expression of defence-related genes or affecting hydrolase activity.

Harnessing the potential of non-coding RNA: An insight into its mechanism and interaction in plant biotic stress

Plants have developed diverse physical and chemical defence mechanisms to ensure their continued growth and well-being in challenging environments. Plants also have evolved intricate molecular mechanisms to regulate their responses to biotic stress. Non-coding RNA (ncRNA) plays a crucial role in this process that affects the expression or suppression of target transcripts. While there have been numerous reviews on the role of molecules in plant biotic stress, few of them specifically focus on how plant ncRNAs enhance resistance through various mechanisms against different pathogens. In this context, we explored the role of ncRNA in exhibiting responses to biotic stress endogenously as well as cross-kingdom regulation of transcript expression. Furthermore, we address the interplay between ncRNAs, which can act as suppressors, precursors, or regulators of other ncRNAs. We also delve into the regulation of ncRNAs in response to attacks from different organisms, such as bacteria, viruses, fungi, nematodes, oomycetes, and insects. Interestingly, we observed that diverse microorganisms interact with distinct ncRNAs. This intricacy leads us to conclude that each ncRNA serves a specific function in response to individual biotic stimuli. This deeper understanding of the molecular mechanisms involving ncRNAs in response to biotic stresses enhances our knowledge and provides valuable insights for future research in the field of ncRNA, ultimately leading to improvements in plant traits.

Genome-wide identification of the B3 transcription factor family in pepper (Capsicum annuum) and expression patterns during fruit ripening

In plants, B3 transcription factors play important roles in a variety of aspects of their growth and development. While the B3 transcription factor has been extensively identified and studied in numerous species, there is limited knowledge regarding its B3 superfamily in pepper. Through the utilization of genome-wide sequence analysis, we identified a total of 106 B3 genes from pepper (Capsicum annuum), they are categorized into four subfamilies: RAV, ARF, LAV, and REM. Chromosome distribution, genetic structure, motif, and cis-acting element of the pepper B3 protein were analyzed. Conserved gene structure and motifs outside the B3 domain provided strong evidence for phylogenetic relationships, allowing potential functions to be deduced by comparison with homologous genes from Arabidopsis. According to the high-throughput transcriptome sequencing analysis, expression patterns differ during different phases of fruit development in the majority of the 106 B3 pepper genes. By using qRT-PCR analysis, similar expression patterns in fruits from various time periods were discovered. In addition, further analysis of the CaRAV4 gene showed that its expression level decreased with fruit ripening and located in the nucleus. B3 transcription factors have been genome-wide characterized in a variety of crops, but the present study is the first genome-wide analysis of the B3 superfamily in pepper. More importantly, although B3 transcription factors play key regulatory roles in fruit development, it is uncertain whether B3 transcription factors are involved in the regulation of the fruit development and ripening process in pepper and their specific regulatory mechanisms because the molecular mechanisms of the process have not been fully explained. The results of the study provide a foundation and new insights into the potential regulatory functions and molecular mechanisms of B3 genes in the development and ripening process of pepper fruits, and provide a solid theoretical foundation for the enhancement of the quality of peppers and their selection and breeding of high-yield varieties.

Long noncoding RNA from Betula platyphylla, BplncSIR1, confers salt tolerance by regulating BpNAC2 to mediate reactive oxygen species scavenging and stomatal movement

Long noncoding RNAs (lncRNAs) play an important role in abiotic stress tolerance. However, their function in conferring abiotic stress tolerance is still unclear. Herein, we characterized the function of a salt-responsive nuclear lncRNA (BplncSIR1) from Betula platyphylla (birch). Birch plants overexpressing and knocking out for BplncSIR1 were generated. BplncSIR1 was found to improve salt tolerance by inducing antioxidant activity and stomatal closure, and also accelerate plant growth. Chromatin isolation by RNA purification (ChIRP) combined with RNA sequencing indicated that BplncSIR1 binds to the promoter of BpNAC2 (encoding NAC domain-containing protein 2) to activate its expression. Plants overexpressing and knocking out for BpNAC2 were generated. Consistent with that of BplncSIR1, overexpression of BpNAC2 also accelerated plant growth and conferred salt tolerance. In addition, BpNAC2 binds to different cis-acting elements, such as G-box and 'CCAAT' sequences, to regulate the genes involved in salt tolerance, resulting in reduced ROS accumulation and decreased water loss rate by stomatal closure. Taken together, BplncSIR1 serves as the regulator of BpNAC2 to induce its expression in response to salt stress, and activated BpNAC2 accelerates plant growth and improves salt tolerance. Therefore, BplncSIR1 might be a candidate gene for molecular breeding to cultivate plants with both a high growth rate and improved salt tolerance.

Insights into the roles of long noncoding RNAs in the communication between plants and the environment

In addition to coding proteins, RNA molecules, especially long noncoding RNAs (lncRNAs), have well-established functions in regulating gene expression. The number of studies focused on the roles played by different types of lncRNAs in a variety of plant biological processes has markedly increased. These lncRNA roles involve plant vegetative and reproductive growth and responses to biotic and abiotic stresses. In this review, we examine the classification, mechanisms, and functions of lncRNAs and then emphasize the roles played by these lncRNAs in the communication between plants and the environment mainly with respect to the following environmental factors: temperature, light, water, salt stress, and nutrient deficiencies. We also discuss the consensus among researchers and the remaining challenges and underscore the exciting ways lncRNAs may affect the biology of plants.

Emphasizing the Role of Long Non-Coding RNAs (lncRNA), Circular RNA (circRNA), and Micropeptides (miPs) in Plant Biotic Stress Tolerance

Biotic stress tolerance in plants is complex as it relies solely on specific innate immune responses from different plant species combating diverse pathogens. Each component of the plant immune system is crucial to comprehend the molecular basis underlying sustainable resistance response. Among many other regulatory components, long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) have recently emerged as novel regulatory control switches in plant development and stress biology. Besides, miPs, the small peptides (100-150 amino acids long) encoded by some of the non-coding portions of the genome also turned out to be paramount regulators of plant stress. Although some studies have been performed in deciphering the role of miPs in abiotic stress tolerance, their function in regulating biotic stress tolerance is still largely elusive. Hence, the present review focuses on the roles of long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) in combating biotic stress in plants. The probable role of miPs in plant-microbe interaction is also comprehensively highlighted. This review enhances our current understanding of plant lncRNAs, circRNAs, and miPs in biotic stress tolerance and raises intriguing questions worth following up.

WRKY transcription factors in plant defense

Environmental stressors caused by climate change are fundamental barriers to agricultural sustainability. Enhancing the stress resilience of crops is a key strategy in achieving global food security. Plants perceive adverse environmental conditions and initiate signaling pathways to activate precise responses that contribute to their survival. WRKY transcription factors (TFs) are essential players in several signaling cascades and regulatory networks that have crucial implications for defense responses in plants. This review summarizes advances in research concerning how WRKY TFs mediate various signaling cascades and metabolic adjustments as well as how epigenetic modifications involved in environmental stress responses in plants can modulate WRKYs and/or their downstream genes. Emerging research shows that clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas)-mediated genome editing of WRKYs could be used to improve crop resilience.

Sl-lncRNA47980, a positive regulator affects tomato resistance to Phytophthora infestans

Emerging evidence suggests that long non-coding RNAs (lncRNAs) involve in defense respond against pathogen attack and show great potentials to improve plant resistance. Tomato late blight, a destructive plant disease, is caused by the oomycete pathogen Phytophthora infestans, which seriously affects the yield and quality of tomato. Our previous research has shown that Sl-lncRNA47980 is involved in response to P. infestans infection, but its molecular mechanism is unknown. Gain- and loss-of-function experiments revealed that Sl-lncRNA47980 as a positive regulator, played a crucial role in enhancing tomato resistance to P. infestans. The Sl-lncRNA47980-overexpressing transgenic plants exhibited an improved ability to scavenge reactive oxygen species (ROS), decreased contents of endogenous gibberellin (GA) and salicylic acid (SA), and increased contents of jasmonic acid (JA), while silencing of Sl-lncRNA47980 showed an opposite trend in the levels of these hormones. Furthermore, it was found that Sl-lncRNA47980 could upregulate the expression of SlGA2ox4 gene through activation of the promoter of SlGA2ox4 to affect GA content. The increased expression of the tomato GA signaling repressor SlDELLA could activate JA-related genes and inhibit SA-related genes to varying degrees respectively. In addition, exogenous application of GA3 and GA synthesis inhibitor uniconazole could increase disease susceptibility of Sl-lncRNA47980-overexpressing plants and the resistance of Sl-lncRNA47980-silenced plants, respectively, to P. infestans. From thus, it was speculated that Sl-lncRNA47980 conferred tomato resistance to P. infestans, which was related to the decrease in endogenous GA content. Our study provided information to link Sl-lncRNA47980 with changes in ROS accumulation and phytohormone levels in plant immunity, thus providing a new candidate gene for tomato breeding.

Noncoding RNAs and their roles in regulating the agronomic traits of crops

Molecular breeding is one of the most effective methods for improving the performance of crops. Understanding the genome features of crops, especially the physiological functions of individual genes, is of great importance to molecular breeding. Evidence has shown that genomes of both animals and plants transcribe numerous non-coding RNAs, which are involved in almost every aspect of development. In crops, an increasing number of studies have proven that non-coding RNAs are new genetic resources for regulating crop traits. In this review, we summarize the current knowledge of non-coding RNAs, which are potential crop trait regulators, and focus on the functions of long non-coding RNAs (lncRNAs) in determining crop grain yield, phased small-interfering RNAs (phasiRNAs) in regulating fertility, small interfering RNAs (siRNAs) and microRNAs (miRNAs) in facilitating plant immune response and disease resistance, and miRNAs mediating nutrient and metal stress. Finally, we also discuss the next-generation method for ncRNA application in crop domestication and breeding.

The effectors of Phytophthora infestans impact host immunity upon regulation of antagonistic hormonal activities

MAIN CONCLUSION

Phytophthora infestans effectors manipulate the antagonism of host hormones to interfere with the immune response of plants at different infection stages. Phytophthora infestans (P. infestans) poses a serious threat to global crop production, and its effectors play an indispensable role in its pathogenicity. However, the function of these effectors during the switch from biotrophy to necrotrophy of P. infestans remains unclear. Further research on the effectors that manipulate the antagonistic response of host hormones is also lacking. In this study, a coexpression analysis and infection assays were performed to identify distinct gene expression changes in both P. infestans and tomato. During the switch from biotrophy to necrotrophy, P. infestans secretes three types of effectors to interfere with host salicylic acid (SA), jasmonic acid (JA), ethylene (ET), and abscisic acid (ABA) levels. The three aforementioned effectors also regulate the host gene expression including NPR1, TGA2.1, PDF1.2, NDR1, ERF3, NCED6, GAI4, which are involved in hormone crosstalk. The changes in plant hormones are mediated by the three types of effectors, which may accelerate infection and drive completion of the P. infestans lifecycle. Our findings provide new insight into plant‒pathogen interactions that may contribute to the prevention growth of hemibiotrophic pathogens.

Recent perspective of non-coding RNAs at the nexus of plant-pathogen interaction

In natural habitats, plants are exploited by pathogens in biotrophic or necrotrophic ways. Concurrently, plants have evolved their defense systems for rapid perception of pathogenic effectors and begin concerted cellular reprogramming pathways to confine the pathogens at the entry sites. During the reorganization of cellular signaling mechanisms following pathogen attack, non-coding RNAs serves an indispensable role either as a source of resistance or susceptibility. Besides the well-studied functions of non-coding RNAs related to plant development and abiotic stress responses, previous and recent discoveries have established that non-coding RNAs like miRNAs, siRNAs, lncRNAs and phasi-RNAs can fine tune plant defense responses by targeting various signaling pathways. In this review, recapitulation of previous reports associated with non-coding RNAs as a defense responder against virus, bacteria and fungus attacks and insightful discussion will lead us to conceive innovative ideas to fight against approaching threats of resistant breaking pathogens.

CmWRKY6-1-CmWRKY15-like transcriptional cascade negatively regulates the resistance to fusarium oxysporum infection in Chrysanthemum morifolium

Chrysanthemum Fusarium wilt is a soil-borne disease that causes serious economic losses to the chrysanthemum industry. However, the molecular mechanism underlying the response of chrysanthemum WRKY to Fusarium oxysporum infection remains largely unknown. In this study, we isolated CmWRKY6-1 from chrysanthemum 'Jinba' and identified it as a transcriptional repressor localized in the nucleus via subcellular localization and transcriptional activation assays. We found that CmWRKY6-1 negatively regulated resistance to F. oxysporum and affected reactive oxygen species (ROS) and salicylic acid (SA) pathways using transgenic experiments and transcriptomic analysis. Moreover, CmWRKY6-1 bound to the W-box element on the CmWRKY15-like promoter and inhibited its expression. Additionally, we observed that CmWRKY15-like silencing in chrysanthemum reduced its resistance to F. oxysporum via transgenic experiments. In conclusion, we revealed the mechanism underlying the CmWRKY6-1-CmWRKY15-like cascade response to F. oxysporum infection in chrysanthemum and demonstrated that CmWRKY6-1 and CmWRKY15-like regulates the immune system.

Plant long noncoding RNAs: Recent progress in understanding their roles in growth, development, and stress responses

Long noncoding RNA (lncRNA) transcripts are longer than 200 nt and are not translated into proteins. LncRNAs function in a wide variety of processes in plants and animals, but, perhaps because of their lower expression and conservation levels, plant lncRNAs had attracted less attention than protein-coding mRNAs. Now, recent studies have made remarkable progress in identifying lncRNAs and understanding their functions. In this review, we discuss a number of lncRNAs that have important functions in growth, development, reproduction, responses to abiotic stresses, and regulation of disease and insect resistance in plants. Additionally, we describe the known mechanisms of action of plant lncRNAs according to their origins within the genome. This review thus provides a guide for identifying and functionally characterizing new lncRNAs in plants.

The RhWRKY33a-RhPLATZ9 regulatory module delays petal senescence by suppressing rapid reactive oxygen species accumulation in rose flowers

Redox homeostasis in plant cells is critical for maintaining normal growth and development because reactive oxygen species (ROS) can function as signaling molecules or toxic compounds. However, how plants fine-tune redox homeostasis during natural or stress-induced senescence remains unclear. Cut roses (Rosa hybrida), an economically important ornamental product worldwide, often undergo stress-induced precocious senescence at the post-harvest bud stage. Here, we identified RhPLATZ9, an age- and dehydration-induced PLATZ (plant AT-rich sequence and zinc-binding) protein, and determined that it functions as a transcriptional repressor in rose flowers during senescence. We also showed that RhWRKY33a regulates RhPLATZ9 expression during flower senescence. RhPLATZ9-silenced flowers and RhWRKY33a-silenced flowers showed accelerated senescence, with higher ROS contents than the control. By contrast, overexpression of RhWRKY33a or RhPLATZ9 delayed flower senescence, and overexpression in rose calli showed lower ROS accumulation than the control. RNA-sequencing analysis revealed that apoplastic NADPH oxidase genes (RhRbohs) were enriched among the upregulated differentially expressed genes in RhPLATZ9-silenced flowers compared to wild-type flowers. Yeast one-hybrid assays, electrophoretic mobility shift assays, dual luciferase assays and chromatin immunoprecipitation quantitative PCR confirmed that the RhRbohD gene is a direct target of RhPLATZ9. These findings suggest that the RhWRKY33a-RhPLATZ9-RhRbohD regulatory module acts as a brake to help maintain ROS homeostasis in petals and thus antagonize age- and stress-induced precocious senescence in rose flowers.

LncRNA109897-JrCCR4-JrTLP1b forms a positive feedback loop to regulate walnut resistance against anthracnose caused by Colletotrichum gloeosporioides

Walnut anthracnose induced by Colletotrichum gloeosporioides is a disastrous disease that severely restricts the development of the walnut industry in China. Long non-coding RNAs (lncRNAs) are involved in adaptive responses to disease, but their roles in the regulation of walnut anthracnose resistance response are not well defined. In this study, transcriptome analysis demonstrated that a C. gloeosporioides-induced lncRNA, lncRNA109897, located upstream from the target gene JrCCR4, upregulated the expression of JrCCR4. JrCCR4 interacted with JrTLP1b and promoted its transcriptional activity. In turn, JrTLP1b induced the transcription of lncRNA109897 to promote its expression. Meanwhile, transient expression in walnut leaves and stable transformation of Arabidopsis thaliana further proved that lncRNA, JrCCR4, and JrTLP1b improve the resistance of C. gloeosporioides. Collectively, these findings provide insights into the mechanism by which the lncRNA109897-JrCCR4-JrTLP1b transcriptional cascade regulates the resistance of walnut to anthracnose.

Genomic survey of high-throughput RNA-Seq data implicates involvement of long intergenic non-coding RNAs (lincRNAs) in cytoplasmic male-sterility and fertility restoration in pigeon pea

BACKGROUND

Long-intergenic non-coding RNAs (lincRNAs) originate from intergenic regions and have no coding potential. LincRNAs have emerged as key players in the regulation of various biological processes in plant development. Cytoplasmic male-sterility (CMS) in association with restorer-of-fertility (Rf) systems makes it a highly reliable tool for exploring heterosis for producing commercial hybrid seeds. To date, there have been no reports of lincRNAs during pollen development in CMS and fertility restorer lines in pigeon pea.

OBJECTIVE

Identification of lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines.

METHODS

We employed a computational approach to identify lincRNAs in the floral buds of cytoplasmic male-sterile (AKCMS11) and fertility restorer (AKPR303) pigeon pea lines using RNA-Seq data.

RESULTS

We predicted a total of 2145 potential lincRNAs of which 966 were observed to be differentially expressed between the sterile and fertile pollen. We identified, 927 cis-regulated and 383 trans-regulated target genes of the lincRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of the target genes revealed that these genes were specifically enriched in pathways like pollen and pollen tube development, oxidative phosphorylation, etc. We detected 23 lincRNAs that were co-expressed with 17 pollen-related genes with known functions. Fifty-nine lincRNAs were predicted to be endogenous target mimics (eTMs) for 25 miRNAs, and found to be associated with pollen development. The, lincRNA regulatory networks revealed that different lincRNA-miRNA-mRNA networks might be associated with CMS and fertility restoration.

CONCLUSION

Thus, this study provides valuable information by highlighting the functions of lincRNAs as regulators during pollen development in pigeon pea and utilization in hybrid seed production.

Unveiling the secrets of non-coding RNA-encoded peptides in plants: A comprehensive review of mining methods and research progress

Non-coding RNAs (ncRNAs) are not conventionally involved in protein encoding. However, recent findings indicate that ncRNAs possess the capacity to code for proteins or peptides. These ncRNA-encoded peptides (ncPEPs) are vital for diverse plant life processes and exhibit significant potential value. Despite their importance, research on plant ncPEPs is limited, with only a few studies conducted and less information on the underlying mechanisms, and the field remains in its nascent stage. This manuscript provides a comprehensive overview of ncPEPs mining methods in plants, focusing on prediction, identification, and functional analysis. We discuss the strengths and weaknesses of various techniques, identify future research directions in the ncPEPs domain, and elucidate the biological functions and agricultural application prospects of plant ncPEPs. By highlighting the immense potential and research value of ncPEPs, we aim to lay a solid foundation for more in-depth studies in plant science.

Laminarin-triggered defence responses are geographically dependent in natural populations of Solanum chilense

Natural plant populations are polymorphic and show intraspecific variation in resistance properties against pathogens. The activation of the underlying defence responses can depend on variation in perception of pathogen-associated molecular patterns or elicitors. To dissect such variation, we evaluated the responses induced by laminarin (a glucan, representing an elicitor from oomycetes) in the wild tomato species Solanum chilense and correlated this to observed infection frequencies of Phytophthora infestans. We measured reactive oxygen species burst and levels of diverse phytohormones upon elicitation in 83 plants originating from nine populations. We found high diversity in basal and elicitor-induced levels of each component. Further we generated linear models to explain the observed infection frequency of P. infestans. The effect of individual components differed dependent on the geographical origin of the plants. We found that the resistance in the southern coastal region, but not in the other regions, was directly correlated to ethylene responses and confirmed this positive correlation using ethylene inhibition assays. Our findings reveal high diversity in the strength of defence responses within a species and the involvement of different components with a quantitatively different contribution of individual components to resistance in geographically separated populations of a wild plant species.

Genome-wide identification and characterization of long non-coding RNA in barley roots in response to Piriformospora indica colonization

Currently, there is very limited information about long noncoding RNAs (lncRNAs) found in barley. It remains unclear whether barley lncRNAs are responsive to Piriformospora indica (P. indica) colonization.We found that barley roots exhibited fast development and that large roots branched after P. indica colonization. Genome-wide high-throughput RNA-seq and bioinformatic analysis showed that 4356 and 5154 differentially expressed LncRNAs (DELs) were found in response to P. indica at 3 and 7 days after colonization (dai), respectively, and 2456 DELs were found at 7 dai compared to 3 dai. Based on the coexpression correlation of lncRNAmRNA, we found that 98.6% of lncRNAs were positively correlated with 3430 mRNAs at 3 dai and 7 dai. Further GO analysis showed that 30 lncRNAs might be involved in the regulation of gene transcription; 23 lncRNAs might participate in cell cycle regulation. Moreover, the metabolite analysis indicated that chlorophyll a, sucrose, protein, gibberellin, and auxin were in accordance with the results of the transcriptome, and the respective lncRNAs were positively correlated with these target RNAs. Gene silencing suggested that lncRNA TCONS_00262342 is probably a key regulator of GA₃ synthesis pathway, which participates in P. indica and barley interactions. We concluded that acting as a molecular material basis and resource, lncRNAs respond to P. indica colonization by regulating metabolite content in barley and coordinate the complex regulatory process of higher life by constructing highly positive correlations with their target mRNAs.

Roles of long non-coding RNAs in plant immunity

Robust plant immune systems are fine-tuned by both protein-coding genes and non-coding RNAs. Long non-coding RNAs (lncRNAs) refer to RNAs with a length of more than 200 nt and usually do not have protein-coding function and do not belong to any other well-known non-coding RNA types. The non-protein-coding, low expression, and non-conservative characteristics of lncRNAs restrict their recognition. Although studies of lncRNAs in plants are in the early stage, emerging studies have shown that plants employ lncRNAs to regulate plant immunity. Moreover, in response to stresses, numerous lncRNAs are differentially expressed, which manifests the actions of low-expressed lncRNAs and makes plant-microbe/insect interactions a convenient system to study the functions of lncRNAs. Here, we summarize the current advances in plant lncRNAs, discuss their regulatory effects in different stages of plant immunity, and highlight their roles in diverse plant-microbe/insect interactions. These insights will not only strengthen our understanding of the roles and actions of lncRNAs in plant-microbe/insect interactions but also provide novel insight into plant immune responses and a basis for further research in this field.

Morphological, ultrastructural and molecular variations in susceptible and resistant genotypes of chickpea infected with Botrytis grey mould

Biotic stress due to fungal infection is detrimental to the growth and development of chickpea. In our study, two chickpea genotypes viz Cicer pinnatifidum (resistant) and PBG5 (susceptible) were inoculated with (1 × 104 spore mL−1) of nectrotrophic fungus Botrytis cinerea at seedling stage. These seedlings were evaluated for morphological, ultrastructural, and molecular differences after 3, 5 and 7 days post inoculation (dpi). Visual symptoms were recorded in terms of water-soaked lesions, rotten pods and twigs with fungal colonies. Light and scanning electron microscopy (SEM) revealed the differences in number of stomata, hyphal network and extent of topographical damage in resistant (C. pinnatifidum) and susceptible (PBG5) genotypes, which were validated by stomatal index studies done by using fluorescence microscopy in the infection process of B. cinerea in leaves of both chickpea genotypes. In case of control (water inoculated) samples, there were differences in PCR analysis done using five primers for screening the genetic variations between two genotypes. The presence of a Botrytis responsive gene (LrWRKY) of size ~300 bp was observed in uninoculated resistant genotype which might have a role in resistance against Botrytis grey mould. The present investigation provides information about the variation in the infection process of B. cinerea in two genotypes which can be further exploited to develop robust and effective strategies to manage grey mould disease.

Promoter Variation of the Key Apple Fruit Texture Related Gene MdPG1 and the Upstream Regulation Analysis

MdPG1 encoding polygalacturonase in apple (Malus × domestica) is a key gene associated with fruit firmness and texture variations among apple cultivars. However, the causative variants of MdPG1 are still not known. In this study, we identified a SNP^A/C variant within an ERF-binding element located in the promoter region of MdPG1. The promoter containing the ERF-binding element with SNP^A, rather than the SNP^C, could be strongly bound and activated by MdCBF2, a member of the AP2/ERF transcription factor family, as determined by yeast-one-hybrid and dual-luciferase reporter assays. We also demonstrated that the presence of a novel long non-coding RNA, lncRNA_PG1, in the promoter of MdPG1 was a causative variant. lncRNA_PG1 was specifically expressed in fruit tissues postharvest. lncRNA_PG1 could reduce promoter activity when it was fused to the promoter of MdPG1 and a tobacco gene encoding Mg-chelatase H subunit (NtCHLH) in transgenic tobacco cells but could not reduce promoter activity when it was supplied in a separate gene construct, indicating a cis-regulatory effect. Our results provide new insights into genetic regulation of MdPG1 allele expression and are also useful for the development of elite apple cultivars.

VqWRKY56 interacts with VqbZIPC22 in grapevine to promote proanthocyanidin biosynthesis and increase resistance to powdery mildew

Powdery mildew (PM) is a severe fungal disease of cultivated grapevine world-wide. Proanthocyanidins (PAs) play an important role in resistance to fungal pathogens; however, little is known about PA-mediated PM resistance in grapevine. We identified a WRKY transcription factor, VqWRKY56, from Vitis quinquangularis, the expression of which was significantly induced by PM. Overexpression (OE) of VqWRKY56 in Vitis vinifera increased PA content and reduced susceptibility to PM. Furthermore, the transgenic plants showed more cell death and increased accumulation of salicylic acid and reactive oxygen species. Transient silencing of VqWRKY56 in V. quinquangularis and V. vinifera reduced PA accumulation and increased the susceptibility to PM. VqWRKY56 interacted with VqbZIPC22 in vitro and in planta. The protein VqWRKY56 can bind to VvCHS3, VvLAR1, and VvANR promoters, and VqbZIPC22 can bind to VvANR promoter. Co-expression of VqWRKY56 and VqbZIPC22 significantly increased the transcript level of VvCHS3, VvLAR1, and VvANR genes. Finally, transient OE of VqbZIPC22 in V. vinifera promoted PA accumulation and improved resistance to PM, while transient silencing in V. quinquangularis had the opposite effect. Our study provides new insights into the mechanism of PA regulation by VqWRKY56 in grapevine and provides a basis for further metabolic engineering of PA biosynthesis to improve PM resistance.

sORFPred: A Method Based on Comprehensive Features and Ensemble Learning to Predict the sORFs in Plant LncRNAs

Long non-coding RNAs (lncRNAs) are important regulators of biological processes. It has recently been shown that some lncRNAs include small open reading frames (sORFs) that can encode small peptides of no more than 100 amino acids. However, existing methods are commonly applied to human and animal datasets and still suffer from low feature representation capability. Thus, accurate and credible prediction of sORFs with coding ability in plant lncRNAs is imperative. This paper proposes a new method termed sORFPred, in which we design a model named MCSEN by combining multi-scale convolution and Squeeze-and-Excitation Networks to fully mine distinct information embedded in sORFs, integrate and optimize multiple sequence-based and physicochemical feature descriptors, and built a two-layer prediction classifier based on Bayesian optimization algorithm and Extra Trees. sORFPred has been evaluated on sORFs datasets of three species and experimentally validated sORFs dataset. Results indicate that sORFPred outperforms existing methods and achieves 97.28% accuracy, 97.06% precision, 97.52% recall, and 97.29% F1-score on Arabidopsis thaliana, which shows a significant improvement in prediction performance compared to various conventional shallow machine learning and deep learning models.

Genome-wide identification of the B3 gene family in soybean and the response to melatonin under cold stress

INTRODUCTION

Melatonin is a multipotent molecule that exists widely in animals and plants and plays an active regulatory role in abiotic stresses. The B3 superfamily is a ubiquitous transcription factor with a B3 functional domain in plants, which can respond temporally to abiotic stresses by activating defense compounds and plant hormones. Despite the fact that the B3 genes have been studied in a variety of plants, their role in soybean is still unknown.

METHODS

The regulation of melatonin on cold resistance of soybean and the response of B3 genes to cold stress were investigated by measuring biochemical indexes of soybean. Meanwhile, the genome-wide identification of B3 gene family was conducted in soybean, and B3 genes were analyzed based on phylogeny, motifs, gene structure, collinearity, and cis-regulatory elements analysis.

RESULTS

We found that cold stress-induced oxidative stress in soybean by producing excessive reactive oxygen species. However, exogenous melatonin treatment could increase the content of endogenous melatonin and other hormones, including IAA and ABA, and enhance the antioxidative system, such as POD activity, CAT activity, and GSH/GSSG, to scavenge ROS. Furthermore, the present study first revealed that melatonin could alleviate the response of soybean to cold stress by inducing the expression of B3 genes. In addition, we first identified 145 B3 genes in soybean that were unevenly distributed on 20 chromosomes. The B3 gene family was divided into 4 subgroups based on the phylogeny tree constructed with protein sequence and a variety of plant hormones and stress response cis-elements were discovered in the promoter region of the B3 genes, indicating that the B3 genes were involved in several aspects of the soybean stress response. Transcriptome analysis and results of qRT-PCR revealed that most GmB3 genes could be induced by cold, the expression of which was also regulated by melatonin. We also found that B3 genes responded to cold stress in plants by interacting with other transcription factors.

DISCUSSION

We found that melatonin regulates the response of soybean to cold stress by regulating the expression of the transcription factor B3 gene, and we identified 145 B3 genes in soybean. These findings further elucidate the potential role of the B3 gene family in soybean to resist low-temperature stress and provide valuable information for soybean functional genomics study.

miRNAs and lncRNAs in tomato: Roles in biotic and abiotic stress responses

Plants are continuously exposed to various biotic and abiotic stresses in the natural environment. To cope with these stresses, they have evolved a multitude of defenses mechanisms. With the rapid development of genome sequencing technologies, a large number of non-coding RNA (ncRNAs) have been identified in tomato, like microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Recently, more and more evidence indicates that many ncRNAs are involved in plant response to biotic and abiotic stresses in tomato. In this review, we summarize recent updates on the regulatory roles of ncRNAs in tomato abiotic/biotic responses, including abiotic (high temperature, drought, cold, salinization, etc.) and biotic (bacteria, fungi, viruses, insects, etc.) stresses. Understanding the molecular mechanisms mediated by ncRNAs in response to these stresses will help us to clarify the future directions for ncRNA research and resistance breeding in tomato.

A long non-coding RNA PelncRNA1 is involved in Phyllostachys edulis response to UV-B stress

Phyllostachys edulis (moso bamboo) is China's most widespread bamboo species, with significant economic and ecological values. Long non-coding RNA (lncRNA) is a type of regulatory RNA that is longer than 200 nucleotides and incapable of encoding proteins, and is frequently involved in regulating biotic and abiotic stress and plant development. However, the biological functions of lncRNA in moso bamboo are unknown. In this study, a lncRNA (named PelncRNA1) differentially expressed following UV-B treatment was discovered in the whole transcriptome sequencing database of moso bamboo. The target genes were filtered and defined by correlation analysis of PelncRNA1 and gene expression pattern. The expression levels of PelncRNA1 and its target genes were verified using qRT-PCR. The results demonstrated that the expression levels of PelncRNA1 and its target genes increased during UV-B treatment. In Arabidopsis transgenic seedlings and moso bamboo protoplasts, PelncRNA1 was discovered to influence the expression of its target genes when overexpressed. In addition, transgenic Arabidopsis showed higher tolerance to UV-B stress. These results suggest that PelncRNA1 and its target genes are involved in the response of moso bamboo to UV-B stress. The novel findings would contribute to our understanding of how lncRNAs regulate the response to abiotic stresses in moso bamboo.

Epigenetic modifications: Allusive clues of lncRNA functions in plants

Long non-coding RNAs (lncRNAs) have been verified as flexible and important factors in various biological processes of multicellular eukaryotes, including plants. The respective intricate crosstalk among multiple epigenetic modifications has been examined to some extent. However, only a small proportion of lncRNAs has been functionally well characterized. Moreover, the relationship between lncRNAs and other epigenetic modifications has not been systematically studied. In this mini-review, we briefly summarize the representative biological functions of lncRNAs in developmental programs and environmental responses in plants. In addition, we particularly discuss the intimate relationship between lncRNAs and other epigenetic modifications, and we outline the underlying avenues and challenges for future research on plant lncRNAs.

Plant Disease Resistance-Related Signaling Pathways: Recent Progress and Future Prospects

Plant-pathogen interactions induce a signal transmission series that stimulates the plant's host defense system against pathogens and this, in turn, leads to disease resistance responses. Plant innate immunity mainly includes two lines of the defense system, called pathogen-associated molecular pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). There is extensive signal exchange and recognition in the process of triggering the plant immune signaling network. Plant messenger signaling molecules, such as calcium ions, reactive oxygen species, and nitric oxide, and plant hormone signaling molecules, such as salicylic acid, jasmonic acid, and ethylene, play key roles in inducing plant defense responses. In addition, heterotrimeric G proteins, the mitogen-activated protein kinase cascade, and non-coding RNAs (ncRNAs) play important roles in regulating disease resistance and the defense signal transduction network. This paper summarizes the status and progress in plant disease resistance and disease resistance signal transduction pathway research in recent years; discusses the complexities of, and interactions among, defense signal pathways; and forecasts future research prospects to provide new ideas for the prevention and control of plant diseases.

From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants

The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.