Plant Responses to Biotic Stress: Old Memories Matter

Plant Signaling Hormones and Transcription Factors: Key Regulators of Plant Responses to Growth, Development, and Stress

Plants constantly encounter a wide range of biotic and abiotic stresses that adversely affect their growth, development, and productivity. Phytohormones such as abscisic acid, jasmonic acid, salicylic acid, and ethylene serve as crucial regulators, integrating internal and external signals to mediate stress responses while also coordinating key developmental processes, including seed germination, root and shoot growth, flowering, and senescence. Transcription factors (TFs) such as WRKY, NAC, MYB, and AP2/ERF play complementary roles by orchestrating complex transcriptional reprogramming, modulating stress-responsive genes, and facilitating physiological adaptations. Recent advances have deepened our understanding of hormonal networks and transcription factor families, revealing their intricate crosstalk in shaping plant resilience and development. Additionally, the synthesis, transport, and signaling of these molecules, along with their interactions with stress-responsive pathways, have emerged as critical areas of study. The integration of cutting-edge biotechnological tools, such as CRISPR-mediated gene editing and omics approaches, provides new opportunities to fine-tune these regulatory networks for enhanced crop resilience. By leveraging insights into transcriptional regulation and hormone signaling, these advancements provide a foundation for developing stress-tolerant, high-yielding crop varieties tailored to the challenges of climate change.

Effect of Pinus pinaster and Pinus radiata resin on biomass growth of Fusarium circinatum

Pines produce and accumulate oleoresin, which is part of the preformed defensive system or is synthesized de novo in response to biotic and abiotic challenges. Fusarium circinatum is a fungal pathogen that causes Pine Pitch Canker disease and is characterized by cankers with abundant resin at the infection site. F. circinatum colonizes the plant using both constitutive and traumatic resin ducts, indicating a resin tolerance that needs to be evaluated. Using a spectrophotometric technique, we assessed the effects of constitutive and induced resin on the growth of F. circinatum. The pathogen was grown in minimum medium supplemented with resin (at 0.8, 1.5 and 3 % concentrations) in the wells of a microplate for 6 days, and the absorbance at 570 nm was measured as an indicator of fungal biomass. The results showed that resin from Pinus pinaster and Pinus radiata enhanced fungal growth, as the absorbances measured with the addition of volatile or nonvolatile fractions extracted from constitutive and induced resins increased above 100 % relative to the solvent used in resin extraction. F. circinatum grew 40 % more in the hexane extract of the induced resin than in the constitutive resin of P. radiata. Terpene profiles determined by GC-MS analysis differed quantitatively and qualitatively by resin type (constitutive or induced) and pine species. The F. circinatum growth with various single terpene components of resin at different concentrations was also measured. The absorbance results showed that α-pinene and citronellol (monoterpenes) promoted growth at specific concentrations, while all others inhibited or did not affect it.

Full-length transcriptome characterization and analysis of Carrizo Citrange and molecular insights into pathogen defense

Citrus huanglongbing (HLB) is a major challenge that impacts the flourishing of the citrus industry. Therefore, analyzing the genomic information of HLB-resistant or tolerant citrus resources is crucial for breeding HLB-resistant citrus varieties. The Carrizo citrange, a hybrid of Citrus sinensis and Poncirus trifoliata, plays a pivotal role in citrus cultivation. However, its genetic explorations are difficult due to the absence of a reference genome or full-length transcriptome. In order to enhance our understanding of the genetic information of citrange, we conducted a full-length transcriptomic sequencing of multiple tissues from the Carrizo citrange using the PacBio Sequel II platform. Moreover, we performed gene ontology (GO) annotation, gene functional annotation, simple sequence repeats (SSR) types analysis, as well as identification of lncRNAs, alternative splicing events, and analysis of pathogen defense-related genes. Results showed that a total of 43,452 isoforms were generated, with 43,307 of them being annotated. GO annotation indicated the involvement of these isoforms in various biological processes, cellular components, and molecular functions. The coding sequence length of the isoforms ranged from 1,000 to 4,000 base pairs (bp). Moreover, we have discovered 54 varieties of transcription factors and regulators, along with 16 classifications of genes associated with resistance. Among all types of SSRs, trimer type SSRs were the most abundant. 130 lncRNAs were predicted to be highly reliable in the isoforms of the Carrizo citrange, with alternative splicing events identified, and the most frequent being retained intron. The analysis of gene family expansion and contraction revealed a significant increase in pathogen defense-related genes within the Carrizo citrange. The results of this study will be of great value for future investigations into gene function in citrange and for expanding the genetic pool for breeding citrus varieties resistant or tolerant to HLB.

Unveiling the role of epigenetic mechanisms and redox signaling in alleviating multiple abiotic stress in plants

Anthropogenic activities and subsequent global climate change instigate drastic crop productivity and yield changes. These changes comprise a rise in the number and severity of plant stress factors, which can arise simultaneously or sequentially. When abiotic stress factors are combined, their impact on plants is more substantial than that of a singleton stress factor. One such impact is the alteration of redox cellular homeostasis, which, in turn, can regulate downstream stress-responsive gene expression and resistance response. The epigenetic regulation of gene expression in response to varied stress factors is an interesting phenomenon, which, conversely, can be stable and heritable. The epigenetic control in plants in response to abiotic stress combinations and their interactions with cellular redox alteration is an emerging field to commemorate crop yield management under climate change. The article highlights the integration of the redox signaling pathways and epigenetic regulations as pivotal components in the complex network of plant responses against multi-combinatorial stresses across time and space. This review aims to lay the foundation for developing novel approaches to mitigate the impact of environmental stresses on crop productivity, bridging the gap between theoretical understanding and practical solutions in the face of a changing climate and anthropogenic disturbances.

The Ability of Different Tea Tree Germplasm Resources in South China to Aggregate Rhizosphere Soil Characteristic Fungi Affects Tea Quality

It is generally recognized that the quality differences in plant germplasm resources are genetically determined, and that only a good "pedigree" can have good quality. Ecological memory of plants and rhizosphere soil fungi provides a new perspective to understand this phenomenon. Here, we selected 45 tea tree germplasm resources and analyzed the rhizosphere soil fungi, nutrient content and tea quality. We found that the ecological memory of tea trees for soil fungi led to the recruitment and aggregation of dominant fungal populations that were similar across tea tree varieties, differing only in the number of fungi. We performed continuous simulation and validation to identify four characteristic fungal genera that determined the quality differences. Further analysis showed that the greater the recruitment and aggregation of Saitozyma and Archaeorhizomyces by tea trees, the greater the rejection of Chaetomium and Trechispora, the higher the available nutrient content in the soil and the better the tea quality. In summary, our study presents a new perspective, showing that ecological memory between tea trees and rhizosphere soil fungi leads to differences in plants' ability to recruit and aggregate characteristic fungi, which is one of the most important determinants of tea quality. The artificial inoculation of rhizosphere fungi may reconstruct the ecological memory of tea trees and substantially improve their quality.

Recruitment and Aggregation Capacity of Tea Trees to Rhizosphere Soil Characteristic Bacteria Affects the Quality of Tea Leaves

There are obvious differences in quality between different varieties of the same plant, and it is not clear whether they can be effectively distinguished from each other from a bacterial point of view. In this study, 44 tea tree varieties (Camellia sinensis) were used to analyze the rhizosphere soil bacterial community using high-throughput sequencing technology, and five types of machine deep learning were used for modeling to obtain characteristic microorganisms that can effectively differentiate different varieties, and validation was performed. The relationship between characteristic microorganisms, soil nutrient transformation, and tea quality formation was further analyzed. It was found that 44 tea tree varieties were classified into two groups (group A and group B) and the characteristic bacteria that distinguished them came from 23 genera. Secondly, the content of rhizosphere soil available nutrients (available nitrogen, available phosphorus, and available potassium) and tea quality indexes (tea polyphenols, theanine, and caffeine) was significantly higher in group A than in group B. The classification result based on both was consistent with the above bacteria. This study provides a new insight and research methodology into the main reasons for the formation of quality differences among different varieties of the same plant.

Genome-Wide Transcriptomic and Metabolomic Analyses Unveiling the Defence Mechanisms of Populus tremula against Sucking and Chewing Insect Herbivores

Plants and insects coevolved as an evolutionarily successful and enduring association. The molecular arms race led to evolutionary novelties regarding unique mechanisms of defence and detoxification in plants and insects. While insects adopt mechanisms to conquer host defence, trees develop well-orchestrated and species-specific defence strategies against insect herbivory. However, current knowledge on the molecular underpinnings of fine-tuned tree defence responses against different herbivore insects is still restricted. In the current study, using a multi-omics approach, we unveiled the defence response of Populus tremula against aphids (Chaitophorus populialbae) and spongy moths (Lymantria dispar) herbivory. Comparative differential gene expression (DGE) analyses revealed that around 272 and 1203 transcripts were differentially regulated in P. tremula after moth and aphid herbivory compared to uninfested controls. Interestingly, 5716 transcripts were differentially regulated in P. tremula between aphids and moth infestation. Further investigation showed that defence-related stress hormones and their lipid precursors, transcription factors, and signalling molecules were over-expressed, whereas the growth-related counterparts were suppressed in P. tremula after aphid and moth herbivory. Metabolomics analysis documented that around 37% of all significantly abundant metabolites were associated with biochemical pathways related to tree growth and defence. However, the metabolic profiles of aphid and moth-fed trees were quite distinct, indicating species-specific response optimization. After identifying the suitable reference genes in P. tremula, the omics data were further validated using RT-qPCR. Nevertheless, our findings documented species-specific fine-tuning of the defence response of P. tremula, showing conservation on resource allocation for defence overgrowth under aphid and moth herbivory. Such findings can be exploited to enhance our current understanding of molecular orchestration of tree responses against herbivory and aid in developing insect pest resistance P. tremula varieties.

Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants

Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.

Understanding plant stress memory traits can provide a way for sustainable agriculture

Being sessile, plants encounter various biotic and abiotic threats in their life cycle. To minimize the damages caused by such threats, plants have acquired sophisticated response mechanisms. One major such response includes memorizing the encountered stimuli in the form of a metabolite, hormone, protein, or epigenetic marks. All of these individually as well as together, facilitate effective transcriptional and post-transcriptional responses upon encountering the stress episode for a second time during the life cycle and in some instances even in the future generations. This review attempts to highlight the recent advances in the area of plant memory. A detailed understanding of plant memory has the potential to offer solutions for developing climate-resilient crops for sustainable agriculture.

Revisiting plant stress memory: mechanisms and contribution to stress adaptation

Highly repetitive adverse environmental conditions are encountered by plants multiple times during their lifecycle. These repetitive encounters with stresses provide plants an opportunity to remember and recall the experiences of past stress-associated responses, resulting in better adaptation towards those stresses. In general, this phenomenon is known as plant stress memory. According to our current understanding, epigenetic mechanisms play a major role in plants stress memory through DNA methylation, histone, and chromatin remodeling, and modulating non-coding RNAs. In addition, transcriptional, hormonal, and metabolic-based regulations of stress memory establishment also exist for various biotic and abiotic stresses. Plant memory can also be generated by priming the plants using various stressors that improve plants' tolerance towards unfavorable conditions. Additionally, the application of priming agents has been demonstrated to successfully establish stress memory. However, the interconnection of all aspects of the underlying mechanisms of plant stress memory is not yet fully understood, which limits their proper utilization to improve the stress adaptations in plants. This review summarizes the recent understanding of plant stress memory and its potential applications in improving plant tolerance towards biotic and abiotic stresses.

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.

Plant Secondary Metabolites: The Weapons for Biotic Stress Management

The rise in global temperature also favors the multiplication of pests and pathogens, which calls into question global food security. Plants have developed special coping mechanisms since they are sessile and lack an immune system. These mechanisms use a variety of secondary metabolites as weapons to avoid obstacles, adapt to their changing environment, and survive in less-than-ideal circumstances. Plant secondary metabolites include phenolic compounds, alkaloids, glycosides, and terpenoids, which are stored in specialized structures such as latex, trichomes, resin ducts, etc. Secondary metabolites help the plants to be safe from biotic stressors, either by repelling them or attracting their enemies, or exerting toxic effects on them. Modern omics technologies enable the elucidation of the structural and functional properties of these metabolites along with their biosynthesis. A better understanding of the enzymatic regulations and molecular mechanisms aids in the exploitation of secondary metabolites in modern pest management approaches such as biopesticides and integrated pest management. The current review provides an overview of the major plant secondary metabolites that play significant roles in enhancing biotic stress tolerance. It examines their involvement in both indirect and direct defense mechanisms, as well as their storage within plant tissues. Additionally, this review explores the importance of metabolomics approaches in elucidating the significance of secondary metabolites in biotic stress tolerance. The application of metabolic engineering in breeding for biotic stress resistance is discussed, along with the exploitation of secondary metabolites for sustainable pest management.

Advances in the study of the function and mechanism of the action of flavonoids in plants under environmental stresses

MAIN CONCLUSION

This review summarizes the anti-stress effects of flavonoids in plants and highlights its role in the regulation of polar auxin transport and free radical scavenging mechanism. As secondary metabolites widely present in plants, flavonoids play a vital function in plant growth, but also in resistance to stresses. This review introduces the classification, structure and synthetic pathways of flavonoids. The effects of flavonoids in plant stress resistance were enumerated, and the mechanism of flavonoids in plant stress resistance was discussed in detail. It is clarified that plants under stress accumulate flavonoids by regulating the expression of flavonoid synthase genes. It was also determined that the synthesized flavonoids are transported in plants through three pathways: membrane transport proteins, vesicles, and bound to glutathione S-transferase (GST). At the same time, the paper explores that flavonoids regulate polar auxin transport (PAT) by acting on the auxin export carrier PIN-FORMED (PIN) in the form of ATP-binding cassette subfamily B/P-glycoprotein (ABCB/PGP) transporter, which can help plants to respond in a more dominant form to stress. We have demonstrated that the number and location of hydroxyl groups in the structure of flavonoids can determine their free radical scavenging ability and also elucidated the mechanism by which flavonoids exert free radical removal in cells. We also identified flavonoids as signaling molecules to promote rhizobial nodulation and colonization of arbuscular mycorrhizal fungi (AMF) to enhance plant-microbial symbiosis in defense to stresses. Given all this knowledge, we can foresee that the in-depth study of flavonoids will be an essential way to reveal plant tolerance and enhance plant stress resistance.

Calcium signalling in weeds under herbicide stress: An outlook

The continuous use of herbicides for controlling weeds has led to the evolution of resistance to all major herbicidal modes of action globally. Every year, new cases of herbicide resistance are reported. Resistance is still in progress in many species, which must be stopped before it becomes a worldwide concern. Several herbicides are known to cause stressful conditions that resemble plant abiotic stresses. Variation in intracellular calcium (Ca²⁺) concentration is a primary event in a wide range of biological processes in plants, including adaptation to various biotic and abiotic stresses. Ca²⁺ acts as a secondary messenger, connecting various environmental stimuli to different biological processes, especially during stress rejoindering in plants. Even though many studies involving Ca²⁺ signalling in plants have been published, there have been no studies on the roles of Ca²⁺ signalling in herbicide stress response. Hence, this mini-review will highlight the possible sensing and molecular communication via Ca²⁺ signals in weeds under herbicide stress. It will also discuss some critical points regarding integrating the sensing mechanisms of multiple stress conditions and subsequent molecular communication. These signalling responses must be addressed in the future, enabling researchers to discover new herbicidal targets.

The captivating role of calcium in plant-microbe interaction

Plant immune response is fascinating due to the complete absence of a humoral system. The adaptive immune response in plants relies on the intracellular orchestration of signalling molecules or intermediates associated with transcriptional reprogramming. Plant disease response phenomena largely depend on pathogen recognition, signal perception, and intracellular signal transduction. The pathogens possess specific pathogen-associated molecular patterns (PAMP) or microbe-associated molecular patterns (MAMP), which are first identified by pattern recognition receptors (PRRs) of host plants for successful infection. After successful pathogen recognition, the defence response is initiated within plants. The first line of non-specific defence response is called PAMP-triggered immunity (PTI), followed by the specific robust signalling is called effector-triggered immunity (ETI). Calcium plays a crucial role in both PTI and ETI. The biphasic induction of reactive oxygen species (ROS) is inevitable in any plant-microbe interaction. Calcium ions play crucial roles in the initial oxidative burst and ROS induction. Different pathogens can induce calcium accumulation in the cytosol ([Ca²⁺]_Cyt), called calcium signatures. These calcium signatures further control the diverse defence-responsive proteins in the intracellular milieu. These calcium signatures then activate calcium-dependent protein kinases (CDPKs), calcium calmodulins (CaMs), calcineurin B-like proteins (CBLs), etc., to impart intricate defence signalling within the cell. Decoding this calcium ionic map is imperative to unveil any plant microbe interplay and modulate defence-responsive pathways. Hence, the present review is unique in developing concepts of calcium signature in plants and their subsequent decoding mechanism. This review also intends to articulate early sensing of calcium oscillation, signalling events, and comprehensive mechanistic roles of calcium within plants during pathogenic ingression. This will accumulate and summarize the exciting roles of calcium ions in plant immunity and provide the foundation for future research.

Plants detect and respond to sounds

Specific sound patterns can affect plant development. Plants are responsive to environmental stimuli such as sound. However, little is known about their sensory apparatus, mechanisms, and signaling pathways triggered by these stimuli. Thus, it is important to understand the effect of sounds on plants and their technological potential. This review addresses the effects of sounds on plants, the sensory elements inherent to sound detection by the cell, as well as the triggering of signaling pathways that culminate in plant responses. The importance of sound standardization for the study of phytoacoustics is demonstrated. Studies on the sounds emitted or reflected by plants, acoustic stress in plants, and recognition of some sound patterns by plants are also explored.

Optical Sensing Technologies to Elucidate the Interplay between Plant and Microbes

Plant-microbe interactions are critical for ecosystem functioning and driving rhizosphere processes. To fully understand the communication pathways between plants and rhizosphere microbes, it is crucial to measure the numerous processes that occur in the plant and the rhizosphere. The present review first provides an overview of how plants interact with their surrounding microbial communities, and in turn, are affected by them. Next, different optical biosensing technologies that elucidate the plant-microbe interactions and provide pathogenic detection are summarized. Currently, most of the biosensors used for detecting plant parameters or microbial communities in soil are centered around genetically encoded optical and electrochemical biosensors that are often not suitable for field applications. Such sensors require substantial effort and cost to develop and have their limitations. With a particular focus on the detection of root exudates and phytohormones under biotic and abiotic stress conditions, novel low-cost and in-situ biosensors must become available to plant scientists.

TIR1/AFB proteins: Active players in abiotic and biotic stress signaling

The TIR1/AFB family of proteins is a group of functionally diverse auxin receptors that are only found in plants. TIR1/AFB family members are characterized by a conserved N-terminal F-box domain followed by 18 leucine-rich repeats. In the past few decades, extensive research has been conducted on the role of these proteins in regulating plant development, metabolism, and responses to abiotic and biotic stress. In this review, we focus on TIR1/AFB proteins that play crucial roles in plant responses to diverse abiotic and biotic stress. We highlight studies that have shed light on the mechanisms by which TIR1/AFB proteins are regulated at the transcriptional and post-transcriptional as well as the downstream in abiotic or biotic stress pathways regulated by the TIR1/AFB family.

Genome-wide analysis of NBS-LRR genes in Rosaceae species reveals distinct evolutionary patterns

The nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes, one of the largest gene families in plants, are evolving rapidly and playing a critical role in plant resistance to pathogens. In this study, a genome-wide search in 12 Rosaceae genomes screened out 2188 NBS-LRR genes, with the gene number varied distinctively across different species. The reconciled phylogeny revealed 102 ancestral genes (7 RNLs, 26 TNLs, and 69 CNLs), which underwent independent gene duplication and loss events during the divergence of the Rosaceae. The NBS-LRR genes exhibited dynamic and distinct evolutionary patterns in the 12 Rosaceae species due to independent gene duplication/loss events, which resulted the discrepancy of NBS-LRR gene number among Rosaceae species. Specifically, Rubus occidentalis, Potentilla micrantha, Fragaria iinumae and Gillenia trifoliata, displayed a “first expansion and then contraction” evolutionary pattern; Rosa chinensis exhibited a “continuous expansion” pattern; F. vesca had a “expansion followed by contraction, then a further expansion” pattern, three Prunus species and three Maleae species shared a “early sharp expanding to abrupt shrinking” pattern. Overall, this study elucidated the dynamic and complex evolutionary patterns of NBS-LRR genes in the 12 Rosaceae species, and could assist further investigation of mechanisms driving these evolutionary patterns.

Herbicide resistance in grass weeds: Epigenetic regulation matters too

Although herbicides have been successfully used for controlling weeds, their continuous use has developed in the evolution of resistance to all major herbicide modes of action worldwide. Reports suggest that the members of Poaceae family are more prone to developing herbicide resistance than other families. In plants, epigenetic mechanisms play critical roles by increasing their stress-adaptive potential in a rapidly changing environment. Epigenetic mechanisms involve alteration of the expression of genetic elements, but without any changes in the DNA sequence. Although the possible roles of epigenetic mechanisms in contributing to survival and fitness under various stresses are well documented in model plants and crops, their contribution to herbicide resistance in weeds is still in its infancy. A few studies with herbicides have shown differential expression of DNA methyltransferases, histone methyltransferases and DNA demethylases in response to the herbicides; however, no further studies were conducted. In the case of herbicide stress, exploring how these epigenetic processes affect the gene expression pattern in individual plants subjected to recurrent selection would be exciting. Hence, our mini-review will focus on the potential contributions of epigenetic mechanisms to the adaptive responses of grass-weedy species to herbicide stress. A better understanding of these epigenetic changes will add novel perceptions to our knowledge of herbicide resistance evolution in weeds enabling the development of herbicides with novel targets.

Identification and Expression Analysis of the Solanum tuberosum StATG8 Family Associated with the WRKY Transcription Factor

Autophagy is an evolutionarily well-conserved cellular catabolic pathway in eukaryotic cells and plays an important role in cellular processes. Autophagy is regulated by autophagy-associated (ATG) proteins. Among these ATG proteins, the ubiquitin-like protein ATG8/LC3 is essential for autophagosome formation and function. In this study, the potato StATG8 family showed clade I and clade II with significantly different sequences. Expression of the StATG8 family was also increased in senescence. Interestingly, the expression of the StATG8 and other core StATG genes decreased in potato tubers as the tubers matured. The StATG8 family also responded to a variety of stresses such as heat, wounding, salicylic acid, and salt stress. We also found that some Arabidopsis WRKY transcription factors interacted with the StATG8 protein in planta. Based on group II-a WRKY, StATG8-WRKY interaction is independent of the ATG8 interacting motif (AIM) or LC3 interacting region (LIR) motif. This study showed that the StATG8 family had diverse functions in tuber maturation and multiple stress responses in potatoes. Additionally, StATG8 may have an unrelated autophagy function in the nucleus with the WRKY transcription factor.

Will epigenetics be a key player in crop breeding?

If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.

Meta-Analysis of Common and Differential Transcriptomic Responses to Biotic and Abiotic Stresses in Arabidopsis thaliana

Environmental stresses adversely affect crop growth and yield, resulting in major losses to plants. These stresses occur simultaneously in nature, and we therefore conducted a meta-analysis in this study to identify differential and shared genes, pathways, and transcriptomic mechanisms involved in Arabidopsis response to biotic and abiotic stresses. The results showed a total of 436/21 significant up-/downregulated differentially expressed genes (DEGs) in response to biotic stresses, while 476 and 71 significant DEGs were respectively up- and downregulated in response to abiotic stresses in Arabidopsis thaliana. In addition, 21 DEGs (2.09%) were commonly regulated in response to biotic and abiotic stresses. Except for WRKY45 and ATXTH22, which were respectively up-/down- and down-/upregulated in response to biotic and abiotic stresses, other common DEGs were upregulated in response to all biotic and abiotic treatments. Moreover, the transcription factors (TFs) bHLH, MYB, and WRKY were the common TFs in response to biotic and abiotic stresses. In addition, ath-miR414 and ath-miR5658 were identified to be commonly expressed in response to both biotic and abiotic stresses. The identified common genes and pathways during biotic and abiotic stresses may provide potential candidate targets for the development of stress resistance breeding programs and for the genetic manipulation of crop plants.