Network of GRAS transcription factors involved in the control of arbuscule development in Lotus japonicus

SYMRK significantly affected AMF symbiosis and plant growth in maize

Arbuscular mycorrhizal fungi (AMF) are important symbiotic microorganisms in the soil that form reciprocal relationships with most plants to enhance their ability to absorb nutrients from the soil. The establishment of symbiosis between plants and AMF involves complex molecular mechanisms, and the SYMRK (Symbiosis receptor-like kinase) plays a pivotal role in the establishment of symbiosis. Maize (Zea mays) is a globally significant crop and one of the hosts for AMF, but research on AMF symbiosis-related genes in maize is limited. In this study, we identified a symbiosis receptor-like kinase in maize, named ZmSYMRK, which corresponds to the ortholog gene OsSYMRK in rice. ZmSYMRK encodes a cell membrane-localized protein kinase that is crucial for AMF colonization. We demonstrated that ZmSYMRK deletion resulted in severe defects in maize symbiosis with AMF. The colonization rates of zmsymrk mutants were significantly reduced at three different time points, and the colonization defects did not recover with prolonged colonization time. Furthermore, the deletion of the ZmSYMRK gene severely affected plant growth under low phosphorus conditions, and the growth defects of the mutants were even more pronounced after symbiosis. We conclude that ZmSYMRK plays a crucial role in both plant growth and the establishment of symbiotic relationships with AMF.

TaLAC129 is a negative regulator of arbuscular mycorrhizal symbiosis but enhanced the growth and yield of bread wheat

Arbuscular mycorrhizal (AM) symbiosis enhances nutrient acquisition and stress resilience in plants, yet the genetic mechanisms regulating this interaction in wheat remain poorly understood. This study explores the variation in AM colonization rates across a diverse set of wheat varieties and aims to identify key genes that regulate the wheat-AM symbiosis. Understanding these molecular mechanisms is crucial for improving nutrient uptake efficiency and stress resistance in wheat breeding programs. Here, we conducted a genome-wide association study (GWAS) of 291 wheat varieties and integrated transcriptomic data to identify TaLAC129, a laccase (LAC)-encoding gene, as a critical negative regulator of AM colonization in wheat roots. Overexpression of TaLAC129 significantly increased root LAC activity and lignin content, concurrently suppressing AM colonization. While this suppression reduced nitrogen (N), phosphorus (P), and potassium (K) uptake in stems, leaves, and glumes, it markedly enhanced nutrient utilization efficiency (NUE) in grains. Furthermore, TaLAC129 overexpression improved agronomic traits, including grains per panicle, 1000-grain weight, and overall yield. Our findings reveal the dual role of TaLAC129 in balancing AM symbiosis and nutrient allocation, offering a novel genetic target for breeding wheat varieties with improved yield and nutrient efficiency. This study provides critical insights into the molecular coordination between symbiotic trade-offs and agricultural productivity in cereal crops.

Symbiotic synergy: How Arbuscular Mycorrhizal Fungi enhance nutrient uptake, stress tolerance, and soil health through molecular mechanisms and hormonal regulation

Arbuscular Mycorrhizal (AM) symbiosis is integral to sustainable agriculture and enhances plant resilience to abiotic and biotic stressors. Through their symbiotic association with plant roots, AM improves nutrient and water uptake, activates antioxidant defenses, and facilitates hormonal regulation, contributing to improved plant health and productivity. Plants release strigolactones, which trigger AM spore germination and hyphal branching, a process regulated by genes, such as D27, CCD7, CCD8, and MAX1. AM recognition by plants is mediated by receptor-like kinases (RLKs) and LysM domains, leading to the formation of arbuscules that optimize nutrient exchange. Hormonal regulation plays a pivotal role in this symbiosis; cytokinins enhance AM colonization, auxins support arbuscule formation, and brassinosteroids regulate root growth. Other hormones, such as salicylic acid, gibberellins, ethylene, jasmonic acid, and abscisic acid, also influence AM colonization and stress responses, further bolstering plant resilience. In addition to plant health, AM enhances soil health by improving microbial diversity, soil structure, nutrient cycling, and carbon sequestration. This symbiosis supports soil pH regulation and pathogen suppression, offering a sustainable alternative to chemical fertilizers and improving soil fertility. To maximize AM 's potential of AM in agriculture, future research should focus on refining inoculation strategies, enhancing compatibility with different crops, and assessing the long-term ecological and economic benefits. Optimizing AM applications is critical for improving agricultural resilience, food security, and sustainable farming practices.

Genome-Wide Identification, Expression, and Protein Interaction of GRAS Family Genes During Arbuscular Mycorrhizal Symbiosis in Poncirus trifoliata

Arbuscular mycorrhizal (AM) fungi establish mutualistic symbiosis with most land plants, facilitating mineral nutrient uptake in exchange for photosynthates. As one of the most commercially used rootstocks in citrus, Poncirus trifoliata heavily depends on AM fungi for nutrient absorption. The GRAS gene family plays essential roles in plant growth and development, signaling transduction, and responses to biotic and abiotic stresses. However, the identification and functional characterization of GRAS family genes in P. trifoliata remains largely unexplored. In this study, a comprehensive genome-wide analysis of PtGRAS family genes was conducted, including their identification, physicochemical properties, phylogenetic relationships, gene structures, conserved domains, chromosome localization, and collinear relationships. Additionally, the expression profiles and protein interaction of these genes under AM symbiosis were systematically investigated. As a result, 41 GRAS genes were identified in the P. trifoliata genome, and classified into nine distinct clades. Collinearity analysis revealed seven segmental duplications but no tandem duplications, suggesting that segmental duplication played a more important role in the expansion of the PtGRAS gene family compared to tandem duplication. Additionally, 18 PtGRAS genes were differentially expressed in response to AM symbiosis, including orthologs of RAD1, RAM1, and DELLA3 in P. trifoliata. Yeast two-hybrid (Y2H) screening further revealed that PtGRAS6 and PtGRAS20 interacted with both PtGRAS12 and PtGRAS18, respectively. The interactions were subsequently validated through bimolecular fluorescence complementation (BiFC) assays. These findings underscored the crucial role of GRAS genes in AM symbiosis in P. trifoliata, and provided valuable candidate genes for improving nutrient uptake and stress resistance in citrus rootstocks through molecular breeding approaches.

The Effect of Rhizophagus intraradices on Cadmium Uptake and OsNRAMP5 Gene Expression in Rice

The molecular mechanism of arbuscular mycorrhizal fungi (AMF) in reducing cadmium (Cd) accumulation in plants remains unclear. In this respect, the effects of Rhizophagus intraradices (Ri) inoculation under Cd stress on rice growth, the uptake of Cd along with other elements, and the expression of Cd transport genes, including OsNRAMP1/5, were studied using wild-type (WT) and osnramp5 mutant rice. The results showed that Ri inoculation did not affect rice growth. The uptake of Cd of the osnramp5 mutant was much lower than the WT, as 27.6%, 17.5%, and 39.9% of Cd were noted in the grains, shoots, and roots, respectively. For the WT, Cd alone significantly promoted the OsNRAMP5 expression in shoots, but Ri inoculation significantly suppressed OsNRAMP5 expression and significantly reduced its grain and shoot Cd by 44.4% and 62.3%, respectively, compared to the Cd alone treatment. In contrast, for the osnramp5 mutant, Ri inoculation did not influence OsNRAMP5 expression or the grain and shoot Cd. Furthermore, the expression of other Cd transporters (OsIRT1, OsZIP3/7, OsCAX1a) in both varieties were not changed under the treatments. In conclusion, Ri inoculating significantly reduced Cd uptake by rice, with the molecular mechanism by negative regulation of expression of the OsNRAMP5 gene.

Decoding the Dialog Between Plants and Arbuscular Mycorrhizal Fungi: A Molecular Genetic Perspective

Arbuscular mycorrhizal (AM) symbiosis, a mutually beneficial interaction between plant roots and AM fungi, plays a key role in plant growth, nutrient acquisition, and stress tolerance, which make it a major focus for sustainable agricultural strategies. This intricate association involves extensive transcriptional reprogramming in host plant cells during the formation of arbuscules, which are specialized fungal structures for nutrient exchange. The symbiosis is initiated by molecular signaling pathways triggered by fungal chitooligosaccharides and strigolactones released by plant roots, which act as chemoattractants and signaling molecules to promote fungal spore germination, colonization, and arbuscule development. Calcium spiking, mediated by LysM domain receptor kinases, serves as a critical second messenger in coordinating fungal infection and intracellular accommodation. GRAS transcription factors are key components that regulate the transcriptional networks necessary for arbuscule development and maintenance, while small RNAs (sRNAs) from both plant and fungi, contribute to modifications in gene expression, including potential bidirectional sRNA exchange to modulate symbiosis. Understanding the molecular mechanisms related to AM symbiosis may provide valuable insights for implementation of strategies related to enhancing plant productivity and resilience.

Conservation of symbiotic signaling since the most recent common ancestor of land plants

Plants have colonized lands 450 million years ago. This terrestrialization was facilitated by developmental and functional innovations. Recent evo-devo approaches have demonstrated that one of these innovations was the mutualistic arbuscular mycorrhizal symbiosis (AMS). The genetic pathways that have been involved in the establishment and functioning of AMS since its evolution remain poorly described. Here, we found that intracellular colonization by AM fungi induces a transcriptional reporter of the common symbiosis pathway, well-described in angiosperms, in the liverwort Marchantia paleacea. Mutants of either of the three main genes of this pathway, SYMRK, CCaMK, and CYCLOPS, disrupt the ability of M. paleacea to associate with AM fungi. Finally, overexpressing gain-of-function CCaMK or CYCLOPS leads to convergent transcriptomic signatures that partially overlap with AMS. Altogether, our data indicate that plants have maintained three genes of the common symbiotic pathway to support symbiotic interactions since their most recent common ancestor.

Zinc finger protein LjRSDL regulates arbuscule degeneration of arbuscular mycorrhizal fungi in Lotus japonicus

In arbuscular mycorrhizal (AM) symbiosis, appropriate regulation of the formation, maintenance, and degeneration of the arbuscule is essential for plants and fungi. In this study, we identified a Cysteine-2/Histidine-2 zinc finger protein (C2H2-ZFP)-encoding gene in Lotus japonicus named Regulator of Symbiosome Differentiation-Like (LjRSDL) that is required for arbuscule degeneration. Evolutionary analysis showed that homologs of LjRSDL exist in mycorrhizal flowering plants. We obtained ProLjRSDL::GUS transgenic hairy roots and showed that LjRSDL was strongly upregulated upon AM colonization, particularly at 18 days post-AM fungi inoculation and specifically expressed in arbuscule-containing cells. The mycorrhization rate increased in the ljrsdl mutant but decreased in LjRSDL-overexpressed L. japonicus. Interestingly, we observed higher proportions of large arbuscule in the ljrsdl mutant but lower proportions of larger arbuscule in LjRSDL-overexpressing plants. Transcriptome analyses indicated that genes involved in arbuscule degeneration were significantly changed upon the dysregulation of LjRSDL and that LjRSDL-dependent regulation in AM symbiosis is mainly via the hormone signal transduction pathway. LjRSDL, therefore, represents a C2H2-ZFP that negatively regulates AM symbiosis. Our study provides insight into understanding plant-AM fungal communication and AM symbiosis development.

Nuclear factors NF-YC3 and NF-YBs positively regulate arbuscular mycorrhizal symbiosis in tomato

The involvement of nuclear factor Y (NF-Y) in transcriptional reprogramming during arbuscular mycorrhizal symbiosis has been demonstrated in several plant species. However, a comprehensive picture is lacking. We showed that the spatial expression of NF-YC3 was observed in cortical cells containing arbuscules via the cis-regulatory element GCC boxes. Moreover, the NF-YC3 promoter was transactivated by the combination of CYCLOPS and autoactive calcium and calmodulin-dependent kinase (CCaMK) via GCC boxes. Knockdown of NF-YC3 significantly reduced the abundance of all intraradical fungal structures and affected arbuscule size. BCP1, SbtM1, and WRI5a, whose expression associated with NF-YC3 levels, might be downstream of NF-YC3. NF-YC3 interacted with NF-YB3a, NF-YB5c, or NF-YB3b, in yeast (Saccharomyces cerevisiae) and in planta, and interacted with NF-YA3a in yeast. Spatial expression of 3 NF-YBs was observed in all cell layers of roots under both mock and mycorrhizal conditions. Simultaneous knockdown of 3 NF-YBs, but not individually, reduced the fungal colonization level, suggesting that there might be functional redundancy of NF-YBs to regulate AM symbiosis. Collectively, our data suggest that NF-YC3 and NF-YBs positively regulate AM symbiosis in tomato, and arbuscule-related NF-YC3 may be an important downstream gene of the common symbiosis signaling pathway.

Ectopic expression of the GRAS-type transcriptional regulator NSP2 in Parasponia triggers contrasting effects on symbioses

Introduction

Plants strictly control root endosymbioses with nutrient-scavenging arbuscular endomycorrhizal fungi or nodule inducing diazotrophic bacteria. The GRAS-type transcriptional regulator NODULATION SIGNALING PATHWAY 2 (NSP2) is a conserved hub in this process. The NSP2-regulated transcriptional network is instrumental in balancing nutrient homeostasis with symbiotic interactions. NSP2 activity is modulated post-transcriptionally by a specific microRNA. Overriding this control mechanism by ectopic expression of a miRNA-resistant NSP2 transgene enhances the symbiotic permissiveness to arbuscular endomycorrhizal fungi. Such engineered plants may possess enhanced capacities for nutrient uptake. However, the trade-off of this strategy on plant development or other symbiotic interactions, like nodulation, is yet to be fully understood.

Method

We used the nodulating Cannabaceae species Parasponia andersonii as an experimental system to study the effect of ectopic NSP2 expression. Parasponia and legumes (Fabaceae) diverged 100 million years ago, providing a unique comparative system to dissect the nodulation trait.

Results

Six independent transgenic Parasponia lines were generated that differed in the level of NSP2 expression in the root from 6 to 95-fold higher when compared to the empty vector control plants. Analysis of these plants revealed a positive correlation between mycorrhization and the NSP2 expression level, as well as with the expression of the symbiosis transcription factor CYCLOPS and the rate-limiting enzyme in the carotenoid biosynthetic pathway PHYTOENE SYNTHASE1 (PSY1). Yet ectopic expression of NSP2 affected plant architecture and root nodule organogenesis.

Discussion

This indicates a significant trade-off when leveraging NSP2 over-expression to enhance endomycorrhization.

Enhancing arbuscular mycorrhiza symbiosis effectiveness through the involvement of the tomato GRAS transcription factor SCL3/SlGRAS18

Arbuscular mycorrhizal (AM) fungi improve plant growth, nutrition, fitness and stress tolerance while AM fungi obtain carbohydrates and lipids from the host. This whole process of mutual benefit requires substantial alterations in the structural and functional aspects of the host root cells. These modifications ultimately culminate in the formation of arbuscules, which are specialized intraradical and highly branched fungal structures. Arbuscule-containing cells undergo massive reprogramming to hosting arbuscule and members of the GRAS transcription factor family have been characterized as AM inducible genes which play a pivotal role in these process. Here, we show a functional analysis for the GRAS transcription factor SCL3/SlGRAS18 in tomato. SlGRAS18 interacts with SlDELLA, a central regulator of AM formation. Silencing of SlGRAS18 positively impacts arbuscule development and the improvement in symbiotic status, favouring flowering and therefore progress in the formation and development of fruits in SlGRAS18 silenced plants which parallel to a discernible pattern of mineral nutrient redistribution in leaves. Our results advance the knowledge of GRAS transcription factors involved in the formation and establishment of AM symbiosis and provide experimental evidence for how specific genetic alterations can lead to more effective AM symbiosis.

SlDELLA interacts with SlPIF4 to regulate arbuscular mycorrhizal symbiosis and phosphate uptake in tomato

Arbuscular mycorrhizal symbiosis (AMS), a complex and delicate process, is precisely regulated by a multitude of transcription factors. PHYTOCHROME-INTERACTING FACTORS (PIFs) are critical in plant growth and stress responses. However, the involvement of PIFs in AMS and the molecular mechanisms underlying their regulator functions have not been well elucidated. Here, we show that SlPIF4 negatively regulates the arbuscular mycorrhizal fungi (AMF) colonization and AMS-induced phosphate uptake in tomato. Protein-protein interaction studies suggest that SlDELLA interacts with SlPIF4, reducing its protein stability and inhibiting its transcriptional activity towards downstream target genes. This interaction promotes the accumulation of strigolactones (SLs), facilitating AMS development and phosphate uptake. As a transcription factor, SlPIF4 directly transcriptionally regulates genes involved in SLs biosynthesis, including SlCCD7, SlCDD8, and SlMAX1, as well as the AMS-specific phosphate transporter genes PT4 and PT5. Collectively, our findings uncover a molecular mechanism by which the SlDELLA-SlPIF4 module regulates AMS and phosphate uptake in tomato. We clarify a molecular basis for how SlPIF4 interacts with SLs to regulate the AMS and propose a potential strategy to improve phosphate utilization efficiency by targeting the AMS-specific phosphate transporter genes PTs.

A dual regulatory role for the arbuscular mycorrhizal master regulator RAM1 in tomato

The REQUIRED FOR ARBUSCULAR MYCORRHIZATION1 (RAM1) transcription factor from the GRAS family is well known for its role as a master regulator of the arbuscular mycorrhizal (AM) symbiosis in dicotyledonous and monocotyledonous species, being essential in transcriptional reprogramming for the development and functionality of the arbuscules. In tomato, SlGRAS27 is the putative orthologue of RAM1 (here named SlRAM1), but has not yet been characterized. A reduced colonization of the root and impaired arbuscule formation were observed in SlRAM1-silenced plants, confirming the functional conservation of the RAM1 orthologue in tomato. However, unexpectedly, SlRAM1-overexpressing (UBIL:SlRAM1) plants also showed decreased mycorrhizal colonization. Analysis of non-mycorrhizal UBIL:SlRAM1 roots revealed an overall regulation of AM-related genes and a reduction of strigolactone biosynthesis. Moreover, external application of the strigolactone analogue GR244DO almost completely reversed the negative effects of SlRAM1 overexpression on the frequency of mycorrhization. However, it only partially recovered the pattern of arbuscule distribution observed in control plants. Our results strongly suggest that SlRAM1 has a dual regulatory role during mycorrhization and, in addition to its recognized action as a positive regulator of arbuscule development, it is also involved in different mechanisms for the negative regulation of mycorrhization, including the repression of strigolactone biosynthesis.

The receptor-like kinase ARK controls symbiotic balance across land plants

The mutualistic arbuscular mycorrhizal (AM) symbiosis arose in land plants more than 450 million years ago and is still widely found in all major land plant lineages. Despite its broad taxonomic distribution, little is known about the molecular components underpinning symbiosis outside of flowering plants. The ARBUSCULAR RECEPTOR-LIKE KINASE (ARK) is required for sustaining AM symbiosis in distantly related angiosperms. Here, we demonstrate that ARK has an equivalent role in symbiosis maintenance in the bryophyte Marchantia paleacea and is part of a broad AM genetic program conserved among land plants. In addition, our comparative transcriptome analysis identified evolutionarily conserved expression patterns for several genes in the core symbiotic program required for presymbiotic signaling, intracellular colonization, and nutrient exchange. This study provides insights into the molecular pathways that consistently associate with AM symbiosis across land plants and identifies an ancestral role for ARK in governing symbiotic balance.

Aquaporin LjNIP1;5 positively modulates drought tolerance by promoting arbuscular mycorrhizal symbiosis in Lotus japonicus

Drought stress often affects crop growth and even causes crop death, while aquaporins can maintain osmotic balance by transporting water across membranes, so it is important to study how to improve drought tolerance of crops by using aquaporins. In this work, we characterize a set of subfamily members named NIPs belonging to the family of aquaporins in Lotus japonicus, grouping 14 family members based on the sequence similarity in the aromatic/arginine (Ar/R) region. Among these members, LjNIP1;5 is one of the genes with the highest expression in roots which is induced by the AM fungus. In Lotus japonicus, LjNIP1;5 is highly expressed in symbiotic roots, and its promoter can be induced by drought stress and AM fungus. Root colonization analysis reveals that ljnip1:5 mutant exhibits lower mycorrhizal colonization than the wild type, with increasing the proportion of large arbuscule, and fewer arbuscule produced by symbiosis under drought stress. In the LjNIP1;5OE plant, we detected a strong antioxidant capacity compared to the control, and LjNIP1;5OE showed higher stem length under drought stress. Taken together, the current results facilitate our comprehensive understanding of the plant adaptive to drought stress with the coordination of the specific fungi.

A journey into the world of small RNAs in the arbuscular mycorrhizal symbiosis

Arbuscular mycorrhizal (AM) symbiosis is a mutualistic interaction between fungi and most land plants that is underpinned by a bidirectional exchange of nutrients. AM development is a tightly regulated process that encompasses molecular communication for reciprocal recognition, fungal accommodation in root tissues and activation of symbiotic function. As such, a complex network of transcriptional regulation and molecular signaling underlies the cellular and metabolic reprogramming of host cells upon AM fungal colonization. In addition to transcription factors, small RNAs (sRNAs) are emerging as important regulators embedded in the gene network that orchestrates AM development. In addition to controlling cell-autonomous processes, plant sRNAs also function as mobile signals capable of moving to different organs and even to different plants or organisms that interact with plants. AM fungi also produce sRNAs; however, their function in the AM symbiosis remains largely unknown. Here, we discuss the contribution of host sRNAs in the development of AM symbiosis by considering their role in the transcriptional reprogramming of AM fungal colonized cells. We also describe the characteristics of AM fungal-derived sRNAs and emerging evidence for the bidirectional transfer of functional sRNAs between the two partners to mutually modulate gene expression and control the symbiosis.

Molecular and Systems Biology Approaches for Harnessing the Symbiotic Interaction in Mycorrhizal Symbiosis for Grain and Oil Crop Cultivation

Mycorrhizal symbiosis, the mutually beneficial association between plants and fungi, has gained significant attention in recent years due to its widespread significance in agricultural productivity. Specifically, arbuscular mycorrhizal fungi (AMF) provide a range of benefits to grain and oil crops, including improved nutrient uptake, growth, and resistance to (a)biotic stressors. Harnessing this symbiotic interaction using molecular and systems biology approaches presents promising opportunities for sustainable and economically-viable agricultural practices. Research in this area aims to identify and manipulate specific genes and pathways involved in the symbiotic interaction, leading to improved cereal and oilseed crop yields and nutrient acquisition. This review provides an overview of the research frontier on utilizing molecular and systems biology approaches for harnessing the symbiotic interaction in mycorrhizal symbiosis for grain and oil crop cultivation. Moreover, we address the mechanistic insights and molecular determinants underpinning this exchange. We conclude with an overview of current efforts to harness mycorrhizal diversity to improve cereal and oilseed health through systems biology.

Comprehensive regulatory networks for tomato organ development based on the genome and RNAome of MicroTom tomato

MicroTom has a short growth cycle and high transformation efficiency, and is a prospective model plant for studying organ development, metabolism, and plant-microbe interactions. Here, with a newly assembled reference genome for this tomato cultivar and abundant RNA-seq data derived from tissues of different organs/developmental stages/treatments, we constructed multiple gene co-expression networks, which will provide valuable clues for the identification of important genes involved in diverse regulatory pathways during plant growth, e.g. arbuscular mycorrhizal symbiosis and fruit development. Additionally, non-coding RNAs, including miRNAs, lncRNAs, and circRNAs were also identified, together with their potential targets. Interacting networks between different types of non-coding RNAs (miRNA-lncRNA), and non-coding RNAs and genes (miRNA-mRNA and lncRNA-mRNA) were constructed as well. Our results and data will provide valuable information for the study of organ differentiation and development of this important fruit. Lastly, we established a database (http://eplant.njau.edu.cn/microTomBase/) with genomic and transcriptomic data, as well as details of gene co-expression and interacting networks on MicroTom, and this database should be of great value to those who want to adopt MicroTom as a model plant for research.

Dynamic transcriptome profiling provides insights into rhizome enlargement in ginger (Zingiber officinale Rosc.)

The rhizome is an economically important part of ginger (Zingiber officinale Rosc.). However, the mechanism of ginger rhizome enlargement remains unclear. In this study, we performed an integrated analysis of the hormone content and transcriptome of ginger at three rhizome enlargement stages: initial enlargement (S1), middle enlargement (S2), and peak enlargement (S3). With rhizome enlargement, the levels of the hormones zeatin (ZT), gibberellic acid (GA), indole acetic acid (IAA), and jasmonic acid (JA) were significantly increased, and this increase was positively correlated with rhizome diameter. Transcriptomic analysis identified a large number of differentially expressed genes (DEGs); the number of DEGs were 2,206 in the transition from S1 to S2, and 1,151 in the transition from S2 to S3. The expression of several genes related to hormone biosynthesis and signalling and cell division or expansion, and transcription factors was significantly altered, which suggests that these genes play essential roles in rhizome enlargement. The results of correlation analysis suggested that the process of ginger rhizome enlargement may be primarily related to the regulation of endogenous cytokinin, GA3, auxin, and JA biosynthesis pathways and signal transduction; GRAS, HB, MYB, MYB122, bZIP60, ARF1, ARF2, E2FB1, and E2FB2, which may regulate the expression of rhizome formation-related genes; and CYC2, CDKB1, CDKB2, EXPA1, and XTH7, which may mediate cell division and expansion. These results provide gene resources and information that will be useful for the molecular breeding in ginger.

Integrated miRNA-mRNA analysis reveals candidate miRNA family regulating arbuscular mycorrhizal symbiosis of Poncirus trifoliata

Over 70% land plants live in mutualistic symbiosis with arbuscular mycorrhizal (AM) fungi, and maintenance of symbiosis requires transcriptional and post-transcriptional regulation. The former has been widely studied, whereas the latter mediated by symbiotic microRNAs (miRNAs) remains obscure, especially in woody plants. Here, we performed high-throughput sequencing of the perennial woody citrus plant Poncirus trifoliata and identified 3750 differentially expressed genes (DEGs) and 42 miRNAs (DEmiRs) upon AM fungal colonization. By analyzing cis-regulatory elements in the promoters of the DEGs, we predicted 329 key AM transcription factors (TFs). A miRNA-mRNA regulatory network was then constructed by integrating these data. Several candidate miRNA families of P. trifoliata were identified whose members target known symbiotic genes, such as miR167h-AMT2;3 and miR156e-EXO70I, or key TFs, such as miR164d-NAC and miR477a-GRAS, thus are involved in AM symbiotic processes of fungal colonization, arbuscule development, nutrient exchange and phytohormone signaling. Finally, analysis of selected miRNA family revealed that a miR159b conserved in mycorrhizal plant species and a Poncirus-specific miR477a regulate AM symbiosis. The role of miR477a was likely to target GRAS family gene RAD1 in citrus plants. Our results not only revealed that miRNA-mRNA network analysis, especially miRNA-TF analysis, is effective in identifying miRNA family regulating AM symbiosis, but also shed light on miRNA-mediated post-transcriptional regulation of AM symbiosis in woody citrus plants.

ARBUSCULAR MYCORRHIZA-INDUCED KINASES AMK8 and AMK24 associate with the receptor-like kinase KINASE3 to regulate arbuscular mycorrhizal symbiosis in Lotus japonicus

Arbuscular mycorrhizal (AM) symbiosis is a widespread, ancient mutualistic association between plants and fungi, and facilitates nutrient uptake into plants. Cell surface receptor-like kinases (RLKs) and receptor-like cytoplasmic kinases (RLCKs) play pivotal roles in transmembrane signaling, while few RLCKs are known to function in AM symbiosis. Here, we show that 27 out of 40 AM-induced kinases (AMKs) are transcriptionally upregulated by key AM transcription factors in Lotus japonicus. Nine AMKs are only conserved in AM-host lineages, among which the SPARK-RLK-encoding gene KINASE3 (KIN3) and the RLCK paralogues AMK8 and AMK24 are required for AM symbiosis. KIN3 expression is directly regulated by the AP2 transcription factor CTTC MOTIF-BINDING TRANSCRIPTION FACTOR1 (CBX1), which regulates the reciprocal exchange of nutrients in AM symbiosis, via the AW-box motif in the KIN3 promoter. Loss of function mutations in KIN3, AMK8, or AMK24 result in reduced mycorrhizal colonization in L. japonicus. AMK8 and AMK24 physically interact with KIN3. KIN3 and AMK24 are active kinases and AMK24 directly phosphorylates KIN3 in vitro. Moreover, CRISPR-Cas9-mediated mutagenesis of OsRLCK171, the sole homolog of AMK8 and AMK24 in rice (Oryza sativa), leads to diminished mycorrhization with stunted arbuscules. Overall, our results reveal a crucial role of the CBX1-driven RLK/RLCK complex in the evolutionarily conserved signaling pathway enabling arbuscule formation.

The RNAome landscape of tomato during arbuscular mycorrhizal symbiosis reveals an evolving RNA layer symbiotic regulatory network

Arbuscular mycorrhizal symbiosis (AMS) is an ancient plant-fungus relationship that is widely distributed in terrestrial plants. The formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous genes. However, the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly understood. In this study, a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato, an emerging AMS model. The annotation of the tomato genome was improved by a multiple-platform sequencing strategy. A total of 3,174 protein-coding genes were upregulated during AMS, 42% of which were alternatively spliced. Comparative-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant angiosperms. Seven additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host plants. However, these orthogroups were absent or not induced in monocots and/or non-AMS hosts, suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory module. Additionally, we detected 587 lncRNAs, ten miRNAs, and 146 circRNAs that responded to AMS, which were incorporated to establish a tomato AMS-responsive, competing RNA-responsive endogenous RNA (ceRNA) network. Finally, a tomato symbiotic transcriptome database (TSTD, https://efg.nju.edu.cn/TSTD) was constructed to serve as a resource for deep deciphering of the AMS regulatory network. These results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.

A phosphate starvation response-regulated receptor-like kinase, OsADK1, is required for mycorrhizal symbiosis and phosphate starvation responses

Most land plants associate with arbuscular mycorrhizal (AM) fungi to secure mineral nutrient acquisition, especially that of phosphorus. A phosphate starvation response (PHR)-centered network regulates AM symbiosis. Here, we identified 520 direct target genes for the rice transcription factor OsPHR1/2/3 during AM symbiosis using transcriptome deep sequencing and DNA affinity purification sequencing. These genes were involved in strigolactone biosynthesis, transcriptional reprogramming, and bidirectional nutrient exchange. Moreover, we identified the receptor-like kinase, Arbuscule Development Kinase 1 (OsADK1), as a new target of OsPHR1/2/3. Electrophoretic mobility shift assays and transactivation assays showed that OsPHR2 can bind directly to the P1BS elements within the OsADK1 promoter to activate its transcription. OsADK1 appeared to be required for mycorrhizal colonization and arbuscule development. In addition, hydroponic experiments suggested that OsADK1 may be involved in plant Pi starvation responses. Our findings validate a role for OsPHR1/2/3 as master regulators of mycorrhizal-related genes involved in various stages of symbiosis, and uncover a new RLK involved in AM symbiosis and plant Pi starvation responses.

A simple and versatile fluorochrome-based procedure for imaging of lipids in arbuscule-containing cells

The arbuscular mycorrhizal (AM) symbiosis is characterized by the reciprocal exchange of nutrients. AM fungi are oleaginous microorganisms that obtain essential fatty acids from host plants. A lipid biosynthesis and delivery pathway has been proposed to operate in inner root cortex cells hosting arbuscules, a cell type challenging to access microscopically. Despite the central role lipids play in the association, lipid distribution patterns during arbuscule development are currently unknown. We developed a simple co-staining method employing fluorophore-conjugated Wheat Germ Agglutinin (WGA) and a lipophilic blue fluorochrome, Ac-201, for the simultaneous imaging of arbuscules and lipids distributed within arbuscule-containing cells in high resolution. We observed lipid distribution patterns in wild-type root infection zones in a variety of plant species. In addition, we applied this methodology to mutants of the Lotus japonicus GRAS transcription factor RAM1 and the Oryza sativa half-size ABC transporter STR1, both proposed to be impaired in the symbiotic lipid biosynthesis-delivery pathway. We found that lipids accumulated in cortical cells hosting stunted arbuscules in Ljram1 and Osstr1, and observed lipids in the arbuscule body of Osstr1, suggesting that in the corresponding plant species, RAM1 and STR1 may not be essential for symbiotic lipid biosynthesis and transfer from arbuscule-containing cells, respectively. The versatility of this methodology has the potential to help elucidate key questions on the complex lipid dynamics fostering AM symbioses.

A mutant-based analysis of the establishment of Nod-independent symbiosis in the legume Aeschynomene evenia

Intensive research on nitrogen-fixing symbiosis in two model legumes has uncovered the molecular mechanisms, whereby rhizobial Nod factors activate a plant symbiotic signaling pathway that controls infection and nodule organogenesis. In contrast, the so-called Nod-independent symbiosis found between Aeschynomene evenia and photosynthetic bradyrhizobia, which does not involve Nod factor recognition nor infection thread formation, is less well known. To gain knowledge on how Nod-independent symbiosis is established, we conducted a phenotypic and molecular characterization of A. evenia lines carrying mutations in different nodulation genes. Besides investigating the effect of the mutations on rhizobial symbiosis, we examined their consequences on mycorrhizal symbiosis and in nonsymbiotic conditions. Analyzing allelic mutant series for AePOLLUX, Ca2+/calmodulin dependent kinase, AeCYCLOPS, nodulation signaling pathway 2 (AeNSP2), and nodule inception demonstrated that these genes intervene at several stages of intercellular infection and during bacterial accommodation. We provide evidence that AeNSP2 has an additional nitrogen-dependent regulatory function in the formation of axillary root hairs at lateral root bases, which are rhizobia-colonized infection sites. Our investigation of the recently discovered symbiotic actor cysteine-rich receptor-like kinase specified that it is not involved in mycorrhization; however, it is essential for both symbiotic signaling and early infection during nodulation. These findings provide important insights on the modus operandi of Nod-independent symbiosis and contribute to the general understanding of how rhizobial-legume symbioses are established by complementing the information acquired in model legumes.

Moss transcription factors regulating development and defense responses to stress

Transcription factors control gene expression, leading to regulation of biological processes that determine plant development and adaptation to the environment. Land colonization by plants occurred 450-470 million years ago and was accompanied by an increase in the complexity of transcriptional regulation associated to transcription factor gene expansions. AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY transcription factor families increased in land plants compared with algae. In angiosperms, they play crucial roles in regulating plant growth and responses to environmental stressors. However, less information is available in bryophytes and only in a few cases is the functional role of moss transcription factors in stress mechanisms known. In this review, we discuss current knowledge of the transcription factor families involved in development and defense responses to stress in mosses and other bryophytes. By exploring and analysing the Physcomitrium patens public database and published transcriptional profiles, we show that a high number of AP2/ERF, bHLH, MYB, NAC, GRAS, and WRKY genes are differentially expressed in response to abiotic stresses and during biotic interactions. Expression profiles together with a comprehensive analysis provide insights into relevant transcription factors involved in moss defenses, and hint at distinct and conserved biological roles between bryophytes and angiosperms.

Molecular Regulation of Arbuscular Mycorrhizal Symbiosis

Plant-microorganism interactions at the rhizosphere level have a major impact on plant growth and plant tolerance and/or resistance to biotic and abiotic stresses. Of particular importance for forestry and agricultural systems is the cooperative and mutualistic interaction between plant roots and arbuscular mycorrhizal (AM) fungi from the phylum Glomeromycotina, since about 80% of terrestrial plant species can form AM symbiosis. The interaction is tightly regulated by both partners at the cellular, molecular and genetic levels, and it is highly dependent on environmental and biological variables. Recent studies have shown how fungal signals and their corresponding host plant receptor-mediated signalling regulate AM symbiosis. Host-generated symbiotic responses have been characterized and the molecular mechanisms enabling the regulation of fungal colonization and symbiosis functionality have been investigated. This review summarizes these and other recent relevant findings focusing on the molecular players and the signalling that regulate AM symbiosis. Future progress and knowledge about the underlying mechanisms for AM symbiosis regulation will be useful to facilitate agro-biotechnological procedures to improve AM colonization and/or efficiency.

A Perspective on Developing a Plant ‘Holobiont’ for Future Saline Agriculture

Soil salinity adversely affects plant growth and has become a major limiting factor for agricultural development worldwide. There is a continuing demand for sustainable technology innovation in saline agriculture. Among various bio-techniques being used to reduce the salinity hazard, symbiotic microorganisms such as rhizobia and arbuscular mycorrhizal (AM) fungi have proved to be efficient. These symbiotic associations each deploy an array of well-tuned mechanisms to provide salinity tolerance for the plant. In this review, we first comprehensively cover major research advances in symbiont-induced salinity tolerance in plants. Second, we describe the common signaling process used by legumes to control symbiosis establishment with rhizobia and AM fungi. Multi-omics technologies have enabled us to identify and characterize more genes involved in symbiosis, and eventually, map out the key signaling pathways. These developments have laid the foundation for technological innovations that use symbiotic microorganisms to improve crop salt tolerance on a larger scale. Thus, with the aim of better utilizing symbiotic microorganisms in saline agriculture, we propose the possibility of developing non-legume ‘holobionts’ by taking advantage of newly developed genome editing technology. This will open a new avenue for capitalizing on symbiotic microorganisms to enhance plant saline tolerance for increased sustainability and yields in saline agriculture.

Innovation and appropriation in mycorrhizal and rhizobial Symbioses

Most land plants benefit from endosymbiotic interactions with mycorrhizal fungi, including legumes and some nonlegumes that also interact with endosymbiotic nitrogen (N)-fixing bacteria to form nodules. In addition to these helpful interactions, plants are continuously exposed to would-be pathogenic microbes: discriminating between friends and foes is a major determinant of plant survival. Recent breakthroughs have revealed how some key signals from pathogens and symbionts are distinguished. Once this checkpoint has been passed and a compatible symbiont is recognized, the plant coordinates the sequential development of two types of specialized structures in the host. The first serves to mediate infection, and the second, which appears later, serves as sophisticated intracellular nutrient exchange interfaces. The overlap in both the signaling pathways and downstream infection components of these symbioses reflects their evolutionary relatedness and the common requirements of these two interactions. However, the different outputs of the symbioses, phosphate uptake versus N fixation, require fundamentally different components and physical environments and necessitated the recruitment of different master regulators, NODULE INCEPTION-LIKE PROTEINS, and PHOSPHATE STARVATION RESPONSES, for nodulation and mycorrhization, respectively.

Expression and roles of GRAS gene family in plant growth, signal transduction, biotic and abiotic stress resistance and symbiosis formation-a review

The GRAS (derived from GAI, RGA and SCR) gene family consists of plant-specific genes, works as a transcriptional regulator and plays a key part in the regulation of plant growth and development. The past decade has witnessed significant progress in understanding and advances on GRAS transcription factors in various plants. A notable concern is to what extent the mechanisms found in plants, particularly crops, are shared by other species, and what other characteristics are dependent on GRAS transcription factor (TFS)-mediated gene expression. GRAS are involved in many processes that are intimately linked to plant growth regulation. However, GRAS also perform additional roles against environmental stresses, allowing plants to function more efficiently. GRAS increase plant growth and development by improving several physiological processes, such as phytohormone, biosynthetic and signalling pathways. Furthermore, the GRAS gene family plays an important role in response to abiotic stresses, e.g. photooxidative stress. Moreover, evidence shows the involvement of GRAS in arbuscule development during plant-mycorrhiza associations. In this review, the diverse roles of GRAS in plant systems are highlighted that could be useful in enhancing crop productivity through genetic modification, especially of crops. This is the first review to report the role and function of the GRAS gene family in plant systems. Furthermore, a large number of studies are reviewed, and several limitations and research gaps identified that must be addressed in future studies.

Multifarious and Interactive Roles of GRAS Transcription Factors During Arbuscular Mycorrhiza Development

Arbuscular mycorrhiza (AM) is a mutualistic symbiotic interaction between plant roots and AM fungi (AMF). This interaction is highly beneficial for plant growth, development and fitness, which has made AM symbiosis the focus of basic and applied research aimed at increasing plant productivity through sustainable agricultural practices. The creation of AM requires host root cells to undergo significant structural and functional modifications. Numerous studies of mycorrhizal plants have shown that extensive transcriptional changes are induced in the host during all stages of colonization. Advances have recently been made in identifying several plant transcription factors (TFs) that play a pivotal role in the transcriptional regulation of AM development, particularly those belonging to the GRAS TF family. There is now sufficient experimental evidence to suggest that GRAS TFs are capable to establish intra and interspecific interactions, forming a transcriptional regulatory complex that controls essential processes in the AM symbiosis. In this minireview, we discuss the integrative role of GRAS TFs in the regulation of the complex genetic re-programming determining AM symbiotic interactions. Particularly, research being done shows the relevance of GRAS TFs in the morphological and developmental changes required for the formation and turnover of arbuscules, the fungal structures where the bidirectional nutrient translocation occurs.

Conserved and Diverse Transcriptional Reprogramming Triggered by the Establishment of Symbioses in Tomato Roots Forming Arum-Type and Paris-Type Arbuscular Mycorrhizae

Arbuscular mycorrhizal (AM) fungi allocate mineral nutrients to their host plants, and the hosts supply carbohydrates and lipids to the fungal symbionts in return. The morphotypes of intraradical hyphae are primarily determined on the plant side into Arum- and Paris-type AMs. As an exception, Solanum lycopersicum (tomato) forms both types of AMs depending on the fungal species. Previously, we have shown the existence of diverse regulatory mechanisms in Arum- and Paris-type AM symbioses in response to gibberellin (GA) among different host species. However, due to the design of the study, it remained possible that the use of different plant species influenced the results. Here, we used tomato plants to compare the transcriptional responses during Arum- and Paris-type AM symbioses in a single plant species. The tomato plants inoculated with Rhizophagus irregularis or Gigaspora margarita exhibited Arum- and Paris-type AMs, respectively, and demonstrated similar colonization rates and shoot biomass. Comparative transcriptomics showed shared expression patterns of AM-related genes in tomato roots upon each fungal infection. On the contrary, the defense response and GA biosynthetic process was transcriptionally upregulated during Paris-type AM symbiosis. Thus, both shared and different transcriptional reprogramming function in establishing Arum- and Paris-type AM symbioses in tomato plants.

Colonization of Mutualistic Mycorrhizal and Parasitic Blast Fungi Requires OsRAM2-Regulated Fatty Acid Biosynthesis in Rice

Arbuscular mycorrhizal (AM) fungi form a mutual association with the majority of land plants, including most angiosperms of the dicotyledon and monocotyledon lineages. The symbiosis is based upon bidirectional nutrient exchange between the host and symbiont that occurs between inner cortical cells of the root and branched AM hyphae called arbuscules that develop within these cells. Lipid transport and its regulation during the symbiosis have been intensively investigated in dicotyledon plants, especially legumes. Here, we characterize OsRAM2 and OsRAM2L, homologs of Medicago truncatula RAM2, and found that plants defective in OsRAM2 were unable to be colonized by AM fungi and showed impaired colonization by Magnaporthe oryzae. The induction of OsRAM2 and OsRAM2L is dependent on OsRAM1 and the common symbiosis signaling pathway pathway genes CCaMK and CYCLOPS, while overexpression of OsRAM1 results in increased expression of OsRAM2 and OsRAM2L. Collectively, our data show that the function and regulation of OsRAM2 is conserved in monocot and dicot plants and reveals that, similar to mutualistic fungi, pathogenic fungi have recruited RAM2-mediated fatty acid biosynthesis to facilitate invasion.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

A novel SCARECROW-LIKE3 transcription factor LjGRAS36 in Lotus japonicus regulates the development of arbuscular mycorrhizal symbiosis

The symbiosis with arbuscular mycorrhizal (AM) fungi improves plants' nutrient uptake. During this process, transcription factors have been highlighted to play crucial roles. Members of the GRAS transcription factor gene family have been reported involved in AM symbiosis, but little is known about SCARECROW-LIKE3 (SCL3) genes belonging to this family in Lotus japonicus. In this study, 67 LjGRAS genes were identified from the L. japonicus genome, seven of which were clustered in the SCL3 group. Three of the seven LjGRAS genes expression levels were upregulated by AM fungal inoculation, and our biochemical results showed that the expression of LjGRAS36 was specifically induced by AM colonization. Functional loss of LjGRAS36 in mutant ljgras36 plants exhibited a significantly reduced mycorrhizal colonization rate and arbuscular size. Transcriptome analysis showed a deficiency of LjGRAS36 led to the dysregulation of the gibberellic acid signal pathway associated with AM symbiosis. Together, this study provides important insights for understanding the important potential function of SCL3 genes in regulating AM symbiotic development.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01161-z.

Stress-associated developmental reprogramming in moss protonemata by synthetic activation of the common symbiosis pathway

Symbioses between angiosperms and rhizobia or arbuscular mycorrhizal fungi are controlled through a conserved signaling pathway. Microbe-derived, chitin-based elicitors activate plant cell surface receptors and trigger nuclear calcium oscillations, which are decoded by a calcium/calmodulin-dependent protein kinase (CCaMK) and its target transcription factor interacting protein of DMI3 (IPD3). Genes encoding CCaMK and IPD3 have been lost in multiple non-mycorrhizal plant lineages yet retained among non-mycorrhizal mosses. Here, we demonstrated that the moss Physcomitrium is equipped with a bona fide CCaMK that can functionally complement a Medicago loss-of-function mutant. Conservation of regulatory phosphosites allowed us to generate predicted hyperactive forms of Physcomitrium CCaMK and IPD3. Overexpression of synthetically activated CCaMK or IPD3 in Physcomitrium led to abscisic acid (ABA) accumulation and ectopic development of brood cells, which are asexual propagules that facilitate escape from local abiotic stresses. We therefore propose a functional role for Physcomitrium CCaMK-IPD3 in stress-associated developmental reprogramming.

Root cortex development is fine-tuned by the interplay of MIGs, SCL3 and DELLAs during arbuscular mycorrhizal symbiosis

Root development is a crucial process that determines the ability of plants to acquire nutrients, adapt to the substrate and withstand changing environmental conditions. Root plasticity is controlled by a plethora of transcriptional regulators that allow, in contrast to tissue development in animals, post-embryonic changes that give rise to new tissue and specialized cells. One of these changes is the accommodation in the cortex of hyperbranched hyphae of symbiotic arbuscular mycorrhizal (AM) fungi, called arbuscules. Arbuscule-containing cells undergo massive reprogramming to coordinate developmental changes with transport processes. Here we describe a novel negative regulator of arbuscule development, MIG3. MIG3 induces and interacts with SCL3, both of which modulate the activity of the central regulator DELLA, restraining cortical cell growth. As in a tug-of-war, MIG3-SCL3 antagonizes the function of the complex MIG1-DELLA, which promotes the cell expansion required for arbuscule development, adjusting cell size during the dynamic processes of the arbuscule life cycle. Our results in the legume plant Medicago truncatula advance the knowledge of root development in dicot plants, showing the existence of additional regulatory elements not present in Arabidopsis that fine-tune the activity of conserved central modules.

A phosphate starvation response-centered network regulates mycorrhizal symbiosis

To secure phosphorus (P) from soil, most land plants use a direct phosphate uptake pathway via root hairs and epidermis and an indirect phosphate uptake pathway via mycorrhizal symbiosis. The interaction between these two pathways is unclear. Here, we mapped a network between transcription factors and mycorrhizal symbiosis-related genes using Y1H. Intriguingly, this gene regulatory network is governed by the conserved P-sensing pathway, centered on phosphate starvation response (PHR) transcription factors. PHRs are required for mycorrhizal symbiosis and regulate symbiosis-related genes via the P1BS motif. SPX-domain proteins suppress OsPHR2-mediated induction of symbiosis-related genes and inhibit mycorrhizal infection. In contrast, plants overexpressing OsPHR2 show improved mycorrhizal infection and are partially resistant to P-mediated inhibition of symbiosis. Functional analyses of network nodes revealed co-regulation of hormonal signaling and mycorrhizal symbiosis. This network deciphers extensive regulation of mycorrhizal symbiosis by endogenous and exogenous signals and highlights co-option of the P-sensing pathway for mycorrhizal symbiosis.

The scarecrow-like transcription factor SlSCL3 regulates volatile terpene biosynthesis and glandular trichome size in tomato (Solanum lycopersicum)

Tomato (Solanum lycopersicum L.) type VI glandular trichomes that occur on the surface of leaves, stems, young fruits and flowers produce and store a blend of volatile monoterpenes and sesquiterpenes. These compounds play important roles in the interaction with pathogens and herbivorous insects. Although the function of terpene synthases in the biosynthesis of volatile terpenes in tomato has been comprehensively investigated, the deciphering of their transcriptional regulation is only just emerging. We selected transcription factors that are over-expressed in trichomes based on existing transcriptome data and silenced them individually by virus-induced gene silencing. Of these, SlSCL3, a scarecrow-like (SCL) subfamily transcription factor, led to a significant decrease in volatile terpene content and expression of the corresponding terpene synthase genes when its transcription level was downregulated. Overexpression of SlSCL3 dramatically increased both the volatile terpene content and glandular trichome size, whereas its homozygous mutants showed reduced terpene biosynthesis. However, its heterozygous mutants also showed a significantly elevated volatile terpene content and enlarged glandular trichomes, similar to the overexpression plants. SlSCL3 modulates the expression of terpene biosynthetic pathway genes by transcriptional activation, but neither direct protein-DNA binding nor interaction with known regulators was observed. Moreover, transcript levels of the endogenous copy of SlSCL3 were decreased in the overexpression plants but increased in the heterozygous and homozygous mutants, suggesting feedback repression of its own promoter. Taken together, our results provide new insights into the role of SlSCL3 in the complex regulation of volatile terpene biosynthesis and glandular trichome development in tomato.

Genome wide identification and expression pattern analysis of the GRAS family in quinoa

GRAS, a key transcription factor in plant growth and development, has not yet been reported in quinoa. Therefore, this study used the latest quinoa genomic data to identify and analyse GRAS genes in quinoa: 52 GRAS genes were identified in quinoa, these being unevenly distributed on 19 chromosomes. Fragment duplication and tandem duplication events were the main reasons for the expansion of the GRAS gene family in quinoa. Protein sequence analysis showed that there were some differences in amino acid numbers and isoelectric points amongst different subfamilies, and the main secondary structures were α-helix and random coil. The CqGRAS gene was divided into 14 subfamilies based on results from phylogenetic analysis. The genes located in the same subfamily had similar gene structures, conserved motifs, and three-level models. Promoter region analysis showed that the GRAS family genes contained multiple homeostasis elements that responded to hormones and adversity. GO enrichment indicated that CqGRAS genes were involved in biological processes, cell components, and molecular functions. By analysing the expression of CqGRAS genes in different tissues and different treatments, it was found that GRAS genes had obvious differential expression in different tissues and stress, which indicates that GRAS genes had tissue or organ expression specificity and thus might play an important role in response to stress. These results laid a foundation for further functional research on the GRAS gene family in quinoa.

Important innate differences in determining symbiotic responsiveness in host and non-hosts of arbuscular mycorrhiza

Genetic components that regulate arbuscular mycorrhizal (AM) interactions in hosts and non-hosts are not completely known. Comparative transcriptomic analysis was combined with phylogenetic studies to identify the factors that distinguish AM host from non-host. Mycorrhized host, non-mycorrhized host and non-host cultivars of tomato (Solanum lycopersicum) were subjected to RNA seq analysis. The top 10 differentially expressed genes were subjected to extensive in silico phylogenetic analysis along with 10 more candidate genes that have been previously reported for AM-plant interactions. Seven distantly related hosts and four non-hosts were selected to identify structural differences in selected gene/protein candidates. The screened genes/proteins were subjected to MEME, CODEML and DIVERGE analysis to identify evolutionary patterns that differentiate hosts from non-hosts. Based on the results, candidate genes were categorized as highly influenced (SYMRK and CCaMK), moderately influenced and minimally influenced by evolutionary constraints. We propose that the amino acid and nucleotide changes specific to non-hosts are likely to correspond to aberrations in functionality towards AM symbiosis. This study paves way for future research aimed at understanding innate differences in genetic make-up of AM hosts and non-hosts, in addition to the theory of gene losses from the "AM-symbiotic toolkit".

The GRAS gene family in watermelons: identification, characterization and expression analysis of different tissues and root-knot nematode infestations

The family of GRAS plant-specific transcription factor plays diverse roles in numerous biological processes. Despite the identification and characterization of GRAS genes family in dozens of plant species, until now, GRAS members in watermelon (Citrullus lanatus) have not been investigated comprehensively. In this study, using bioinformatic analysis, we identified 37 GRAS genes in the watermelon genome (ClGRAS). These genes are classified into 10 distinct subfamilies based on previous research, and unevenly distributed on 11 chromosomes. Furthermore, a complete analysis was conducted to characterize conserved motifs and gene structures, which revealed the members within same subfamily that have analogous conserved gene structure and motif composition. Additionally, the expression pattern of ClGRAS genes was characterized in fruit flesh and rind tissues during watermelon fruit development and under red light (RL) as well as root knot nematode infestation. Finally, for verification of the availability of public transcriptome data, we also evaluated the expression levels of randomly selected four ClGRAS genes under RL and nematode infection by using qRT-PCR. The qRT-PCR results indicated that several ClGRAS genes were differentially expressed, implying their vital role in RL induction of watermelon resistance against root-knot nematodes. The results obtained in this study could be useful in improving the quality of watermelon.

Lipid exchanges drove the evolution of mutualism during plant terrestrialization

Symbiosis with arbuscular mycorrhizal fungi (AMF) improves plant nutrition in most land plants, and its contribution to the colonization of land by plants has been hypothesized. Here, we identify a conserved transcriptomic response to AMF among land plants, including the activation of lipid metabolism. Using gain of function, we show the transfer of lipids from the liverwort Marchantia paleacea to AMF and its direct regulation by the transcription factor WRINKLED (WRI). Arbuscules, the nutrient-exchange structures, were not formed in loss-of-function wri mutants in M. paleacea, leading to aborted mutualism. Our results show the orthology of the symbiotic transfer of lipids across land plants and demonstrate that mutualism with arbuscular mycorrhizal fungi was present in the most recent ancestor of land plants 450 million years ago.

GIBBERELLINS IN REGULATION OF PLANT GROWTH AND DEVELOPMENT UNDER ABIOTIC STRESSES

Background. Gibberellins (GAs), a class of diterpenoid phytohormones, play an important role in regulation of plant growth and development. Among more than 130 different gibberellin molecules, only a few are bioactive. GA1, GA3, GA4, and GA7 regulate plant growth through promotion the degradation of the DELLA proteins, a family of nuclear growth repressors – negative regulator of GAs signaling. Recent studies on GAs biosynthesis, metabolism, transport, and signaling, as well as crosstalk with other phytohormones and environment have achieved great progress thanks to molecular genetics and functional genomics. Aim. In this review, we focused on the role of GAs in regulation of plant gtowth in abiotic stress conditions. Results. We represented a key information on GAs biosynthesis, signaling and functional activity; summarized current understanding of the crosstalk between GAs and auxin, cytokinin, abscisic acid and other hormones and what is the role of GAs in regulation of adaptation to drought, salinization, high and low temperature conditions, and heavy metal pollution. We emphasize that the effects of GAs depend primarily on the strength and duration of stress and the phase of ontogenesis and tolerance of the plant. By changing the intensity of biosynthesis, the pattern of the distribution and signaling of GAs, plants are able to regulate resistance to abiotic stress, increase viability and even avoid stress. The issues of using retardants – inhibitors of GAs biosynthesis to study the functional activity of hormones under abiotic stresses were discussed. Special attention was focused on the use of exogenous GAs for pre-sowing priming of seeds and foliar treatment of plants. Conclusion. Further study of the role of gibberellins in the acquisition of stress resistance would contribute to the development of biotechnology of exogenous use of the hormone to improve growth and increase plant yields under adverse environmental conditions.

DLK2 regulates arbuscule hyphal branching during arbuscular mycorrhizal symbiosis

D14 and KAI2 receptors enable plants to distinguish between strigolactones (SLs) and karrikins (KARs), respectively, in order to trigger appropriate environmental and developmental responses. Both receptors are related to the regulation of arbuscular mycorrhiza (AM) formation and are members of the RsbQ-like family of α,β-hydrolases. DLK2 proteins, whose function remains unknown, constitute a third clade from the RsbQ-like protein family. We investigated whether the tomato SlDLK2 is a new regulatory component in the AM symbiosis. Genetic approaches were conducted to analyze SlDLK2 expression and to understand SlDLK2 function in AM symbiosis. We show that SlDLK2 expression in roots is AM-dependent and is associated with cells containing arbuscules. SlDLK2 ectopic expression arrests arbuscule branching and downregulates AM-responsive genes, even in the absence of symbiosis; while the opposite effect was observed upon SlDLK2 silencing. Moreover, SlDLK2 overexpression in Medicago truncatula roots showed the same altered phenotype observed in tomato roots. Interestingly, SlDLK2 interacts with DELLA, a protein that regulates arbuscule formation/degradation in AM roots. We propose that SlDLK2 is a new component of the complex plant-mediated mechanism regulating the life cycle of arbuscules in AM symbiosis.

Constitutive Overexpression of RAM1 Leads to an Increase in Arbuscule Density in Brachypodium distachyon

Arbuscular mycorrhizal (AM) symbiosis is a mutually beneficial association of plants and fungi of the subphylum Glomeromycotina. Endosymbiotic AM fungi colonize the inner cortical cells of the roots, where they form branched hyphae called arbuscules that function in nutrient exchange with the plant. To support arbuscule development and subsequent bidirectional nutrient exchange, the root cortical cells undergo substantial transcriptional reprogramming. REDUCED ARBUSCULAR MYCORRHIZA1 (RAM1), previously studied in several dicot plant species, is a major regulator of this cortical cell transcriptional program. Here, we generated ram1 mutants and RAM1 overexpressors in a monocot, Brachypodium distachyon. The AM phenotypes of two ram1 lines revealed that RAM1 is only partly required to enable arbuscule development in B. distachyon Transgenic lines constitutively overexpressing BdRAM1 showed constitutive expression of AM-inducible genes even in the shoots. Following inoculation with AM fungi, BdRAM1-overexpressing plants showed higher arbuscule densities relative to controls, indicating the potential to manipulate the relative proportion of symbiotic interfaces via modulation of RAM1 However, the overexpressors also show altered expression of hormone biosynthesis genes and aberrant growth patterns, including stunted bushy shoots and poor seed set. While these phenotypes possibly provide additional clues about the scope of influence of BdRAM1, they also indicate that directed approaches to increase the density of symbiotic interfaces will require a more focused, potentially cell type specific manipulation of transcription factor gene expression.

Association Mapping and Development of Marker-Assisted Selection Tools for the Resistance to White Pine Blister Rust in the Alberta Limber Pine Populations

Since its introduction to North America in the early 1900s, white pine blister rust (WPBR) caused by the fungal pathogen Cronartium ribicola has resulted in substantial economic losses and ecological damage to native North American five-needle pine species. The high susceptibility and mortality of these species, including limber pine (Pinus flexilis), creates an urgent need for the development and deployment of resistant germplasm to support recovery of impacted populations. Extensive screening for genetic resistance to WPBR has been underway for decades in some species but has only started recently in limber pine using seed families collected from wild parental trees in the USA and Canada. This study was conducted to characterize Alberta limber pine seed families for WPBR resistance and to develop reliable molecular tools for marker-assisted selection (MAS). Open-pollinated seed families were evaluated for host reaction following controlled infection using C. ribicola basidiospores. Phenotypic segregation for presence/absence of stem symptoms was observed in four seed families. The segregation ratios of these families were consistent with expression of major gene resistance (MGR) controlled by a dominant R locus. Based on linkage disequilibrium (LD)-based association mapping used to detect single nucleotide polymorphism (SNP) markers associated with MGR against C. ribicola, MGR in these seed families appears to be controlled by Cr4 or other R genes in very close proximity to Cr4. These associated SNPs were located in genes involved in multiple molecular mechanisms potentially underlying limber pine MGR to C. ribicola, including NBS-LRR genes for recognition of C. ribicola effectors, signaling components, and a large set of defense-responsive genes with potential functions in plant effector-triggered immunity (ETI). Interactions of associated loci were identified for MGR selection in trees with complex genetic backgrounds. SNPs with tight Cr4-linkage were further converted to TaqMan assays to confirm their effectiveness as MAS tools. This work demonstrates the successful translation and deployment of molecular genetic knowledge into specific MAS tools that can be easily applied in a selection or breeding program to efficiently screen MGR against WPBR in Alberta limber pine populations.

The effects of gibberellin on the expression of symbiosis-related genes in Paris-type arbuscular mycorrhizal symbiosis in Eustoma grandiflorum

Arbuscular mycorrhiza (AM) is a symbiotic interaction in terrestrial plants that is colonized by fungi in the Glomeromycotina. The morphological types of AM, including the Arum-type and Paris-type, are distinct, depending on the host plant species. A part of the regulatory pathways in Arum-type AM symbiosis has been revealed because most model plants form the Arum-type AM with a model AM fungus, Rhizophagus irregularis. Moreover, gibberellin (GA) is known to severely inhibit AM fungal colonization in Arum-type AM symbiosis. Recently, we showed that exogenous GA treatment significantly promoted AM fungal colonization in Paris-type AM symbiosis in Eustoma grandiflorum. In this study, we focused on the transcriptional changes in AM symbiosis-related genes in GA-treated E. grandiflorum. The expression levels of all examined E. grandiflorum genes were maintained or increased by GA treatment compared with those of the control treatment. Our new results suggest that signaling pathway(s) required for establishing AM symbiosis in E. grandiflorum may be distinct from the well-characterized pathway for that in model plants.