MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1 and ETHYLENE INSENSITIVE3-LIKE2 Regulate Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice

Ethylene Signaling under Stressful Environments: Analyzing Collaborative Knowledge

Ethylene is a gaseous plant growth hormone that regulates various plant developmental processes, ranging from seed germination to senescence. The mechanisms underlying ethylene biosynthesis and signaling involve multistep mechanisms representing different control levels to regulate its production and response. Ethylene is an established phytohormone that displays various signaling processes under environmental stress in plants. Such environmental stresses trigger ethylene biosynthesis/action, which influences the growth and development of plants and opens new windows for future crop improvement. This review summarizes the current understanding of how environmental stress influences plants’ ethylene biosynthesis, signaling, and response. The review focuses on (a) ethylene biosynthesis and signaling in plants, (b) the influence of environmental stress on ethylene biosynthesis, (c) regulation of ethylene signaling for stress acclimation, (d) potential mechanisms underlying the ethylene-mediated stress tolerance in plants, and (e) summarizing ethylene formation under stress and its mechanism of action.

Dwarf and High Tillering1 represses rice tillering through mediating the splicing of D14 pre-mRNA

Strigolactones (SLs) constitute a class of plant hormones that regulate many aspects of plant development, including repressing tillering in rice (Oryza sativa). However, how SL pathways are regulated is still poorly understood. Here, we describe a rice mutant dwarf and high tillering1 (dht1), which exhibits pleiotropic phenotypes (such as dwarfism and increased tiller numbers) similar to those of mutants defective in SL signaling. We show that DHT1 encodes a monocotyledon-specific hnRNP-like protein that acts as a previously unrecognized intron splicing factor for many precursor mRNAs (pre-mRNAs), including for the SL receptor gene D14. We find that the dht1 (DHT1I232F) mutant protein is impaired in its stability and RNA binding activity, causing defective splicing of D14 pre-mRNA and reduced D14 expression, and consequently leading to the SL signaling-defective phenotypes. Overall, our findings deepen our understanding of the functional diversification of hnRNP-like proteins and establish a connection between posttranscriptional splicing and SL signaling in the regulation of plant development.

Increasing SnRK1 activity with the AMPK activator A-769662 accelerates seed germination in rice

Sucrose non-fermenting-1-related protein kinase 1 (SnRK1) plays a key role in rice germination. The small molecule drug, A-769662, activates AMP-activated protein kinase, a mammalian homolog of SnRK1. However, it is unknown whether A-769662 activates SnRK1, thereby affecting germination. SnRK1 in desalted extracts from germinating rice seeds was strongly activated by adding A-769662 in vitro. Applying 50 or 100 μM A-769662 accelerated germination and increased the root length, shoot length, and seedling fresh weight. 50 μM A-769662 treatment increased the catalytic activity and phosphorylation of SnRK1 during germination. Transcriptome analysis and biochemical validation were performed to investigate the mechanism whereby A-769662 treatment promoted rice germination. A-769662 treatment promoted starch hydrolysis by increasing the expression and activity of amylase and inhibited starch biosynthesis by decreasing the expression of OsAGPL2, OsAGPS2a, Wx, and SSIIa. The abscisic acid (ABA) level and gene expression of ABA-induced transcription factors, including OsNF-YC9, OsNF-YC12, OsWRKY24, OsPYL8, OsMKKK62, and OsMKKK63, which reduced the inhibition of germination by ABA were decreased under 50 μM A-769662 treatment. The increased expression of the OsACO3 and OsACO5 genes and increased ethylene levels under A-769662 treatment, which counteracted the inhibition of ABA on germination and, thus, promoted germination. These results demonstrate the activation of A-769662 on SnRK1 and further reveal the regulatory mechanism of A-769662 in rice seed germination and nutrient remobilization.

Arabidopsis ETHYLENE INSENSITIVE 3 directly regulates the expression of PG1β-like family genes in response to aluminum stress

The genes in the subfamily PG1β (beta subunit of poly-galacturonase isoenzyme 1) have a clear effect on the biosynthesis pathway of pectin, a main component of the cell wall. However, the detailed functions of the PG1β-like gene members in Arabidopsis (AtPG1-3) have not yet been determined. In this study, we investigated their functional roles in response to aluminum (Al) stress. Our results indicate that the PG1β-like gene members are indeed involved in the Al-stress response and they can modulate its accumulation in roots to achieve optimum root elongation and hence better seedling growth. We found that transcription factor EIN3 (ETHYLENE INSENSITIVE 3) alters pectin metabolism and the EIN3 gene responds to Al stress to affect the pectin content in the root cell walls, leading to exacerbation of the inhibition of root growth, as reflected by the phenotypes of overexpressing lines. We determined that EIN3 can directly bind to the promoter regions of PG1-3, which act downstream of EIN3. Thus, our results show that EIN3 responds to Al stress in Arabidopsis directly through regulating the expression of PG1-3. Hence, EIN3 mediates their functions by acting as a biomarker in their molecular biosynthesis pathways, and consequently orchestrates their biological network in response to Al stress.

The OsEIL1-OsERF115-target gene regulatory module controls grain size and weight in rice

Grain size is one of the essential determinants of rice yield. Our previous studies revealed that ethylene plays an important role in grain-size control; however, the precise mechanism remains to be determined. Here, we report that the ethylene response factor OsERF115 functions as a key downstream regulator for ethylene-mediated grain development. OsERF115 encodes an AP2/ERF-type transcriptional factor that is specifically expressed in young spikelets and developing caryopses. Overexpression of OsERF115 significantly increases grain length, width, thickness and weight by promoting longitudinal elongation and transverse division of spikelet hull cells, as well as enhancing grain-filling activity, whereas its knockout mutations lead to the opposite effects, suggesting that OsERF115 positively regulates grain size and weight. OsERF115 transcription is strongly induced by ethylene, and OsEIL1 directly binds to the promoter to activate its expression. OsERF115 acts as a transcriptional repressor to directly or indirectly modulate a set of grain-size genes during spikelet growth and endosperm development. Importantly, haplotype analysis reveals that the SNP variations in the EIN3-binding sites of OsERF115 promoter are significantly associated with the OsERF115 expression levels and grain weight, suggesting that natural variations in the OsERF115 promoter contribute to grain-size diversity. In addition, the OsERF115 orthologues are identified only in grass species, implying a conserved and unique role in the grain development of cereal crops. Our results provide insights into the molecular mechanism of ethylene-mediated grain-size control and a potential strategy based on the OsEIL1-OsERF115-target gene regulatory module for genetic improvement of rice yield.

The coordination of melatonin and anti-bacterial activity by EIL5 underlies ethylene-induced disease resistance in cassava

Ethylene and melatonin are widely involved in plant development and environmental stress responses. However, the role of their direct relationship in the immune response and the underlying molecular mechanisms in plants remain elusive. Here, we found that Xanthomonas axonopodis pv. manihotis (Xam) infection increased endogenous ethylene levels, which positively modulated plant disease resistance through activating melatonin accumulation in cassava. In addition, the ethylene-responsive transcription factor ETHYLENE INSENSITIVE LIKE5 (MeEIL5), a positive regulator of disease resistance, was essential for ethylene-induced melatonin accumulation and disease resistance in cassava. Notably, the identification of heat stress transcription factor 20 (MeHsf20) as an interacting protein of MeEIL5 indicated the association between ethylene and melatonin in plant disease resistance. MeEIL5 physically interacted with MeHsf20 to promote the transcriptional activation of the gene encoding N-acetylserotonin O-methyltransferase 2 (MeASMT2), thereby improving melatonin accumulation. Moreover, MeEIL5 promoted the physical interaction of MeHsf20 and pathogen-related gene 3 (MePR3), resulting in improved anti-bacterial activity of MePR3. This study illustrates the dual roles of MeEIL5 in fine-tuning MeHsf20-mediated coordination of melatonin biosynthesis and anti-bacterial activity, highlighting the ethylene-responsive MeEIL5 as the integrator of ethylene and melatonin signals in the immune response in cassava.

OsMPK4 promotes phosphorylation and degradation of IPA1 in response to salt stress to confer salt tolerance in rice

Salt stress adversely affects plant growth, development, and crop yield. Rice (Oryza sativa L.) is one of the most salt-sensitive cereal crops, especially at the early seedling stage. Mitogen-activated protein kinase (MAPK/MPK) cascades have been shown to play critical roles in salt response in Arabidopsis. However, the roles of the MPK cascade signaling in rice salt response and substrates of OsMPK remain largely unknown. Here, we report that the salt-induced OsMPK4-Ideal Plant Architecture 1 (IPA1) signaling pathway regulates the salt tolerance in rice. Under salt stress, OsMPK4 could interact with IPA1 and phosphorylate IPA1 at Thr180, leading to degradation of IPA1. Genetic evidence shows that IPA1 is a negative regulator of salt tolerance in rice, whereas OsMPK4 promotes salt response in an IPA1-dependent manner. Taken together, our results uncover an OsMPK4-IPA1 signal cascade that modulates the salt stress response in rice and sheds new light on the breeding of salt-tolerant rice varieties.

Ammonium transporter 1 increases rice resistance to sheath blight by promoting nitrogen assimilation and ethylene signalling

Sheath blight (ShB) significantly threatens rice yield production. However, the underlying mechanism of ShB defence in rice remains largely unknown. Here, we identified a highly ShB-susceptible mutant Ds-m which contained a mutation at the ammonium transporter 1;1 (AMT1;1) D³⁵⁸ N. AMT1;1 D³⁵⁸ N interacts with AMT1;1, AMT1;2 and AMT1;3 to inhibit the ammonium transport activity. The AMT1 RNAi was more susceptible and similar to the AMT1;1 D³⁵⁸ N mutant; however, plants with higher NH₄⁺ uptake activity were less susceptible to ShB. Glutamine synthetase 1;1 (GS1;1) mutant gs1;1 and overexpressors (GS1;1 OXs) were more and less susceptible to ShB respectively. Furthermore, AMT1;1 overexpressor (AMT1;1 OX)/gs1;1 and gs1;1 exhibited a similar response to ShB, suggesting that ammonium assimilation rather than accumulation controls the ShB defence. Genetic and physiological assays further demonstrated that plants with higher amino acid or chlorophyll content promoted rice resistance to ShB. Interestingly, the expression of ethylene-related genes was higher in AMT1;1 OX and lower in RNAi mutants than in wild-type. Also, ethylene signalling positively regulated rice resistance to ShB and NH₄⁺ uptake, suggesting that ethylene signalling acts downstream of AMT and also NH₄⁺ uptake is under feedback control. Taken together, our data demonstrated that the AMT1 promotes rice resistance to ShB via the regulation of diverse metabolic and signalling pathways.

OsEIL1 protects rice growth under NH4+ nutrition by regulating OsVTC1-3-dependent N-glycosylation and root NH4+ efflux

Rice is known for its superior adaptation to ammonium (NH₄⁺ ) as a nitrogen source. Compared to many other cereals, it displays lower NH₄⁺ efflux in roots and higher nitrogen-use efficiency on NH₄⁺ . A critical role for GDP-mannose pyrophosphorylase (VTC1) in controlling root NH₄⁺ fluxes was previously documented in Arabidopsis, but the molecular pathways involved in regulating VTC1-dependent NH₄⁺ efflux remain unclear. Here, we report that ETHYLENE-INSENSITIVE3-LIKE1 (OsEIL1) acts as a key transcription factor regulating OsVTC1-3-dependent NH₄⁺ efflux and protein N-glycosylation in rice grown under NH₄⁺ nutrition. We show that OsEIL1 in rice plays a contrasting role to Arabidopsis-homologous ETHYLENE-INSENSITIVE3 (AtEIN3) and maintains rice growth under NH₄⁺ by stabilizing protein N-glycosylation and reducing root NH₄⁺ efflux. OsEIL1 constrains NH₄⁺ efflux by activation of OsVTC1-3, but not OsVTC1-1 or OsVTC1-8. OsEIL1 binds directly to the promoter EIN3-binding site (EBS) of OsVTC1-3 in vitro and in vivo and acts to increase the transcription of OsVTC1-3. Our work demonstrates an important link between excessive root NH₄⁺ efflux and OsVTC1-3-mediated protein N-glycosylation in rice grown under NH₄⁺ nutrition and identifies OsEIL1 as a direct genetic regulator of OsVTC1-3 expression.

A viral protein orchestrates rice ethylene signaling to coordinate viral infection and insect vector-mediated transmission

Arthropod-borne viruses cause serious threats to human health and global agriculture by rapidly spreading via insect vectors. Southern rice black-streaked dwarf virus (SRBSDV) is the most damaging rice-infecting virus that is frequently transmitted by planthoppers. However, the molecular mechanisms underlying its propagation in the host plants and epidemics in the field are largely unknown. Here, we showed that the SRBSDV-encoded P6 protein is a key effector that regulates rice ethylene signaling to coordinate viral infection and transmission. In early SRBSDV infection, P6 interacts with OsRTH2 in the cytoplasm to activate ethylene signaling and enhance SRBSDV proliferation; this also repels the insect vector to reduce infestation. In late infection, P6 enters the nucleus, where it interacts with OsEIL2, a key transcription factor of ethylene signaling. The P6-OsEIL2 interaction suppresses ethylene signaling by preventing the dimerization of OsEIL2, thereby facilitating viral transmission by attracting the insect vector. Collectively, these findings reveal a novel molecular mechanism by which an arbovirus modulates the host defense system to promote viral infection and transmission.

Warm temperature compromises JA-regulated basal resistance to enhance Magnaporthe oryzae infection in rice

Changes in global temperatures profoundly affect the occurrence of plant diseases. It is well known that rice blast can easily become epidemic in relatively warm weather. However, the molecular mechanism remains unclear. In this study, we show that enhanced blast development at a warm temperature (22°C) compared with the normal growth temperature (28°C) is rice plant-determined. Comparative transcriptome analysis revealed that jasmonic acid (JA) biosynthesis and signaling genes in rice could be effectively induced by Magnaporthe oryzae at 28°C but not at 22°C. Phenotypic analyses of the osaoc1 and osmyc2 mutants, OsCOI1 RNAi lines, and OsMYC2-OE plants further demonstrated that compromised M. oryzae-induced JA biosynthesis and signaling lead to enhanced blast susceptibility at the warm temperature. Consistent with these results, we found that exogenous application of methyl jasmonate served as an effective strategy for improving blast resistance under the warm environmental conditions. Furthermore, decreased activation of JA signaling resulted in the downregulated expression of some key basal resistance genes at 22°C when compared with 28°C. Among these affected genes, OsCEBiP (chitin elicitor-binding protein precursor) was found to be directly regulated by OsMYB22 and its interacting protein OsMYC2, a key component of JA signaling, and this contributed to temperature-modulated blast resistance. Taken together, these results suggest that warm temperature compromises basal resistance in rice and enhances M. oryzae infection by reducing JA biosynthesis and signaling, providing potential new strategies for managing rice blast disease under warm climate conditions.

Orchestration of ethylene and gibberellin signals determines primary root elongation in rice

Primary root growth in cereal crops is fundamental for early establishment of the seedling and grain yield. In young rice (Oryza sativa) seedlings, the primary root grows rapidly for 7-10 days after germination and then stops; however, the underlying mechanism determining primary root growth is unclear. Here, we report that the interplay of ethylene and gibberellin (GA) controls the orchestrated development of the primary root in young rice seedlings. Our analyses advance the knowledge that primary root growth is maintained by higher ethylene production, which lowers bioactive GA contents. Further investigations unraveled that ethylene signaling transcription factor ETHYLENE INSENSITIVE3-LIKE 1 (OsEIL1) activates the expression of the GA metabolism genes GIBBERELLIN 2-OXIDASE 1 (OsGA2ox1), OsGA2ox2, OsGA2ox3, and OsGA2ox5, thereby deactivating GA activity, inhibiting cell proliferation in the root meristem, and ultimately gradually inhibiting primary root growth. Mutation in OsGA2ox3 weakened ethylene-induced GA inactivation and reduced the ethylene sensitivity of the root. Genetic analysis revealed that OsGA2ox3 functions downstream of OsEIL1. Taken together, we identify a molecular pathway impacted by ethylene during primary root elongation in rice and provide insight into the coordination of ethylene and GA signals during root development and seedling establishment.

Comparative Analysis of Seed Transcriptome and Coexpression Analysis Reveal Candidate Genes for Enhancing Seed Size/Weight in Brassica juncea

Seed size/weight is a multigenic trait that is governed by complex transcriptional regulatory pathways. An understanding of the genetic basis of seed size is of great interest in the improvement of seed yield and quality in oilseed crops. A global transcriptome analysis was performed at the initial stages of seed development in two lines of Brassica juncea, small-seeded EH-2 and large-seeded PJ. The anatomical analyses revealed significant differences in cell number and cell size in the outer layer of the seed coat between EH-2 and PJ. Pairwise comparisons at each developmental stage identified 5,974 differentially expressed genes (DEGs) between the two lines, of which 954 genes belong to different families of transcription factors. Two modules were found to be significantly correlated with an increased seed size using weighted gene coexpression network analysis. The DEG and coexpression datasets were integrated with the thousand seed weight (Tsw) quantitative trait loci (QTL) mapped earlier in the EPJ (EH-2 × PJ) doubled haploid (DH) population, which identified forty potential key components controlling seed size. The candidate genes included genes regulating the cell cycle, cell wall biogenesis/modification, solute/sugar transport, and hormone signaling. The results provide a valuable resource to widen the current understanding of regulatory mechanisms underlying seed size in B. juncea.

Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice (Oryza sativa L.)

Soil salinity poses a serious threat to the sustainable production of rice (Oryza sativa L.) throughout the world. Thus, the detection of loci and alleles responsible for salt tolerance is fundamental to accelerating the improvement of rice and producing the resilient varieties that will ensure future harvests. In this study, we collected a set of 191 mini-core rice populations from around the world, evaluated their salt tolerance based on plant growth and development phenotypes at the seedling stage, and divided a standard evaluation score (SES) of visual salt injury into five different grades. We used ∼3.82 million single nucleotide polymorphisms (SNPs) to identify 155 significant SNPs and 275 genes associated with salt sensitivity based on a genome-wide association study (GWAS) of SES. In particular, two candidate genes, ZFP179 and OsDSR2, were associated with salt tolerance, and OsHKT1;1 was co-detected in the entire GWAS of all the panels and indica. Additionally, we investigated the transcriptional changes in cultivars 93-11 and PA64s under normal and salinity stress conditions and found 517 co-upregulated and 223 co-downregulated genes. These differentially expressed genes (DEGs) were highly enriched in "response to chemical" and "stress" based on the gene ontology enrichment analysis. Notably, 30 candidate genes that were associated with the salt tolerance analysis were obtained by integrating GWAS and transcriptomic DEG analyses, including 13 cloned genes that had no reports of tolerance to salt and 17 candidate genes whose functions were unknown. To further explore these genes and their alleles, we performed haplotype analysis, genome-wide domestication detection, and transcriptome analysis to breed improved varieties. This data and the genetic resources provided will be valuable for the development of salt tolerant rice varieties.

Early responses to salt stress in quinoa genotypes with opposite behavior

Soil salinity is among the major abiotic stresses that plants must cope with, mainly in arid and semiarid regions. The tolerance to high salinity is an important agronomic trait to sustain food production. Quinoa is a halophytic annual pseudo-cereal species with high nutritional value that can secrete salt out of young leaves in external non-glandular cells called epidermal bladder cells (EBC). Previous work showed high salt tolerance, but low EBC density was associated with an improved response in the early phases of salinity stress, mediated by tissue-tolerance traits mainly in roots. We compared the transcript profiling of two quinoa genotypes with contrasting salt tolerance patterning to identify the candidate genes involved in the differentially early response among genotypes. The transcriptome profiling, supported by in vitro physiological analyses, provided insights into the early-stage molecular mechanisms, both at the shoot and root level, based on the sensitive/tolerance traits. Results showed the presence of numerous differentially expressed genes among genotypes, tissues, and treatments, with genes involved in hormonal and stress response upregulated mainly in the sensitive genotype, suggesting that tolerance may be correlated to restricted changes in gene expression, at least after a short salt stress. These data, showing constitutive differences between the two genotypes, represent a solid basis for further studies to characterize the salt tolerance traits. Additionally, new information provided by this work might be useful for the development of plant breeding or genome engineering programs in quinoa.

Regulatory short RNAs: A decade's tale for manipulating salt tolerance in plants

Salt stress is a globally increasing environmental detriment to crop growth and productivity. Exposure to salt stress evokes a complex medley of cellular signals, which rapidly reprogram transcriptional and metabolic networks to shape plant phenotype. To date, genetic engineering approaches were used with success to enhance salt tolerance; however, their performance is yet to be evaluated under realistic field conditions. Regulatory short non-coding RNAs (rsRNAs) are emerging as next-generation candidates for engineering salt tolerance in crops. In view of this, the present review provides a comprehensive analysis of a decade's worth of functional studies on non-coding RNAs involved in salt tolerance. Further, we have integrated this knowledge of rsRNA-mediated regulation with the current paradigm of salt tolerance to highlight two regulatory complexes (RCs) for regulating salt tolerance in plants. Finally, a knowledge-driven roadmap is proposed to judiciously utilize RC component(s) for enhancing salt tolerance in crops.

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.

Genetic and Molecular Factors Determining Grain Weight in Rice

Grain weight is one of the major factors determining single plant yield production of rice and other cereal crops. Research has begun to reveal the regulatory mechanisms underlying grain weight as well as grain size, highlighting the importance of this research for plant molecular biology. The developmental trait of grain weight is affected by multiple molecular and genetic aspects that lead to dynamic changes in cell division, expansion and differentiation. Additionally, several important biological pathways contribute to grain weight, such as ubiquitination, phytohormones, G-proteins, photosynthesis, epigenetic modifications and microRNAs. Our review integrates early and more recent findings, and provides future perspectives for how a more complete understanding of grain weight can optimize strategies for improving yield production. It is surprising that the acquired wealth of knowledge has not revealed more insights into the underlying molecular mechanisms. To accelerating molecular breeding of rice and other cereals is becoming an emergent and critical task for agronomists. Lastly, we highlighted the importance of leveraging gene editing technologies as well as structural studies for future rice breeding applications.

Analysis of Phytohormone Signal Transduction in Sophora alopecuroides under Salt Stress

Salt stress seriously restricts crop yield and quality, leading to an urgent need to understand its effects on plants and the mechanism of plant responses. Although phytohormones are crucial for plant responses to salt stress, the role of phytohormone signal transduction in the salt stress responses of stress-resistant species such as Sophora alopecuroides has not been reported. Herein, we combined transcriptome and metabolome analyses to evaluate expression changes of key genes and metabolites associated with plant hormone signal transduction in S. alopecuroides roots under salt stress for 0 h to 72 h. Auxin, cytokinin, brassinosteroid, and gibberellin signals were predominantly involved in regulating S. alopecuroides growth and recovery under salt stress. Ethylene and jasmonic acid signals may negatively regulate the response of S. alopecuroides to salt stress. Abscisic acid and salicylic acid are significantly upregulated under salt stress, and their signals may positively regulate the plant response to salt stress. Additionally, salicylic acid (SA) might regulate the balance between plant growth and resistance by preventing reduction in growth-promoting hormones and maintaining high levels of abscisic acid (ABA). This study provides insight into the mechanism of salt stress response in S. alopecuroides and the corresponding role of plant hormones, which is beneficial for crop resistance breeding.

Application of Upstream Open Reading Frames (uORFs) Editing for the Development of Stress-Tolerant Crops

Global population growth and climate change are posing increasing challenges to the production of a stable crop supply using current agricultural practices. The generation of genetically modified (GM) crops has contributed to improving crop stress tolerance and productivity; however, many regulations are still in place that limit their commercialization. Recently, alternative biotechnology-based strategies, such as gene-edited (GE) crops, have been in the spotlight. Gene-editing technology, based on the clustered regularly interspaced short palindromic repeats (CRISPR) platform, has emerged as a revolutionary tool for targeted gene mutation, and has received attention as a game changer in the global biotechnology market. Here, we briefly introduce the concept of upstream open reading frames (uORFs) editing, which allows for control of the translation of downstream ORFs, and outline the potential for enhancing target gene expression by mutating uORFs. We discuss the current status of developing stress-tolerant crops, and discuss uORF targets associated with salt stress-responsive genes in rice that have already been verified by transgenic research. Finally, we overview the strategy for developing GE crops using uORF editing via the CRISPR-Cas9 system. A case is therefore made that the mutation of uORFs represents an efficient method for developing GE crops and an expansion of the scope of application of genome editing technology.

Anesthetics and plants: no pain, no brain, and therefore no consciousness

Plants have a rich variety of interactions with their environment, including adaptive responses mediated by electrical signaling. This has prompted claims that information processing in plants is similar to that in animals and, hence, that plants are conscious, intelligent organisms. In several recent reports, the facts that general anesthetics cause plants to lose their sensory responses and behaviors have been taken as support for such beliefs. These lipophilic substances, however, alter multiple molecular, cellular, and systemic functions in almost every organism. In humans and other animals with complex brains, they eliminate the experience of pain and disrupt consciousness. The question therefore arises: do plants feel pain and have consciousness? In this review, we discuss what can be learned from the effects of anesthetics in plants. For this, we describe the mechanisms and structural prerequisites for pain sensations in animals and show that plants lack the neural anatomy and all behaviors that would indicate pain. By explaining the ubiquitous and diverse effects of anesthetics, we discuss whether these substances provide any empirical or logical evidence for "plant consciousness" and whether it makes sense to study the effects of anesthetics on plants for this purpose. In both cases, the answer is a resounding no.

Two Cyc2CL transcripts (Cyc2CL-1 and Cyc2CL-2) may play key roles in the petal and stamen development of ray florets in chrysanthemum

BACKGROUND

Chrysanthemum morifolium is one of the most popular ornamental crops. The capitulum, which is the main ornamental part of chrysanthemum plants, consists of ligulate marginal ray florets, an attractive corolla (petals), and radially hermaphroditic disc florets, but no stamens. In Asteraceae species, the zygomorphic ray florets evolved from the actinomorphic disc florets. During this process, the zygomorphic ligulate corolla arose and the stamens were aborted. Although molecular genetic research has clarified ray floret development to some extent, the precise molecular mechanism underlying ray floret development in chrysanthemum remained unclear.

RESULTS

A CYC2-like gene, Cyc2CL, was cloned from C. morifolium 'Fenditan'. Subsequent analyses revealed that the alternative splicing of Cyc2CL, which occurred in the flower differentiation stage, resulted in the production of Cyc2CL-1 and Cyc2CL-2 in the apical buds. Prior to this stage, only Cyc2CL-1 was produced in the apical buds. A fluorescence in situ hybridization analysis of labeled Cyc2CL-1 and Cyc2CL-2 RNA indicated that Cyc2CL-2 was first expressed in the involucre tissue during the final involucre differentiation stage, but was subsequently expressed in the receptacle and floret primordia as the floral bud differentiation stage progressed. Moreover, Cyc2CL-2 was highly expressed in the inflorescence tissue during the corolla formation stage, and the expression remained high until the end of the floral bud differentiation stage. Furthermore, the overexpression of Cyc2CL-1 and Cyc2CL-2 in transgenic Arabidopsis inhibited stamen and petal development. Therefore, both Cyc2CL-1 and Cyc2CL-2 encode candidate regulators of petal development and stamen abortion and are important for the ray floret development in chrysanthemum.

CONCLUSION

In this study, we characterized the alternatively spliced transcripts of the CYC2-like gene that differ subtly regarding expression and function. The data presented herein will be useful for clarifying the regulatory mechanisms associated with the CYC2-like gene and may also be important for identifying the key genes and molecular mechanisms controlling the development of ray florets in chrysanthemum.

Clock component OsPRR73 positively regulates rice salt tolerance by modulating OsHKT2;1-mediated sodium homeostasis

The roles of clock components in salt stress tolerance remain incompletely characterized in rice. Here, we show that, among OsPRR (Oryza sativa Pseudo-Response Regulator) family members, OsPRR73 specifically confers salt tolerance in rice. Notably, the grain size and yield of osprr73 null mutants were significantly decreased in the presence of salt stress, with accumulated higher level of reactive oxygen species and sodium ions. RNA sequencing and biochemical assays identified OsHKT2;1, encoding a plasma membrane-localized Na+ transporter, as a transcriptional target of OsPRR73 in mediating salt tolerance. Correspondingly, null mutants of OsHKT2;1 displayed an increased tolerance to salt stress. Immunoprecipitation-mass spectrometry (IP-MS) assays further identified HDAC10 as nuclear interactor of OsPRR73 and co-repressor of OsHKT2;1. Consistently, H3K9ac histone marks at OsHKT2;1 promoter regions were significantly reduced in osprr73 mutant. Together, our findings reveal that salt-induced OsPRR73 expression confers salt tolerance by recruiting HDAC10 to transcriptionally repress OsHKT2;1, thus reducing cellular Na+ accumulation. This exemplifies a new molecular link between clock components and salt stress tolerance in rice.

Ethylene Signaling Facilitates Plant Adaption to Physical Barriers

The morphological changes are usually observed in the terrestrial plants to respond to physical barriers. The phytohormone ethylene plays an essential role in the morphological development of plants encountering exogenous mechanical impedance, which enables plants to grow optimally in response to physical barriers. Ethylene is shown to regulate these developmental processes directly or in concert with other phytohormones, especially auxin. In this mini review, the involvement of ethylene action in seedling emergence from the soil, root movement within the soil, and parasitic plant invasion of the host plant are described.

Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms

Ethylene is a gaseous hormone which plays important roles in both plant growth and development and stress responses. Based on studies in the dicot model plant species Arabidopsis, a linear ethylene signaling pathway has been established, according to which ethylene is perceived by ethylene receptors and transduced through CONSTITUTIVE TRIPLE RESPONSE 1 (CTR1) and ETHYLENE-INSENSITIVE 2 (EIN2) to activate transcriptional reprogramming. In addition to this canonical signaling pathway, an alternative ethylene receptor-mediated phosphor-relay pathway has also been proposed to participate in ethylene signaling. In contrast to Arabidopsis, rice, a monocot, grows in semiaquatic environments and has a distinct plant structure. Several novel regulators and/or mechanisms of the rice ethylene signaling pathway have recently been identified, indicating that the ethylene signaling pathway in rice has its own unique features. In this review, we summarize the latest progress and compare the conserved and divergent aspects of the ethylene signaling pathway between Arabidopsis and rice. The crosstalk between ethylene and other plant hormones is also reviewed. Finally, we discuss how ethylene regulates plant growth, stress responses and agronomic traits. These analyses should help expand our knowledge of the ethylene signaling mechanism and could further be applied for agricultural purposes.

Advances and Challenges in the Breeding of Salt-Tolerant Rice

Soil salinization and a degraded ecological environment are challenging agricultural productivity and food security. Rice (Oryza sativa), the staple food of much of the world’s population, is categorized as a salt-susceptible crop. Improving the salt tolerance of rice would increase the potential of saline-alkali land and ensure food security. Salt tolerance is a complex quantitative trait. Biotechnological efforts to improve the salt tolerance of rice hinge on a detailed understanding of the molecular mechanisms underlying salt stress tolerance. In this review, we summarize progress in the breeding of salt-tolerant rice and in the mapping and cloning of genes and quantitative trait loci (QTLs) associated with salt tolerance in rice. Furthermore, we describe biotechnological tools that can be used to cultivate salt-tolerant rice, providing a reference for efforts aimed at rapidly and precisely cultivating salt-tolerance rice varieties.

How Plant Hormones Mediate Salt Stress Responses

Salt stress is one of the major environmental stresses limiting plant growth and productivity. To adapt to salt stress, plants have developed various strategies to integrate exogenous salinity stress signals with endogenous developmental cues to optimize the balance of growth and stress responses. Accumulating evidence indicates that phytohormones, besides controlling plant growth and development under normal conditions, also mediate various environmental stresses, including salt stress, and thus regulate plant growth adaptation. In this review, we mainly discuss and summarize how plant hormones mediate salinity signals to regulate plant growth adaptation. We also highlight how, in response to salt stress, plants build a defense system by orchestrating the synthesis, signaling, and metabolism of various hormones via multiple crosstalks.

A brief appraisal of ethylene signaling under abiotic stress in plants

For years, ethylene has been known to humankind as the plant hormone responsible for fruit ripening. However, the multitasking aspect of ethylene is still being investigated as ever. It is one of the most diversified signaling molecules which acclimatize plant under adverse conditions. It promotes adventitious root formation, stem and petiole elongation, opening and closing of stomatal aperture, reduces salinity and metal stress, etc. Presence of ethylene checks the production and scavenging of reactive oxygen species by strengthening the antioxidant machinery. Meanwhile, it interacts with other signaling molecules and initiates a cascade of adaptive responses. In the present mini review, the biosynthesis and sources of ethylene production, interaction with other signaling molecules, and its exogenous application under different abiotic stresses have been discussed.

Molecular Mechanisms Supporting Rice Germination and Coleoptile Elongation under Low Oxygen

Rice germinates under submergence by exploiting the starch available in the endosperm and translocating sugars from source to sink organs. The availability of fermentable sugar under water allows germination with the protrusion of the coleoptile, which elongates rapidly and functions as a snorkel toward the air above. Depending on the variety, rice can produce a short or a long coleoptile. Longer length entails the involvement of a functional transport of auxin along the coleoptile. This paper is an overview of rice coleoptiles and the studies undertaken to understand its functioning and role under submergence.

Ethylene: A Master Regulator of Salinity Stress Tolerance in Plants

Salinity stress is one of the major threats to agricultural productivity across the globe. Research in the past three decades, therefore, has focused on analyzing the effects of salinity stress on the plants. Evidence gathered over the years supports the role of ethylene as a key regulator of salinity stress tolerance in plants. This gaseous plant hormone regulates many vital cellular processes starting from seed germination to photosynthesis for maintaining the plants' growth and yield under salinity stress. Ethylene modulates salinity stress responses largely via maintaining the homeostasis of Na+/K+, nutrients, and reactive oxygen species (ROS) by inducing antioxidant defense in addition to elevating the assimilation of nitrates and sulfates. Moreover, a cross-talk of ethylene signaling with other phytohormones has also been observed, which collectively regulate the salinity stress responses in plants. The present review provides a comprehensive update on the prospects of ethylene signaling and its cross-talk with other phytohormones to regulate salinity stress tolerance in plants.

Role of ethylene crosstalk in seed germination and early seedling development: A review

Seed germination and early seedling development are two critical phases in plant lifecycle that largely determine crop yield. Phytohormones play an essential role in governing these developmental processes; of these, ethylene (ET; C₂H₄), the smallest gaseous hormone, plays a major role via crosstalk with other hormones. Typically, the mechanism of hormone (for instance, auxin, cytokinins, ET, and gibberellins) action is determined by cellular context, revealing either synergistic or antagonistic relations. Significant progress has been made, so far, on unveiling ET crosstalk with other hormones and environmental signals, such as light. In particular, stimulatory and inhibitory effects of ET on hypocotyl growth in light and dark, respectively, and its interaction with other hormones provide an ideal model to study the growth-regulatory pathways. In this review, we aim at exploring the mechanisms of multifarious phenomena that occur via ET crosstalk during the germination of seeds (overcoming dormancy), and all through the development of seedlings. Understanding the remarkably complex mechanism of ET crosstalk that emerges from the interaction between hormones and other molecular players to modulate plant growth, remains a challenge in plant developmental biology.

Transitions in wheat endosperm metabolism upon transcriptional induction of oil accumulation by oat endosperm WRINKLED1

BACKGROUND

Cereal grains, including wheat (Triticum aestivum L.), are major sources of food and feed, with wheat being dominant in temperate zones. These end uses exploit the storage reserves in the starchy endosperm of the grain, with starch being the major storage component in most cereal species. However, oats (Avena sativa L.) differs in that the starchy endosperm stores significant amounts of oil. Understanding the control of carbon allocation between groups of storage compounds, such as starch and oil, is therefore important for understanding the composition and hence end use quality of cereals. WRINKLED1 is a transcription factor known to induce triacylglycerol (TAG; oil) accumulation in several plant storage tissues.

RESULTS

An oat endosperm homolog of WRI1 (AsWRI1) expressed from the endosperm-specific HMW1Dx5 promoter resulted in drastic changes in carbon allocation in wheat grains, with reduced seed weight and a wrinkled seed phenotype. The starch content of mature grain endosperms of AsWRI1-wheat was reduced compared to controls (from 62 to 22% by dry weight (dw)), TAG was increased by up to nine-fold (from 0.7 to 6.4% oil by dw) and sucrose from 1.5 to 10% by dw. Expression of AsWRI1 in wheat grains also resulted in multiple layers of elongated peripheral aleurone cells. RNA-sequencing, lipid analyses, and pulse-chase experiments using ¹⁴C-sucrose indicated that futile cycling of fatty acids could be a limitation for oil accumulation.

CONCLUSIONS

Our data show that expression of oat endosperm WRI1 in the wheat endosperm results in changes in metabolism which could underpin the application of biotechnology to manipulate grain composition. In particular, the striking effect on starch synthesis in the wheat endosperm indicates that an important indirect role of WRI1 is to divert carbon allocation away from starch biosynthesis in plant storage tissues that accumulate oil.

The GDSL Lipase MHZ11 Modulates Ethylene Signaling in Rice Roots

Ethylene plays important roles in plant growth and development, but the regulation of ethylene signaling is largely unclear, especially in crops such as rice (Oryza sativa). Here, by analysis of the ethylene-insensitive mutant mao huzi 11 (mhz11), we identified the GDSL lipase MHZ11, which modulates ethylene signaling in rice roots. MHZ11 localized to the endoplasmic reticulum membrane and has acyl-hydrolyzing activity. This activity affects the homeostasis of sterols in rice roots and is required for root ethylene response. MHZ11 overexpression caused constitutive ethylene response in roots. Genetically, MHZ11 acts with the ethylene receptor ETHYLENE RESPONSE SENSOR2 (OsERS2) upstream of CONSTITUTIVE TRIPLE RESPONSE2 (OsCTR2) and ETHYLENE INSENSITIVE2 (OsEIN2). The mhz11 mutant maintains more OsCTR2 in the phosphorylated form whereas MHZ11 overexpression promotes ethylene-mediated inhibition of OsCTR2 phosphorylation. MHZ11 colocalized with the ethylene receptor OsERS2, and its effect on OsCTR2 phosphorylation requires ethylene perception and initiation of ethylene signaling. The mhz11 mutant overaccumulated sterols and blocking sterol biosynthesis partially rescued the mhz11 ethylene response, likely by reducing receptor-OsCTR2 interaction and OsCTR2 phosphorylation. We propose that MHZ11 reduces sterol levels to impair receptor-OsCTR2 interactions and OsCTR2 phosphorylation for triggering ethylene signaling. Our study reveals a mechanism by which MHZ11 participates in ethylene signaling for regulation of root growth in rice.

Physiological and transcriptomic analyses reveal the mechanisms underlying the salt tolerance of Zoysia japonica Steud

BACKGROUND

Areas with saline soils are sparsely populated and have fragile ecosystems, which severely restricts the sustainable development of local economies. Zoysia grasses are recognized as excellent warm-season turfgrasses worldwide, with high salt tolerance and superior growth in saline-alkali soils. However, the mechanism underlying the salt tolerance of Zoysia species remains unknown.

RESULTS

The phenotypic and physiological responses of two contrasting materials, Zoysia japonica Steud. Z004 (salt sensitive) and Z011 (salt tolerant) in response to salt stress were studied. The results show that Z011 was more salt tolerant than was Z004, with the former presenting greater K+/Na+ ratios in both its leaves and roots. To study the molecular mechanisms underlying salt tolerance further, we compared the transcriptomes of the two materials at different time points (0 h, 1 h, 24 h, and 72 h) and from different tissues (leaves and roots) under salt treatment. The 24-h time point and the roots might make significant contributions to the salt tolerance. Moreover, GO and KEGG analyses of different comparisons revealed that the key DEGs participating in the salt-stress response belonged to the hormone pathway, various TF families and the DUF family.

CONCLUSIONS

Zoysia salt treatment transcriptome shows the 24-h and roots may make significant contributions to the salt tolerance. The auxin signal transduction family, ABA signal transduction family, WRKY TF family and bHLH TF family may be the most important families in Zoysia salt-stress regulation.

Ethylene insensitive3-like2 (OsEIL2) confers stress sensitivity by regulating OsBURP16, the β subunit of polygalacturonase (PG1β-like) subfamily gene in rice

The transcription factors EIN3 (ETHYLENE-INSENSITIVE 3) and EILs (EIN3-Likes) play important roles in plant development and defense responses; however, their mechanism in these processes remain unclear. Here, we report that OsEIL2, an EIN3-like transcription factor from rice (Oryza sativa), plays important roles in abiotic stress and leaf senescence. OsEIL2 is a nuclear-localized protein with transactivation activity in the C-terminus (amino acids 344-583) and can be induced by NaCl, polyethylene glycol (PEG), dark, and abscisic acid (ABA) treatment. Transgenic plants of overexpressing OsEIL2 (OsEIL2-OX) show reduced tolerance to salt and drought stress compared with the controls. While the transgenic plants of overexpressing OsEIL2-RNA interference (OsEIL2-RNAi) exhibit enhanced tolerance to salt and drought stress compared with the controls. Moreover, seedlings of OsEIL2-overexpressing transgenic plants exhibit delayed leaf development and an accelerated dark-induced senescence phenotype, whereas OsEIL2-RNAi plants display the opposite phenotype. We further found that OsEIL2 functions upstream of OsBURP14 and OsBURP16. OsBURP14 and OsBURP16 are the members of the β subunit of polygalacturonase subfamilies. OsBURP16 overexpression reduced pectin content and cell adhesion and increased abiotic stress sensitivity in rice. OsEIL2 binds directly to the promoter of OsBURP14 and OsBURP16 and activates their transcript levels. We also found that OsEIL2 overexpression decreased the pectin content by increasing polygalacturonase (PG) activity. Taken together, these results revealed a new mechanism of OsEIL2 in abiotic stress responses. These findings provide new insights into plant resistance to abiotic stress.

Research advances of WRINKLED1 (WRI1) in plants

WRINKLED 1 (WRI1), a member of the AP2/EREBP class of transcription factors, regulates carbon allocation between the glycolytic and fatty acid biosynthetic pathways and plays important roles in other biological events. Previous studies have suggested that post-translational modifications and interacting partners modulate the activity of WRI1. We systematically summarised the structure of WRI1 as well as its molecular interactions during transcription and translation in plants. This work elucidates the genetic evolution and regulatory functions of WRI1 at the molecular level and describes a new pathway involving WRI1 that can be used to produce triacylglycerols (TAGs) in plants.

Histidine kinase MHZ1/OsHK1 interacts with ethylene receptors to regulate root growth in rice

Ethylene plays essential roles during adaptive responses to water-saturating environments in rice, but knowledge of its signaling mechanism remains limited. Here, through an analysis of a rice ethylene-response mutant mhz1, we show that MHZ1 positively modulates root ethylene responses. MHZ1 encodes the rice histidine kinase OsHK1. MHZ1/OsHK1 is autophosphorylated at a conserved histidine residue and can transfer the phosphoryl signal to the response regulator OsRR21 via the phosphotransfer proteins OsAHP1/2. This phosphorelay pathway is required for root ethylene responses. Ethylene receptor OsERS2, via its GAF domain, physically interacts with MHZ1/OsHK1 and inhibits its kinase activity. Genetic analyses suggest that MHZ1/OsHK1 acts at the level of ethylene perception and works together with the OsEIN2-mediated pathway to regulate root growth. Our results suggest that MHZ1/OsHK1 mediates the ethylene response partially independently of OsEIN2, and is directly inhibited by ethylene receptors, thus revealing mechanistic details of ethylene signaling for root growth regulation.

Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.

Novel crosstalk between ethylene- and jasmonic acid-pathway responses to a piercing-sucking insect in rice

Ethylene (ET) and jasmonic acid (JA) play important roles in plant defenses against biotic stresses. Crosstalk between JA and ET has been well studied in mediating pathogen resistance, but its roles in piercing-sucking insect resistance are unclear. The brown planthopper (BPH; Nilaparvata lugens) is the most notorious piercing-sucking insect specific to rice (Oryza sativa) that severely affects yield. A genetic analysis revealed that OsEBF1 and OsEIL1, which are in the ET signaling pathway, positively and negatively regulated BPH resistance, respectively. Molecular and biochemical analyses revealed direct interactions between OsEBF1 and OsEIL1. OsEBF1, an E3 ligase, mediated the degradation of OsEIL1 through the ubiquitination pathway, indicating the negative regulation of the ET-signaling pathway in response to BPH infestation. An RNA sequencing analysis revealed that a JA biosynthetic pathway-related gene, OsLOX9, was downregulated significantly in the oseil1 mutant. Biochemical analyses, including yeast one-hybrid, dual luciferase, and electrophoretic mobility shift assay, confirmed the direct regulation of OsLOX9 by OsEIL1. This study revealed the synergistic and negative regulation of JA and ET pathways in response to piercing-sucking insect attack. The synergistic mechanism was realized by transcriptional regulation of OsEIL1 on OsLOX9. OsEIL1-OsLOX9 is a novel crosstalk site in these two phytohormone signaling pathways.

A class B heat shock factor selected for during soybean domestication contributes to salt tolerance by promoting flavonoid biosynthesis

Soybean (Glycine max) production is severely affected in unfavorable environments. Identification of the regulatory factors conferring stress tolerance would facilitate soybean breeding. In this study, through coexpression network analysis of salt-tolerant wild soybeans, together with molecular and genetic approaches, we revealed a previously unidentified function of a class B heat shock factor, HSFB2b, in soybean salt stress response. We showed that HSFB2b improves salt tolerance through the promotion of flavonoid accumulation by activating one subset of flavonoid biosynthesis-related genes and by inhibiting the repressor gene GmNAC2 to release another subset of genes in the flavonoid biosynthesis pathway. Moreover, four promoter haplotypes of HSFB2b were identified from wild and cultivated soybeans. Promoter haplotype II from salt-tolerant wild soybean Y20, with high promoter activity under salt stress, is probably selected for during domestication. Another promoter haplotype, III, from salt-tolerant wild soybean Y55, had the highest promoter activity under salt stress, had a low distribution frequency and may be subjected to the next wave of selection. Together, our results revealed the mechanism of HSFB2b in soybean salt stress tolerance. Its promoter variations were identified, and the haplotype with high activity may be adopted for breeding better soybean cultivars that are adapted to stress conditions.

MiR319 mediated salt tolerance by ethylene

Salinity-induced accumulation of certain microRNAs accompanied by gaseous phytohormone ethylene production has been recognized as a mechanism of plant salt tolerance. MicroRNA319 (miR319) has been characterized as an important player in abiotic stress resistance in some C3 plants, such as Arabidopsis thaliana and rice. However, its role in the dedicated biomass plant switchgrass (Panicum virgatum L.), a C4 plant, has not been reported. Here, we show crosstalk between miR319 and ethylene (ET) for increasing salt tolerance. By overexpressing Osa-MIR319b and a target mimicry form of miR319 (MIM319), we showed that miR319 positively regulated ET synthesis and salt tolerance in switchgrass. By experimental treatments, we demonstrated that ET-mediated salt tolerance in switchgrass was dose-dependent, and miR319 regulated the switchgrass salt response by fine-tuning ET synthesis. Further experiments showed that the repression of a miR319 target, PvPCF5, in switchgrass also led to enhanced ethylene accumulation and salt tolerance in transgenic plants. Genome-wide transcriptome analysis demonstrated that overexpression of miR319 (OE-miR319) down-regulated the expression of key genes in the methionine (Met) cycle but promoted the expression of genes in ethylene synthesis. The results enrich our understanding of the synergistic effects of the miR319-PvPCF5 module and ethylene synthesis in the salt tolerance of switchgrass, a C4 bioenergy plant.

OsLUGL is involved in the regulating auxin level and OsARFs expression in rice (Oryza sativa L.)

Specification of floral organ identity is critical for floral morphology and inflorescence architecture. Floral organ identity in plants is controlled by floral homeotic A/B/C/D/E-class genes. Although multiple genes regulate floral organogenesis, our understanding of the regulatory network remains fragmentary. Here, we characterized a rice floral organ gene KAIKOUXIAO (KKX), mutation of which produces an uncharacteristic open hull, abnormal seed and semi-sterility. KKX encodes a putative LEUNIG-like (LUGL) transcriptional regulator OsLUGL. OsLUGL is preferentially expressed in young panicles and its protein can interact with OsSEU, which functions were reported as an adaptor for LEUNIG. OsLUGL-OsSEU functions together as a transcriptional co-regulatory complex to control organ identity. SEP3 (such as OsMADS8) and AP1 (such as OsMADS18) serve as the DNA-binding partner of OsLUGL-OsSEU complex. Further studies indicated that OsMADS8 and OsMADS18 could bind to the promoter of OsGH3-8. The altered expression of OsGH3-8 might cause the increased auxin level and the decreased expression of OsARFs. Overall, our results demonstrate a possible pathway whereby OsLUGL-OsSEU-OsAP1-OsSEP3 complex as a transcriptional co-regulator by targeting the promoter of OsGH3-8, then affecting auxin level, OsARFs expression and thereby influencing floral development. These findings provide a valuable insight into the molecular functions of OsLUGL in rice floral development.

GhEIN3, a cotton (Gossypium hirsutum) homologue of AtEIN3, is involved in regulation of plant salinity tolerance

Ethylene insensitive 3 (EIN3), a key transcription factor in ethylene signal transduction, play important roles in plant stress signaling pathways. In this study, we isolated and characterized an EIN3-like gene from cotton (Gossypium hirsutum), designated as GhEIN3. GhEIN3 is highly expressed in vegetative tissues, and its expression is induced by 1-aminocyclopropane-1-carboxylic acid (ACC) and NaCl. Ectopic expression of GhEIN3 in Arabidopsis elevated plants' response to ethylene, which exhibit smaller leaves, more root hairs, shorter roots and hypocotyls. The germination rate, survival rate and root length of GhEIN3 transgenic plants were significantly improved compared to wild type under salt stress. GhEIN3 transgenic plants accumulated less H₂O₂ and malondialdehyde (MDA), while higher superoxide dismutase (SOD) and peroxidase (POD) activities were detected under salt stress. In addition, expression of several genes related to reactive oxygen species (ROS) pathway and ABA signaling pathway was increased in the GhEIN3 transgenic plants under salt stress. In contrast, virus-induced gene silencing (VIGS) of GhEIN3 in cotton enhanced the sensitivity of transgenic plants to salt stress, accumulating higher H₂O₂ and MDA and lower SOD and POD activities compared to control plants. Collectively, our results revealed that GhEIN3 might be involved in the regulation of plant response to salt stress by regulating ABA and ROS pathway during plant growth and development.

Transcriptomic and phosphoproteomic profiling and metabolite analyses reveal the mechanism of NaHCO3-induced organic acid secretion in grapevine roots

BACKGROUND

Organic acid secretion is a widespread physiological response of plants to alkalinity. However, the characteristics and underlying mechanism of the alkali-induced secretion of organic acids are poorly understood.

RESULTS

Oxalate was the main organic acid synthesized and secreted in grapevine (a hybrid of Vitis amurensis, V. berlandieri and V. riparia) roots, while acetate synthesis and malate secretion were also promoted under NaHCO₃ stress. NaHCO₃ stress enhanced the H⁺ efflux rate of grapevine roots, which is related to the plasma membrane H⁺-ATPase activity. Transcriptomic profiling revealed that carbohydrate metabolism was the most significantly altered biological process under NaHCO₃ stress; a total of seven genes related to organic acid metabolism were significantly altered, including two phosphoenolpyruvate carboxylases and phosphoenolpyruvate carboxylase kinases. Additionally, the expression levels of five ATP-binding cassette transporters, particularly ATP-binding cassette B19, and two Al-activated malate transporter 2 s were substantially upregulated by NaHCO₃ stress. Phosphoproteomic profiling demonstrated that the altered phosphoproteins were primarily related to binding, catalytic activity and transporter activity in the context of their molecular functions. The phosphorylation levels of phosphoenolpyruvate carboxylase 3, two plasma membrane H⁺-ATPases 4 and ATP-binding cassette B19 and pleiotropic drug resistance 12 were significantly increased. Additionally, the inhibition of ethylene synthesis and perception completely blocked NaHCO₃-induced organic acid secretion, while the inhibition of indoleacetic acid synthesis reduced NaHCO₃-induced organic acid secretion.

CONCLUSIONS

Our results demonstrated that oxalate was the main organic acid produced under alkali stress and revealed the necessity of ethylene in mediating organic acid secretion. Additionally, we further identified several candidate genes and phosphoproteins responsible for organic acid metabolism and secretion.

Rice OsDOF15 contributes to ethylene-inhibited primary root elongation under salt stress

In early seedlings, the primary root adapts rapidly to environmental changes through the modulation of endogenous hormone levels. The phytohormone ethylene inhibits primary root elongation, but the underlying molecular mechanism of how ethylene-reduced root growth is modulated in environmental changes remains poorly understood. Here, we show that a novel rice (Oryza sativa) DOF transcription factor OsDOF15 positively regulates primary root elongation by regulating cell proliferation in the root meristem, via restricting ethylene biosynthesis. Loss-of-function of OsDOF15 impaired primary root elongation and cell proliferation in the root meristem, whereas OsDOF15 overexpression enhanced these processes, indicating that OsDOF15 is a key regulator of primary root elongation. This regulation involves the direct interaction of OsDOF15 with the promoter of OsACS1, resulting in the repression of ethylene biosynthesis. The control of ethylene biosynthesis by OsDOF15 in turn regulates cell proliferation in the root meristem. OsDOF15 transcription is repressed by salt stress, and OsDOF15-mediated ethylene biosynthesis plays a role in inhibition of primary root elongation by salt stress. Thus, our data reveal how the ethylene-inhibited primary root elongation is finely controlled by OsDOF15 in response to environmental signal, a novel mechanism of plants responding to salt stress and transmitting the information to ethylene biosynthesis to restrict root elongation.

The EIL transcription factor family in soybean: Genome-wide identification, expression profiling and genetic diversity analysis

The ETHYLENE INSENSITIVE3-LIKE (EIL) transcription factor family plays a critical role in the ethylene signaling pathway, which regulates a broad spectrum of plant growth and developmental processes, as well as defenses to myriad stresses. Although genome-wide analysis of this family has been carried out for several plant species, no comprehensive analysis of the EIL gene family in soybean has been reported so far. Furthermore, there are few studies on the functions of EIL genes in soybean. In this study, we identified 12 soybean (Gm) EIL genes, which we divided into three groups based on their phylogenetic relationships. We then detected their duplication status and found that most of the GmEIL genes have duplicated copies derived from two whole-genome duplication events. These duplicated genes underwent strong negative selection during evolution. We further analyzed the transcript profiles of GmEIL genes using the transcriptome data and found that their spatio-temporal and stress expression patterns varied considerably. For example, GmEIL1-GmEIL5 were found to be strongly expressed in almost every sample, while GmEIL8-GmEIL12 exhibited low expression, or were not expressed at all. Additionally, these genes showed different responses to dehydration, salinity and phosphate starvation. Finally, we surveyed genetic variations of these genes in 302 resequenced wild soybeans, landraces and improved soybean cultivars. Our data showed that most GmEIL genes are well conserved, and are not modified in domesticated or improved cultivars. Together, these findings provide a potentially valuable resource for characterizing the GmEIL gene family and lay the basis for further elucidation of their molecular mechanisms.

Cytosolic lipid droplets as engineered organelles for production and accumulation of terpenoid biomaterials in leaves

Cytosolic lipid droplets are endoplasmic reticulum-derived organelles typically found in seeds as reservoirs for physiological energy and carbon to fuel germination. Here, we report synthetic biology approaches to co-produce high-value sesqui- or diterpenoids together with lipid droplets in plant leaves. The formation of cytosolic lipid droplets is enhanced in the transient Nicotiana benthamiana system through ectopic production of WRINKLED1, a key regulator of plastid fatty acid biosynthesis, and a microalgal lipid droplet surface protein. Engineering of the pathways providing the universal C5-building blocks for terpenoids and installation of terpenoid biosynthetic pathways through direction of the enzymes to native and non-native compartments boost the production of target terpenoids. We show that anchoring of distinct biosynthetic steps onto the surface of lipid droplets leads to efficient production of terpenoid scaffolds and functionalized terpenoids. The co-produced lipid droplets "trap" the terpenoids in the cells.

Analysing the rice young panicle transcriptome reveals the gene regulatory network controlled by TRIANGULAR HULL1

BACKGROUND

TRIANGULAR HULL1 (TH1), a member of the rice ALOG gene family, has been characterized as a rice lemma/palea-related gene. To understand the gene regulatory network that controlled by TH1, we analyzed the transcriptome from a TH1 knock out (KO) line, which was generated by CRISPR/Cas9. Our study may shed some light on the molecular mechanism of lemma/palea development.

RESULTS

We obtained 20 T₀ th1-C transgenic plants by CRISPR/Cas9. Among the 20 plants, there were eight bi-allelic mutations, five homozygous mutations, three heterozygous mutations, and four Non-KO plants. By comparing with the wild type and the heterozygous knock out (KO) line, the homozygous KO lines showed defects in lemma/palea development as well as in grain filling. Further more, we studied the gene regulatory network that controlled by TH1 by comparing the transcriptome of a homozygous TH1 KO line with its Non-KO line as a control. A total of 622 genes were identified as differentially expressed genes (DEGs), of which 297 genes were significantly up-regulated while 325 genes were down-regulated. One hundred thirty eight of the DEGs were assigned to the 59 KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways. Among these annotated DEGs, 15 genes were related to plant hormone signal transduction, eight genes were related to starch and sucrose metabolism. These were the two largest groups of DEGs according to the KEGG pathway analysis.

CONCLUSIONS

Our results indicated that hormone related genes and starch/sucrose metabolism related genes might act as downstream targets of TH1; they might be responsible for lemma/palea development and grain filling respectively.

Overexpression of OsARD1 Improves Submergence, Drought, and Salt Tolerances of Seedling Through the Enhancement of Ethylene Synthesis in Rice

Acireductone dioxygenase (ARD) is a metal-binding metalloenzyme and involved in the methionine salvage pathway. In rice, OsARD1 binds Fe²⁺ and catalyzes the formation of 2-keto-4-methylthiobutyrate (KMTB) to produce methionine, which is an initial substrate in ethylene synthesis pathway. Here, we report that overexpression of OsARD1 elevates the endogenous ethylene release rate, enhances the tolerance to submergence stress, and reduces the sensitivity to drought, salt, and osmotic stresses in rice. OsARD1 is strongly induced by submergence, drought, salinity, PEG6000, and mechanical damage stresses and exhibits high expression level in senescent leaves. Transgenic plants overexpressing OsARD1 (OsARD1-OE) display fast elongation growth to escape submergence stress. The ethylene content is significantly maximized in OsARD1-OE plants compared with the wide type. OsARD1-OE plants display increased shoot elongation and inhibition of root elongation under the submergence stress and grow in dark due to increase of ethylene. The elongation of coleoptile under anaerobic germination is also significantly promoted in OsARD1-OE lines due to the increase of ethylene content. The sensitivity to drought and salt stresses is reduced in OsARD1-OE transgenic lines. Water holding capacity is enhanced, and the stomata and trichomes on leaves increase in OsARD1-OE lines. Drought and salt tolerance and ethylene synthesis-related genes are upregulated in OsARD1-OE plants. Subcellular localization shows that OsARD1 displays strong localization signal in cell nucleus, suggesting OsARD1 may interact with the transcription factors. Taken together, the results provide the understanding of the function of OsARD1 in ethylene synthesis and abiotic stress response in rice.