Functions and application of the AP2/ERF transcription factor family in crop improvement

Identification of ERF genes in peanuts and functional analysis of AhERF008 and AhERF019 in abiotic stress response

Ethylene-responsive factor (ERF) play an important role in regulating gene expression in plant development and response to stresses. In peanuts (Arachis hypogaea L.), which produce flowers aerially and pods underground, only a few ERF genes have been identified so far. This study identifies 63 ERF unigenes from 247,313 peanut EST sequences available in the NCBI database. The phylogeny, gene structures, and putative conserved motifs in the peanut ERF proteins were analysed. Comparative analysis revealed the absence of two subgroups (A1 and A3) of the ERF family in peanuts; only 10 subgroups were identified in peanuts compared to 12 subgroups in Arabidopsis and soybeans. AP2/ERF domains were found to be conserved among peanuts, Arabidopsis, and soybeans. Outside the AP2/ERF domain, many soybean-specific conserved motifs were also detected in peanuts. The expression analysis of ERF family genes representing each clade revealed differential expression patterns in response to biotic and abiotic stresses. Overexpression of AhERF008 influenced the root gravity of Arabidopsis, whereas overexpression of AhERF019 enhanced tolerance to drought, heat, and salt stresses in Arabidopsis. The information generated in this study will be helpful to further investigate the function of ERFs in plant development and stress response.

Scratching the surface: genetic regulation of cuticle assembly in fleshy fruit

The hydrophobic cuticular membrane of land plants performs a number of important roles during fruit development, including protection from a range of abiotic and biotic stresses. The components of the fleshy fruit cuticle are synthesized and secreted from the epidermal cells. While the biosynthetic and transport pathways of the cuticle have been thoroughly investigated for a number of decades, the regulatory mechanisms allowing fine tuning of cuticle deposition are only now beginning to be elucidated. Transcription factors belonging to the APETALA2, homeodomain-leucine zipper IV, and MYB families have been shown to be important regulators of both cuticle biosynthesis and epidermal cell differentiation, highlighting the connection between these processes. The involvement of MADS-box transcription factors demonstrates the link between fruit ripening and cuticle deposition. Epigenetic and post-transcriptional regulatory mechanisms also play a role in the control of cuticle biosynthesis, in addition to phytohormones, such as abscisic acid, that have been shown to stimulate cuticle deposition. These various levels of genetic regulation allow the plant constantly to maintain and adjust the cuticle in response to environmental and developmental cues.

Overexpression of a pepper CaERF5 gene in tobacco plants enhances resistance to Ralstonia solanacearum infection

ETHYLENE RESPONSE FACTORs (ERF) transcription factors (TFs) constitute a large transcriptional regulator family belonging to the AP2/ERF superfamily and are implicated in a range of biological processes. However, the specific roles of individual ERF family members in biotic or abiotic stress responses and the underlying molecular mechanism still need to be elucidated. In the present study, a cDNA encoding a member of ethylene response factor (ERF) transcription factor, CaERF5, was isolated from pepper. Sequence analysis showed that CaERF5 contains a typical 59 amino acid AP2/ERF DNA-binding domain, two highly conserved amino acid residues (14th alanine (A) and 19th aspartic acid (D)), a putative nuclear localisation signal (NLS), a CMIX-2 motif in the N-terminal region and two putative MAP kinase phosphorylation site CMIX-5 and CMIX-6 motifs. It belongs to group IXb of the ERF subfamily. A CaERF5-green fluorescence protein (GFP) fusion transiently expressed in onion epidermal cells localised to the nucleus. CaERF5 transcripts were induced by Ralstonia solanacearum infection, salicylic acid (SA), methyl jasmonate (MeJA) and ethephon (ETH) treatments. Constitutive expression of the CaERF5 gene in tobacco plants upregulated transcript levels of a set of defence- related genes and enhanced resistance to R. solanacearum infection. Our results suggest that CaERF5 acts as a positive regulator in plant resistance to R. solanacearum infection and show that overexpression of this transcription factor can be used as a tool to enhance disease resistance in crop species.

Genome-wide analysis of the distribution of AP2/ERF transcription factors reveals duplication and CBFs genes elucidate their potential function in Brassica oleracea

BACKGROUND

Cabbage (Brassica oleracea) is one of the most important leaf vegetables grown worldwide. The entire cabbage genome sequence and more than fifty thousand proteins have been obtained to date. However a high degree of sequence similarity and conserved genome structure remain between cabbage and Arabidopsis; therefore, Arabidopsis is a viable reference species for comparative genomics studies. Transcription factors (TFs) are important regulators involved in plant development and physiological processes and the AP2/ERF protein family contains transcriptional factors that play a crucial role in plant growth and development, as well as response to biotic and abiotic stress conditions in plants. However, no detailed expression profile of AP2/ERF-like genes is available for B. oleracea.

RESULTS

In the present study, 226 AP2/ERF TFs were identified from B. oleracea based on the available genome sequence. Based on sequence similarity, the AP2/ERF superfamily was classified into five groups (DREB, ERF, AP2, RAV and Soloist) and 15 subgroups. The identification, classification, phylogenetic construction, conserved motifs, chromosome distribution, functional annotation, expression patterns and interaction network were then predicted and analyzed. AP2/ERF transcription factor expression levels exhibited differences in response to varying abiotic stresses based on expressed sequence tags (ESTs). BoCBF1a, 1b, 2, 3 and 4, which were highly conserved in Arabidopsis and B. rapa CBF/DREB genes families were well characterized. Expression analysis enabled elucidation of the molecular and genetic level expression patterns of cold tolerance (CT) and susceptible lines (CS) of cabbage and indicated that all BoCBF genes responded to abiotic stresses.

CONCLUSIONS

Comprehensive analysis of the physiological functions and biological roles of AP2/ERF superfamily genes and BoCBF family genes in B. oleracea is required to fully elucidate AP2/ERF, which will provide rich resources and opportunities to understand abiotic stress tolerance in crops.

Related to ABA-Insensitive3(ABI3)/Viviparous1 and AtABI5 transcription factor coexpression in cotton enhances drought stress adaptation

Drought tolerance is an important trait being pursued by the agbiotech industry. Abscisic acid (ABA) is a stress hormone that mediates a multitude of processes in growth and development, water use efficiency (WUE) and gene expression during seed development and in response to environmental stresses. Arabidopsis B3-domain transcription factor Related to ABA-Insensitive3 (ABI3)/Viviparous1 (namely AtRAV2) and basic leucine zipper (bZIPs) AtABI5 or AtABF3 transactivated ABA-inducible promoter:GUS reporter expression in a maize mesophyll protoplast transient assay and showed synergies in reporter transactivation when coexpressed. Transgenic cotton (Gossypium hirsutum) expressing AtRAV1/2 and/or AtABI5 showed resistance to imposed drought stress under field and greenhouse conditions and exhibited improved photosynthesis and WUEs associated with absorption through larger root system and greater leaf area. We observed synergy for root biomass accumulation in the greenhouse, intrinsic WUE in the field and drought tolerance in stacked AtRAV and AtABI5 double-transgenic cotton. We assessed AtABI5 and AtRAV1/2 involvement in drought stress adaptations through reactive oxygen species scavenging and osmotic adjustment by marker gene expression in cotton. Deficit irrigation-grown AtRAV1/2 and AtABI5 transgenics had 'less-stressed' molecular and physiological phenotypes under drought, likely due to improved photoassimilation and root and shoot sink strengths and enhanced expression of endogenous GhRAV and genes for antioxidant and osmolyte biosynthesis. Overexpression of bZIP and RAV TFs could impact sustainable cotton agriculture and potentially other crops under limited irrigation conditions.

Day and night heat stress trigger different transcriptomic responses in green and ripening grapevine (vitis vinifera) fruit

BACKGROUND

Global climate change will noticeably affect plant vegetative and reproductive development. The recent increase in temperatures has already impacted yields and composition of berries in many grapevine-growing regions. Physiological processes underlying temperature response and tolerance of the grapevine fruit have not been extensively investigated. To date, all studies investigating the molecular regulation of fleshly fruit response to abiotic stress were only conducted during the day, overlooking possible critical night-specific variations. The present study explores the night and day transcriptomic response of grapevine fruit to heat stress at several developmental stages. Short heat stresses (2 h) were applied at day and night to vines bearing clusters sequentially ordered according to the developmental stages along their vertical axes. The recently proposed microvine model (DRCF-Dwarf Rapid Cycling and Continuous Flowering) was grown in climatic chambers in order to circumvent common constraints and biases inevitable in field experiments with perennial macrovines. Post-véraison berry heterogeneity within clusters was avoided by constituting homogenous batches following organic acids and sugars measurements of individual berries. A whole genome transcriptomic approach was subsequently conducted using NimbleGen 090818 Vitis 12X (30 K) microarrays.

RESULTS

Present work reveals significant differences in heat stress responsive pathways according to day or night treatment, in particular regarding genes associated with acidity and phenylpropanoid metabolism. Precise distinction of ripening stages led to stage-specific detection of malic acid and anthocyanin-related transcripts modulated by heat stress. Important changes in cell wall modification related processes as well as indications for heat-induced delay of ripening and sugar accumulation were observed at véraison, an effect that was reversed at later stages.

CONCLUSIONS

This first day - night study on heat stress adaption of the grapevine berry shows that the transcriptome of fleshy fruits is differentially affected by abiotic stress at night. The present results emphasize the necessity of including different developmental stages and especially several daytime points in transcriptomic studies.

CMYB1 encoding a MYB transcriptional activator is involved in abiotic stress and circadian rhythm in rice

Through analysis of cold-induced transcriptome, a novel gene encoding a putative MYB transcription factor was isolated and designated Cold induced MYB 1 (CMYB1). Tissue-specific gene expression analysis revealed that CMYB1 was highly expressed in rice stems and nodes. qRT-PCR assay indicated that CMYB1 was dramatically induced by cold stress (>100-folds) and induced by exogenous ABA and osmotic stress. Interestingly, CMYB1 showed rhythmic expression profile in rice leaves at different developmental stages. Subcellular localization assay suggested that CMYB1-GFP (green fluorescent protein) fusion protein was localized in the nuclei. Moreover, CMYB1 exhibited the transcriptional activation activity when transiently expressed in rice protoplast cells. Taken together, CMYB1 probably functions as a transcriptional activator in mediating stress and rhythm responsive gene expression in rice.

Expression patterns of ERF genes underlying abiotic stresses in di-haploid Populus simonii × P. nigra

176 ERF genes from Populus were identified by bioinformatics analysis, 13 of these in di-haploid Populus simonii × P. nigra were investigate by real-time RT-PCR, the results demonstrated that 13 ERF genes were highly responsive to salt stress, drought stress and ABA treatment, and all were expressed in root, stem, and leaf tissues, whereas their expression levels were markedly different in the various tissues. In roots, PthERF99, 110, 119, and 168 were primarily downregulated under drought and ABA treatment but were specifically upregulated under high salt condition. Interestingly, in poplar stems, all ERF genes showed the similar trends in expression in response to NaCl stress, drought stress, and ABA treatment, indicating that they may not play either specific or unique roles in stems in abiotic stress responses. In poplar leaves, PthERF168 was highly induced by ABA treatment, but was suppressed by high salinity and drought stresses, implying that PthERF168 participated in the ABA signaling pathway. The results of this study indicated that ERF genes could play essential but distinct roles in various plant tissues in response to different environment cues and hormonal treatment.

EsDREB2B, a novel truncated DREB2-type transcription factor in the desert legume Eremosparton songoricum, enhances tolerance to multiple abiotic stresses in yeast and transgenic tobacco

BACKGROUND

Dehydration-Responsive Element-Binding Protein2 (DREB2) is a transcriptional factor which regulates the expression of several stress-inducible genes. DREB2-type proteins are particularly important in plant responses to drought, salt and heat. DREB2 genes have been identified and characterized in a variety of plants, and DREB2 genes are promising candidate genes for the improvement of stress tolerance in plants. However, little is known about these genes in plants adapted to water-limiting environments.

RESULTS

In this study, we describe the characterization of EsDREB2B, a novel DREB2B gene identified from the desert plant Eremosparton songoricum. Phylogenetic analysis and motif prediction indicate that EsDREB2B encodes a truncated DREB2 polypeptide that belongs to a legume-specific DREB2 group. In E. songoricum, EsDREB2B transcript accumulation was induced by a variety of abiotic stresses, including drought, salinity, cold, heat, heavy metal, mechanical wounding, oxidative stress and exogenous abscisic acid (ABA) treatment. Consistent with the predicted role as a transcription factor, EsDREB2B was targeted to the nucleus of onion epidermal cells and exhibited transactivation activity of a GAL4-containing reporter gene in yeast. In transgenic yeast, overexpression of EsDREB2B increased tolerance to multiple abiotic stresses. Our findings indicate that EsDREB2B can enhance stress tolerance in other plant species. Heterologous expression of EsDREB2B in tobacco showed improved tolerance to multiple abiotic stresses, and the transgenic plants exhibited no reduction in foliar growth. We observed that EsDREB2B is a functional DREB2-orthologue able to influence the physiological and biochemical response of transgenic tobacco to stress.

CONCLUSIONS

Based upon these findings, EsDREB2B encodes an abiotic stress-inducible, transcription factor which confers abiotic stress-tolerance in yeast and transgenic tobacco.

Farinose flavonoids are associated with high freezing tolerance in fairy primrose (Primula malacoides) plants

The deposition of surface (farinose) flavonoids on aerial parts of some Primula species is a well-documented but poorly understood phenomenon. Here, we show that flavonoid deposition on the leaves and winter buds may contribute strongly to preventing freezing damage in these plants. The ice nucleation temperature of fairy primrose (Primula malacoides) leaves covered with natural flavone was approximately 6 °C lower compared to those that had their flavone artificially removed. Additionally, farinose flavonoids on the leaves reduced subsequent electrolyte leakage (EL) from the cells exposed to freezing temperatures. Interestingly, exogenous application of flavone at 4 mg/g fresh weight to P. malacoides leaves, which had the original flavone mechanically removed, restored freezing tolerance, and diminished EL from the cells to pretreatment values. Our results suggest that farinose flavonoids may function as mediators of freezing tolerance in P. malacoides, and exogenous application of flavone could be used to reduce freezing damage during sudden but predictable frost events in other plant species.

Fruit specific variability in capsaicinoid accumulation and transcription of structural and regulatory genes in Capsicum fruit

Accumulation of capsaicinoids in the placental tissue of ripening chile (Capsicum spp.) fruit follows the coordinated expression of multiple biosynthetic enzymes producing the substrates for capsaicin synthase. Transcription factors are likely agents to regulate expression of these biosynthetic genes. Placental RNAs from habanero fruit (Capsicum chinense) were screened for expression of candidate transcription factors; with two candidate genes identified, both in the ERF family of transcription factors. Characterization of these transcription factors, Erf and Jerf, in nine chile cultivars with distinct capsaicinoid contents demonstrated a correlation of expression with pungency. Amino acid variants were observed in both ERF and JERF from different chile cultivars; none of these changes involved the DNA binding domains. Little to no transcription of Erf was detected in non-pungent Capsium annuum or C. chinense mutants. This correlation was characterized at an individual fruit level in a set of jalapeño (C. annuum) lines again with distinct and variable capsaicinoid contents. Both Erf and Jerf are expressed early in fruit development, 16-20 days post-anthesis, at times prior to the accumulation of capsaicinoids in the placental tissues. These data support the hypothesis that these two members of the complex ERF family participate in regulation of the pungency phenotype in chile.

Analyses of hypomethylated oil palm gene space

Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.

Composition, roles, and regulation of cullin-based ubiquitin e3 ligases

Due to their sessile nature, plants depend on flexible regulatory systems that allow them to adequately regulate developmental and physiological processes in context with environmental cues. The ubiquitin proteasome pathway, which targets a great number of proteins for degradation, is cellular tool that provides the necessary flexibility to accomplish this task. Ubiquitin E3 ligases provide the needed specificity to the pathway by selectively binding to particular substrates and facilitating their ubiquitylation. The largest group of E3 ligases known in plants is represented by CULLIN-REALLY INTERESTING NEW GENE (RING) E3 ligases (CRLs). In recent years, a great amount of knowledge has been generated to reveal the critical roles of these enzymes across all aspects of plant life. This review provides an overview of the different classes of CRLs in plants, their specific complex compositions, the variety of biological processes they control, and the regulatory steps that can affect their activities.

Pathogenesis related-10 proteins are small, structurally similar but with diverse role in stress signaling

Pathogenesis related-10 proteins are small proteins with cytosolic localization, conserved three dimensional structures and single intron at 185 bp position. These proteins have a broad spectrum of roles significantly in biotic and abiotic stresses. The RNase activity, ligand binding activity, posttranslational modification (phosphorylation) and phytohormone signaling provide some information into the mechanism of the regulation of PR-10 proteins, however the presence of isoforms makes it difficult to decipher its exact mode of function. The involvement of phosphorylation/dephosphorylation events in its activation is interesting and provides unique and unbiased insights into the complexity of its regulation. Studies on upstream region of different PR-10 genes indicate the presence of cis-acting elements for WRKY, RAVI, bZ1P, ERF, SEBF and Pti4 transcription factors indicating their role in regulating PR-10 promoter. In this review, we discuss in detail the structure and mechanism of regulation of PR-10 proteins.

Defense responses in two ecotypes of Lotus japonicus against non-pathogenic Pseudomonas syringae

Lotus japonicus is a model legume broadly used to study many important processes as nitrogen fixing nodule formation and adaptation to salt stress. However, no studies on the defense responses occurring in this species against invading microorganisms have been carried out at the present. Understanding how this model plant protects itself against pathogens will certainly help to develop more tolerant cultivars in economically important Lotus species as well as in other legumes. In order to uncover the most important defense mechanisms activated upon bacterial attack, we explored in this work the main responses occurring in the phenotypically contrasting ecotypes MG-20 and Gifu B-129 of L. japonicus after inoculation with Pseudomonas syringae DC3000 pv. tomato. Our analysis demonstrated that this bacterial strain is unable to cause disease in these accessions, even though the defense mechanisms triggered in these ecotypes might differ. Thus, disease tolerance in MG-20 was characterized by bacterial multiplication, chlorosis and desiccation at the infiltrated tissues. In turn, Gifu B-129 plants did not show any symptom at all and were completely successful in restricting bacterial growth. We performed a microarray based analysis of these responses and determined the regulation of several genes that could play important roles in plant defense. Interestingly, we were also able to identify a set of defense genes with a relative high expression in Gifu B-129 plants under non-stress conditions, what could explain its higher tolerance. The participation of these genes in plant defense is discussed. Our results position the L. japonicus-P. syringae interaction as a interesting model to study defense mechanisms in legume species.

Analysis of Brassica napus ESTs: gene discovery and expression patterns of AP2/ERF-family transcription factors

Starting from expressed sequence tag sequences and using the conserved amino acid sequence of the Arabidopsis thaliana AP2/ERF domain as a probe, we used in silico cloning to identify 87 genes that encode putative AP2/ERF transcription factors (TFs) from the Brassica napus. Almost all of the putative AP2/ERF factors from B. napus were similar to genes previously defined as AP2/ERF genes from A. thaliana. Based on the number of AP2-domains and the function of the genes, the AP2/ERF TFs from B. napus were classified into four subfamilies, named the AP2, DREB, ERF, and RAV subfamilies. We then predicted and analyzed cDNA sequences and amino acid sequences, amino acid compositions, physical and chemical characteristics, phylogenetic trees, conserved domain sequences, functional domains, molecular models, and folding states of the proteins they are predicted to encode. Expression analysis showed that four factors, which belonged to the ERF and DREB subfamilies, were induced by abiotic stresses, as well as by hormone treatment. This suggests that those AP2/ERF factors may be involved in signaling pathways responsive to abiotic and biotic stresses. The results from this study, reported herein, form a basis for future functional analyses of B. napus TFs that belong to the AP2/ERF family.

LaAP2L1, a heterosis-associated AP2/EREBP transcription factor of Larix, increases organ size and final biomass by affecting cell proliferation in Arabidopsis

In Larix and in some crops, heterosis is prevalent and has been widely used in breeding to produce excellent varieties. However, the molecular basis of heterosis in Larix remains ambiguous. LaAP2L1, a member of the AP2/EREBP transcription factor family, has been suggested to be involved in heterosis in Larix hybrids. Here, the function and regulation of LaAP2L1 were further explored. Overexpression of LaAP2L1 led to markedly enlarged organs and heterosis-like traits in Arabidopsis. Fresh weight of leaves was almost twice as great as in vector controls. Likewise, seed yield of 35S::LaAP2L1 individual plants was >200% greater than that of control plants. The enlarged organs and heterosis-like traits displayed by 35S::LaAP2L1 plants were mainly due to enhanced cell proliferation and prolonged growth duration. At the molecular level, LaAP2L1 upregulated the expression of ANT, EBP1, and CycD3;1 and inhibited the expression of ARGOS in 35S::LaAP2L1 plants, suggesting an important molecular role of LaAP2L1 in regulating plant organ development. These findings provide new insights into the formation of heterosis in woody plants and suggest that LaAP2L1 has potential applications in breeding high-yielding crops and energy plants. In addition, 50 AP2/EREBP transcription factors, including LaAP2L1, in Larix were identified by transcriptome sequencing, and phylogenetic analysis was conducted. This provided information that will be important in further revealing the functions of these transcription factors.

Characterization of a Pollen-Specific and Desiccation-Associated AP2/ERF Type Transcription Factor Gene from Castor Bean (Ricinus communis L.)

DREB transcription factors (TF) belong to the superfamily of AP2/ERF and their involvement in protein-protein interactions and DNA binding has been proposed. AP2/ERF proteins have important functions in the transcriptional regulation of a variety of biological processes related to growth and development, as well as various responses to environmental stimuli, regulating expression of plant biotic and abiotic stress-responsive genes. In this study an AP2/ERF TF gene (named RcDREB1) was isolated from castor bean (Ricinus communis L.) and its expression was analyzed in developing seeds, leaves, ovules, stems and petals of plants cultivated under field conditions. Transcripts were only observed in pollen grains, peaking during anthesis. The RcDREB1 deduced amino acid sequence was compared to other AP2/ERF TF proteins and presented 38–78% identity. Phylogenetic analysis classified it as a member of the CBF/DREB subfamily, rooting with the subgroup A-5. The RcDREB1 promoter was fused to the gus reporter gene and used to transform tobacco. Transgenic plants were exposed to various abiotic stress treatments (low and high tempera- tures, drought, salinity and exogenous ABA) and no detectable GUS expression was observed, suggesting that the RcDREB1 promoter is not active under tested conditions. In silico analyses revealed the presence of three copies of the regulatory late pollen-specific element (AGAAA) in the RcDREB1 5′-region. Interestingly, GUS expression was only observed in pollen grains, starting when the flower opened and initiating the senescence process; at this point, desiccated mature pollen grains are released from anthers. In addition, dehydrated developing pollen grains also expressed the gus gene. This is the first study on a DREB gene presenting pollen-specific expression.

Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis)

Background

Chinese cabbage (Brassica rapa ssp. pekinensis) is a member of one of the most important leaf vegetables grown worldwide, which has experienced thousands of years in cultivation and artificial selection. The entire Chinese cabbage genome sequence, and more than forty thousand proteins have been obtained to date. The genome has undergone triplication events since its divergence from Arabidopsis thaliana (13 to 17 Mya), however a high degree of sequence similarity and conserved genome structure remain between the two species. Arabidopsis is therefore a viable reference species for comparative genomics studies. Variation in the number of members in gene families due to genome triplication may contribute to the broad range of phenotypic plasticity, and increased tolerance to environmental extremes observed in Brassica species. Transcription factors are important regulators involved in plant developmental and physiological processes. The AP2/ERF proteins, one of the most important families of transcriptional regulators, play a crucial role in plant growth, and in response to biotic and abiotic stressors. Our analysis will provide resources for understanding the tolerance mechanisms in Brassica rapa ssp. pekinensis.

Results

In the present study, 291 putative AP2/ERF transcription factor proteins were identified from the Chinese cabbage genome database, and compared with proteins from 15 additional species. The Chinese cabbage AP2/ERF superfamily was classified into four families, including AP2, ERF, RAV, and Soloist. The ERF family was further divided into DREB and ERF subfamilies. The AP2/ERF superfamily was subsequently divided into 15 groups. The identification, classification, phylogenetic reconstruction, conserved motifs, chromosome distribution, functional annotation, expression patterns, and interaction networks of the AP2/ERF transcription factor superfamily were predicted and analyzed. Distribution mapping results showed AP2/ERF superfamily genes were localized on the 10 Chinese cabbage chromosomes. AP2/ERF transcription factor expression levels exhibited differences among six tissue types based on expressed sequence tags (ESTs). In the AP2/ERF superfamily, 214 orthologous genes were identified between Chinese cabbage and Arabidopsis. Orthologous gene interaction networks were constructed, and included seven CBF and four AP2 genes, primarily involved in cold regulatory pathways and ovule development, respectively.

Conclusions

The evolution of the AP2/ERF transcription factor superfamily in Chinese cabbage resulted from genome triplication and tandem duplications. A comprehensive analysis of the physiological functions and biological roles of AP2/ERF superfamily genes in Chinese cabbage is required to fully elucidate AP2/ERF, which provides us with rich resources and opportunities to understand crop stress tolerance mechanisms.

Xanthomonas type III effector XopD desumoylates tomato transcription factor SlERF4 to suppress ethylene responses and promote pathogen growth

XopD, a type III secretion effector from Xanthomonas euvesicatoria (Xcv), the causal agent of bacterial spot of tomato, is required for pathogen growth and delay of host symptom development. XopD carries a C-terminal SUMO protease domain, a host range determining nonspecific DNA-binding domain and two EAR motifs typically found in repressors of stress-induced transcription. The precise target(s) and mechanism(s) of XopD are obscure. We report that XopD directly targets the tomato ethylene responsive transcription factor SlERF4 to suppress ethylene production, which is required for anti-Xcv immunity and symptom development. SlERF4 expression was required for Xcv ΔxopD-induced ethylene production and ethylene-stimulated immunity. XopD colocalized with SlERF4 in subnuclear foci and catalyzed SUMO1 hydrolysis from lysine 53 of SlERF4, causing SlERF4 destabilization. Mutation of lysine 53 prevented SlERF4 sumoylation, decreased SlERF4 levels, and reduced SlERF4 transcription. These data suggest that XopD desumoylates SlERF4 to repress ethylene-induced transcription required for anti-Xcv immunity.

APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors: mediators of stress responses and developmental programs

Transcription factors belonging to the APETALA2/Ethylene Responsive Factor (AP2/ERF) family are conservatively widespread in the plant kingdom. These regulatory proteins are involved in the control of primary and secondary metabolism, growth and developmental programs, as well as responses to environmental stimuli. Due to their plasticity and to the specificity of individual members of this family, AP2/ERF transcription factors represent valuable targets for genetic engineering and breeding of crops. In this review, we integrate the evidence collected from functional and structural studies to describe their different mechanisms of action and the regulatory pathways that affect their activity.

The phytohormone crosstalk paradigm takes center stage in understanding how plants respond to abiotic stresses

The highly coordinated, dynamic nature of growth requires plants to perceive and react to various environmental signals in an interactive manner. Elaborate signaling networks mediate this plasticity in growth and the ability to adapt to changing environmental conditions. The fluctuations of stress-responsive hormones help alter the cellular dynamics and hence play a central role in coordinately regulating the growth responses under stress. Recent experimental data unequivocally demonstrated that interactions among various phytohormones are the rule rather than exception in integrating the diverse input signals and readjusting growth as well as acquiring stress tolerance. The presence of multiple and often redundant signaling intermediates for each phytohormone appears to help in such crosstalk. Furthermore, there are several examples of similar developmental changes occurring in response to distinct abiotic stress signals, which can be explained by the crosstalk in phytohormone signaling. Therefore, in this brief review, we have highlighted the major phytohormone crosstalks with a focus on the response of plants to abiotic stresses. The recent findings have made it increasingly apparent that such crosstalk will also explain the extreme pleiotropic responses elicited by various phytohormones. Indeed, it would not be presumptuous to expect that in the coming years this paradigm will take a central role in explaining developmental regulation.

A wheat PI4K gene whose product possesses threonine autophophorylation activity confers tolerance to drought and salt in Arabidopsis

Phosphoinositides are involved in regulation of recruitment and activity of signalling proteins in cell membranes. Phosphatidylinositol (PI) 4-kinases (PI4Ks) generate PI4-phosphate the precursor of regulatory phosphoinositides. No type II PI4K research on the abiotic stress response has previously been reported in plants. A stress-inducible type II PI4K gene, named TaPI4KIIγ, was obtained by de novo transcriptome sequencing of drought-treated wheat (Triticum aestivum). TaPI4KIIγ, localized on the plasma membrane, underwent threonine autophosphorylation, but had no detectable lipid kinase activity. Interaction of TaPI4KIIγ with wheat ubiquitin fusion degradation protein (TaUDF1) indicated that it might be hydrolysed by the proteinase system. Overexpression of TaPI4KIIγ revealed that it could enhance drought and salt stress tolerance during seed germination and seedling growth. A ubdkγ7 mutant, identified as an orthologue of TaPI4KIIγ in Arabidopsis, was sensitive to salt, polyethylene glycol (PEG), and abscisic acid (ABA), and overexpression of TaPI4KIIγ in the ubdkγ7 mutant compensated stress sensitivity. TaPI4KIIγ promoted root growth in Arabidopsis, suggesting that TaPI4KIIγ might enhance stress resistance by improving root growth. Overexpression of TaPI4KIIγ led to an altered expression level of stress-related genes and changes in several physiological traits that made the plants more tolerant to stress. The results provided evidence that overexpression of TaPI4KIIγ could improve drought and salt tolerance.

Ethylene signaling and regulation in plant growth and stress responses

Gaseous phytohormone ethylene affects many aspects of plant growth and development. The ethylene signaling pathway starts when ethylene binds to its receptors. Since the cloning of the first ethylene receptor ETR1 from Arabidopsis, a large number of studies have steadily improved our understanding of the receptors and downstream components in ethylene signal transduction pathway. This article reviews the regulation of ethylene receptors, signal transduction, and the posttranscriptional modulation of downstream components. Functional roles and importance of the ethylene signaling components in plant growth and stress responses are also discussed. Cross-reactions of ethylene with auxin and other phytohormones in plant organ growth will be analyzed. The studies of ethylene signaling in plant growth, development, and stress responses in the past decade greatly advanced our knowledge of how plants respond to endogenous signals and environmental factors.

Banana ethylene response factors are involved in fruit ripening through their interactions with ethylene biosynthesis genes

The involvement of ethylene response factor (ERF) transcription factor (TF) in the transcriptional regulation of ethylene biosynthesis genes during fruit ripening remains largely unclear. In this study, 15 ERF genes, designated as MaERF1-MaERF15, were isolated and characterized from banana fruit. These MaERFs were classified into seven of the 12 known ERF families. Subcellular localization showed that MaERF proteins of five different subfamilies preferentially localized to the nucleus. The 15 MaERF genes displayed differential expression patterns and levels in peel and pulp of banana fruit, in association with four different ripening treatments caused by natural, ethylene-induced, 1-methylcyclopropene (1-MCP)-delayed, and combined 1-MCP and ethylene treatments. MaERF9 was upregulated while MaERF11 was downregulated in peel and pulp of banana fruit during ripening or after treatment with ethylene. Furthermore, yeast-one hybrid (Y1H) and transient expression assays showed that the potential repressor MaERF11 bound to MaACS1 and MaACO1 promoters to suppress their activities and that MaERF9 activated MaACO1 promoter activity. Interestingly, protein-protein interaction analysis revealed that MaERF9 and -11 physically interacted with MaACO1. Taken together, these results suggest that MaERFs are involved in banana fruit ripening via transcriptional regulation of or interaction with ethylene biosynthesis genes.

Induction of endodormancy in crown buds of leafy spurge (Euphorbia esula L.) implicates a role for ethylene and cross-talk between photoperiod and temperature

Leafy spurge is a model for studying well-defined phases of dormancy in underground adventitious buds (UABs) of herbaceous perennial weeds, which is a primary factor facilitating their escape from conventional control measures. A 12-week ramp down in both temperature (27 → 10 °C) and photoperiod (16 → 8 h light) is required to induce a transition from para- to endo-dormancy in UABs of leafy spurge. To evaluate the effects of photoperiod and temperature on molecular networks of UABs during this transition, we compared global transcriptome data-sets obtained from leafy spurge exposed to a ramp down in both temperature and photoperiod (RDtp) versus a ramp down in temperature (RDt) alone. Analysis of data-sets indicated that transcript abundance for genes associated with circadian clock, photoperiodism, flowering, and hormone responses (CCA1, COP1, HY5, MAF3, MAX2) preferentially increased in endodormant UABs. Gene-set enrichment analyses also highlighted metabolic pathways involved in endodormancy induction that were associated with ethylene, auxin, flavonoids, and carbohydrate metabolism; whereas, sub-network enrichment analyses identified hubs (CCA1, CO, FRI, miR172A, EINs, DREBs) of molecular networks associated with carbohydrate metabolism, circadian clock, flowering, and stress and hormone responses. These results helped refine existing models for the transition to endodormancy in UABs of leafy spurge, which strengthened the roles of circadian clock associated genes, DREBs, COP1-HY5, carbohydrate metabolism, and involvement of hormones (ABA, ethylene, and strigolactones). We further examined the effects of ethylene by application of 1-aminocyclopropane-1-carboxylate (ACC) to paradormant plants without a ramp down treatment. New vegetative growth from UABs of ACC-treated plants resulted in a dwarfed phenotype that mimicked the growth response in RDtp-induced endodormant UABs. The results of this study provide new insights into dormancy regulation suggesting a short-photoperiod treatment provides an additive cross-talk effect with temperature signals that may impact ethylene's effect on AP2/ERF family members.

Using RNA-Seq to profile soybean seed development from fertilization to maturity

To understand gene expression networks leading to functional properties and compositional traits of the soybean seed, we have undertaken a detailed examination of soybean seed development from a few days post-fertilization to the mature seed using Illumina high-throughput transcriptome sequencing (RNA-Seq). RNA was sequenced from seven different stages of seed development, yielding between 12 million and 78 million sequenced transcripts. These have been aligned to the 79,000 gene models predicted from the soybean genome recently sequenced by the Department of Energy Joint Genome Institute. Over one hundred gene models were identified with high expression exclusively in young seed stages, starting at just four days after fertilization. These were annotated as being related to many basic components and processes such as histones and proline-rich proteins. Genes encoding storage proteins such as glycinin and beta-conglycinin had their highest expression levels at the stages of largest fresh weight, confirming previous knowledge that these storage products are being rapidly accumulated before the seed begins the desiccation process. Other gene models showed high expression in the dry, mature seeds, perhaps indicating the preparation of pathways needed later, in the early stages of imbibition. Many highly-expressed gene models at the dry seed stage are, as expected, annotated as hydrophilic proteins associated with low water conditions, such as late embryogenesis abundant (LEA) proteins and dehydrins, which help preserve the cellular structures and nutrients within the seed during desiccation. More significantly, the power of RNA-Seq to detect genes expressed at low levels revealed hundreds of transcription factors with notable expression in at least one stage of seed development. Results from a second biological replicate demonstrate high reproducibility of these data revealing a comprehensive view of the transciptome of seed development in the cultivar Williams, the reference cultivar for the first soybean genome sequence.

Physiological, biochemical and molecular responses to a combination of drought and ozone in Medicago truncatula

Drought and tropospheric ozone are escalating climate change problems that can co-occur. In this study, we observed Medicago truncatula cultivar Jemalong that is sensitive to ozone and drought stress when applied singly, showed tolerance when subjected to a combined application of these stresses. Lowered stomatal conductance may be a vital tolerance mechanism to overcome combined ozone and drought. Sustained increases in both reduced ascorbate and glutathione in response to combined stress may play a role in lowering reactive oxygen species and nitric oxide toxicity. Transcriptome analysis indicated that genes associated with glucan metabolism, responses to temperature and light signalling may play a role in dampening ozone responses due to drought-induced stomatal closure during combined occurrence of these two stresses. Gene ontologies for jasmonic acid signalling and innate immunity were enriched among the 300 differentially expressed genes unique to combined stress. Differential expression of transcription factors associated with redox, defence signalling, jasmonate responses and chromatin modifications may be important for evoking novel gene networks during combined occurrence of drought and ozone. The alterations in redox milieu and distinct transcriptome changes in response to combined stress could aid in tweaking the metabolome and proteome to annul the detrimental effects of ozone and drought in Jemalong.

Isolation and molecular characterization of GmERF7, a soybean ethylene-response factor that increases salt stress tolerance in tobacco

Ethylene-response factors (ERFs) play an important role in regulating gene expression in plant responses to biotic and abiotic stresses. In this study, a new ERF transcription factor, GmERF7, was isolated from soybean. Sequence analysis showed that GmERF7 contained an AP2/ERF domain with 58 amino acids, two putative nuclear localization signal (NLS) domains, an acidic amino acid-rich transcriptional activation domain and a conserved N-terminal motif [MCGGAI(I/L)]. The expression of GmERF7 was induced by drought, salt, methyl jasmonate (MeJA), ethylene (ETH) and abscisic acid (ABA) treatments. However, the expression of GmERF7 decreased under cold treatment. GmERF7 localized to the nucleus when transiently expressed in onion epidermal cells. Furthermore, GmERF7 protein bound to the GCC-box element in vitro and activated the expression of the β-glucuronidase (GUS) reporter gene in tobacco leaves. Activities of GmERF7 promoter (GmERF7P) upregulated in tobacco leaves with 10h drought, salt and ETH treatments. However, activities of GmERF7P decreased with 10h cold and ABA treatments. Overexpression of GmERF7 in tobacco plants led to higher levels of chlorophyll and soluble carbohydrates and a lower level of malondialdehyde compared with wild-type tobacco plants under salt stress conditions, which indicated that GmERF7 enhanced salt tolerance in transgenic plants.

Heat shock protein 90 in plants: molecular mechanisms and roles in stress responses

The heat shock protein 90 (Hsp90) family mediates stress signal transduction, and plays important roles in the control of normal growth of human cells and in promoting development of tumor cells. Hsp90s have become a currently important subject in cellular immunity, signal transduction, and anti-cancer research. Studies on the physiological functions of Hsp90s began much later in plants than in animals and fungi. Significant progress has been made in understanding complex mechanisms of HSP90s in plants, including ATPase-coupled conformational changes and interactions with cochaperone proteins. A wide range of signaling proteins interact with HSP90s. Recent studies revealed that plant Hsp90s are important in plant development, environmental stress response, and disease and pest resistance. In this study, the plant HSP90 family was classified into three clusters on the basis of phylogenetic relationships, gene structure, and biological functions. We discuss the molecular functions of Hsp90s, and systematically review recent progress of Hsp90 research in plants.

Expression profile in rice panicle: insights into heat response mechanism at reproductive stage

Rice at reproductive stage is more sensitive to environmental changes, and little is known about the mechanism of heat response in rice panicle. Here, using rice microarray, we provided a time course gene expression profile of rice panicle at anther developmental stage 8 after 40°C treatment for 0 min, 20 min, 60 min, 2 h, 4 h, and 8 h. The identified differentially expressed genes were mainly involved in transcriptional regulation, transport, cellular homeostasis, and stress response. The predominant transcription factor gene families responsive to heat stress were Hsf, NAC, AP2/ERF, WRKY, MYB, and C₂H₂. KMC analysis discovered the time-dependent gene expression pattern under heat stress. The motif co-occurrence analysis on the promoters of genes from an early up-regulated cluster showed the important roles of GCC box, HSE, ABRE, and CE3 in response to heat stress. The regulation model central to ROS combined with transcriptome and ROS quantification data in rice panicle indicated the great importance to maintain ROS balance and the existence of wide cross-talk in heat response. The present study increased our understanding of the heat response in rice panicle and provided good candidate genes for crop improvement.

Ectopic expression of dehydration responsive element binding proteins (StDREB2) confers higher tolerance to salt stress in potato

Dehydration responsive element binding proteins (DREB) are members of a larger family of transcription factors, many of which have been reported to contribute to plant responses to abiotic stresses in several species. While, little is known about their role in potato (Solanum tuberosum). This report describes the cloning and characterization of a DREB transcription factor cDNA, StDREB2, isolated from potato (cv Nicola) plants submitted to salt treatment. Based on a multiple sequence alignment, this protein was classified into the A-5 group of DREB subfamily. Expression studies revealed that StDREB2 was induced in leaves, roots and stems upon various abiotic stresses and in response to exogenous treatment with abscisic acid (ABA). In agreement with this expression pattern, over-expression of StDREB2 in transgenic potato plants resulted in enhanced tolerance to salt stress. These data suggest that the isolated StDREB2 encodes a functional protein involved in plant response to different abiotic stresses. An electrophoretic mobility shift assay (EMSA) indicated that the StDREB2 protein bound specifically to the DRE core element (ACCGAGA) in vitro. Moreover, Semi quantitative RT-PCR analysis revealed that the transcript level of a putative target gene i.e. δ(1)-pyrroline-5-carboxylate synthase (P5CS) was up-regulated in transgenic plants submitted to salt stress conditions. A concomitant increase in proline accumulation was also observed under these conditions. Taking together, all these data suggest that StDREB2 takes part in the processes underlying plant responses to abiotic stresses probably via the regulation of ABA hormone signaling and through a mechanism allowing proline synthesis.

A TFIIIA-type zinc finger protein confers multiple abiotic stress tolerances in transgenic rice (Oryza sativa L.)

The TFIIIA-type zinc finger transcription factors are involved in plant development and abiotic stress responses. Most TFIIIA-type zinc finger proteins are transcription repressors due to existence of an EAR-motif in their amino acid sequences. In this work, we found that ZFP182, a TFIIIA-type zinc finger protein, forms a homodimer in the nucleus and exhibits trans-activation activity in yeast cells. The deletion analysis indicated that a Leu-rich region at C-terminus is required for the trans-activation. Overexpression of ZFP182 significantly enhanced multiple abiotic stress tolerances, including salt, cold and drought tolerances in transgenic rice. Overexpression of ZFP182 promotes accumulation of compatible osmolytes, such as free proline and soluble sugars, in transgenic rice. ZFP182 activates the expression of OsP5CS encoding pyrroline-5-carboxylate synthetase and OsLEA3 under stress conditions, while OsDREB1A and OsDREB1B were regulated by ZFP182 under both normal and stress conditions. Interestingly, site-directed mutagenesis assay showed that DRE-like elements in ZFP182 promoter are involved in dehydration-induced expression of ZFP182. The yeast two-hybrid assay revealed that ZFP182 interacted with several ribosomal proteins including ZIURP1, an ubiquitin fused to ribosomal protein L40. The in vivo and in vitro interactions of ZFP182 and ZIURP1 were further confirmed by bimolecular fluorescence complementation and His pull-down assays. Our studies provide new clues in the understanding of the mechanisms for TFIIIA-type zinc finger transcription factor mediated stress tolerance and a candidate gene for improving stress tolerance in crops.

De novo sequencing and comparative analysis of the blueberry transcriptome to discover putative genes related to antioxidants

Blueberry (Vaccinium spp.) is an important small fruit crop rich in antioxidants. However, tissue-specific transcriptome and genomic data in public databases are not sufficient for an understanding of the molecular mechanisms associated with antioxidants, especially the biosynthesis of anthocyanins. Here, we obtained more than 64 million sequencing reads from blueberry skin and pulp using Illumina sequencing technology. De novo assemblies yielded 34,464 unigenes, among them 1236 transcripts and 862 putative transcription factors involved in the main antioxidant biosynthesis pathway were identified. Comparative transcript profiling allowed the identification of 92 differentially expressed genes with potential relevance in regulating the fruit metabolism and anthocyanin content during ripening. A series of qRT-PCR confirmed the high expression level of the anthocyanin pathway genes in the skin of the blue fruit from the in silico study. This sequence collection provides a significant resource for the blueberry research and breeding work.

A proximal promoter region of Arabidopsis DREB2C confers tissue-specific expression under heat stress

The dehydration-responsive element-binding factor 2C (DREB2C) is a member of the CBF/DREB subfamily of proteins, which contains a single APETALA2/Ethylene responsive element-binding factor (AP2/ERF) domain. To identify the expression pattern of the DREB2C gene, which contains multiple transcription cis-regulatory elements in its promoter, an approximately 1.4 kb upstream DREB2C sequence was fused to the β-glucuronidase reporter gene (GUS) and the recombinant p1244 construct was transformed into Arabidopsis thaliana (L.) Heynh. The promoter of the gene directed prominent GUS activity in the vasculature in diverse young dividing tissues. Upon applying heat stress (HS), GUS staining was also enhanced in the vasculature of the growing tissues. Analysis of a series of 5'-deletions of the DREB2C promoter revealed that a proximal upstream sequence sufficient for the tissue-specific spatial and temporal induction of GUS expression by HS is localized in the promoter region between -204 and -34 bps relative to the transcriptional start site. Furthermore, electrophoretic mobility shift assay (EMSA) demonstrated that nuclear protein binding activities specific to a -120 to -32 bp promoter fragment increased after HS. These results indicate that the TATA-proximal region and some latent trans-acting factors may cooperate in HS-induced activation of the Arabidopsis DREB2C promoter.

An alfalfa (Medicago sativa L.) ethylene response factor gene, MsERF11, enhances salt tolerance in transgenic Arabidopsis

A novel orthologue of ethylene response factor gene, MsERF11, was isolated from alfalfa in this study. It has an open reading frame of 807 bp, encoding a predicted polypeptide of 268 amino acids. Sequence similarity analysis clearly suggested that MsERF11 encoded an ethylene response factor protein. The results of transient expression of MsERF11 in onion epidermal cells indicated that MsERF11 is a nuclear protein. The expression pattern of MsERF11 gene was analyzed by real-time quantitative PCR and a higher level of expression was observed in leaves than was observed in roots, stems, flower buds and flowers. Furthermore, the expression was induced by PEG6000, NaCl, Al2(SO4)3 and six different hormones. Over-expressing MsERF11 resulted in enhanced tolerances to salt stress in transgenic Arabidopsis plants. This research indicates that MsERF11 has the potential to be used for improving crop's salt tolerance in areas where salinity is a limiting factor for agricultural productivity.

KEY MESSAGE

MsERF11 was isolated from alfalfa. Its expression was induced by different abiotic stresses and hormones. Over-expressing MsERF11 resulted in enhanced salt tolerance in transgenic Arabidopsis plants.

Genome-wide transcription factor gene prediction and their expressional tissue-specificities in maize

Transcription factors (TFs) are important regulators of gene expression. To better understand TF-encoding genes in maize (Zea mays L.), a genome-wide TF prediction was performed using the updated B73 reference genome. A total of 2298 TF genes were identified, which can be classified into 56 families. The largest family, known as the MYB superfamily, comprises 322 MYB and MYB-related TF genes. The expression patterns of 2 014 (87.64%) TF genes were examined using RNA-seq data, which resulted in the identification of a subset of TFs that are specifically expressed in particular tissues (including root, shoot, leaf, ear, tassel and kernel). Similarly, 98 kernel-specific TF genes were further analyzed, and it was observed that 29 of the kernel-specific genes were preferentially expressed in the early kernel developmental stage, while 69 of the genes were expressed in the late kernel developmental stage. Identification of these TFs, particularly the tissue-specific ones, provides important information for the understanding of development and transcriptional regulation of maize.

Reference gene selection in the desert plant Eremosparton songoricum

Eremosparton songoricum (Litv.) Vass. (E. songoricum) is a rare and extremely drought-tolerant desert plant that holds promise as a model organism for the identification of genes associated with water deficit stress. Here, we cloned and evaluated the expression of eight candidate reference genes using quantitative real-time reverse transcriptase polymerase chain reactions. The expression of these candidate reference genes was analyzed in a diverse set of 20 samples including various E. songoricum plant tissues exposed to multiple environmental stresses. GeNorm analysis indicated that expression stability varied between the reference genes in the different experimental conditions, but the two most stable reference genes were sufficient for normalization in most conditions. EsEF and Esα-TUB were sufficient for various stress conditions, EsEF and EsACT were suitable for samples of differing germination stages, and EsGAPDHand EsUBQ were most stable across multiple adult tissue samples. The Es18S gene was unsuitable as a reference gene in our analysis. In addition, the expression level of the drought-stress related transcription factor EsDREB2 verified the utility of E. songoricum reference genes and indicated that no single gene was adequate for normalization on its own. This is the first systematic report on the selection of reference genes in E. songoricum, and these data will facilitate future work on gene expression in this species.

The interaction of plant biotic and abiotic stresses: from genes to the field

Plant responses to different stresses are highly complex and involve changes at the transcriptome, cellular, and physiological levels. Recent evidence shows that plants respond to multiple stresses differently from how they do to individual stresses, activating a specific programme of gene expression relating to the exact environmental conditions encountered. Rather than being additive, the presence of an abiotic stress can have the effect of reducing or enhancing susceptibility to a biotic pest or pathogen, and vice versa. This interaction between biotic and abiotic stresses is orchestrated by hormone signalling pathways that may induce or antagonize one another, in particular that of abscisic acid. Specificity in multiple stress responses is further controlled by a range of molecular mechanisms that act together in a complex regulatory network. Transcription factors, kinase cascades, and reactive oxygen species are key components of this cross-talk, as are heat shock factors and small RNAs. This review aims to characterize the interaction between biotic and abiotic stress responses at a molecular level, focusing on regulatory mechanisms important to both pathways. Identifying master regulators that connect both biotic and abiotic stress response pathways is fundamental in providing opportunities for developing broad-spectrum stress-tolerant crop plants.

Drought tolerance through biotechnology: improving translation from the laboratory to farmers' fields

Water availability is a significant constraint to crop production, and increasing drought tolerance of crops is one step to gaining greater yield stability. Excellent progress has been made using models to identify pathways and genes that can be manipulated through biotechnology to improve drought tolerance. A current focus is on translation of results from models in controlled environments to crops in the field. Field testing to demonstrate improved yields under water-limiting conditions is challenging and expensive. More extensive phenotyping of transgenic lines in the greenhouse may contribute to improved predictions about field performance. It is possible that multiple mechanisms of drought tolerance may be needed to provide benefit across the diversity of water stress environments relevant to economic yield.