Jasmonate Response Research Articles

DELLAs Modulate Jasmonate Signaling via Competitive Binding to JAZs

Gibberellins (GAs) modulate jasmonate (JA) signaling, which is essential for stress response and development in plants. However, the molecular details of such phytohormone interaction remain largely unknown. Here, we show that the JA ZIM-domain 1 (JAZ1) protein, a key repressor of JA signaling, interacts in vivo with DELLA proteins, repressors of the GA pathway. DELLAs prevent inhibitory JAZ1 interaction with a key transcriptional activator of JA responses, MYC2, and, thus, enhance the ability of MYC2 to regulate its target genes. Conversely, GA triggers degradation of DELLAs, which allows JAZ1 to bind MYC2 and suppress MYC2-dependent JA-signaling outputs. Therefore, our results reveal one means by which GAs suppress cellular competence to respond to JA. Because DELLAs serve as central regulators that mediate the crosstalk of various phytohormones, our model also suggests a candidate mechanism by which JA signaling may be fine-tuned by other signaling pathways through DELLAs.

Low oleic acid-derived repression of jasmonic acid-inducible defense responses requires the WRKY50 and WRKY51 proteins.

Signaling induced upon a reduction in oleic acid (18:1) levels simultaneously up-regulates salicylic acid (SA)-mediated responses and inhibits jasmonic acid (JA)-inducible defenses, resulting in enhanced resistance to biotrophs but increased susceptibility to necrotrophs. SA and the signaling component Enhanced Disease Susceptibility1 function redundantly in this low-18:1-derived pathway to induce SA signaling but do not function in the repression of JA responses. We show that repression of JA-mediated signaling under low-18:1 conditions is mediated via the WRKY50 and WRKY51 proteins. Knockout mutations in WRKY50 and WRKY51 lowered SA levels but did not restore pathogenesis-related gene expression or pathogen resistance to basal levels in the low-18:1-containing Arabidopsis (Arabidopsis thaliana) mutant, suppressor of SA insensitivity2 (ssi2). In contrast, both JA-inducible PDF1.2 (defensin) expression and basal resistance to Botrytis cinerea were restored. Simultaneous mutations in both WRKY genes (ssi2 wrky50 wrky51) did not further enhance the JA or Botrytis-related responses. The ssi2 wrky50 and ssi2 wrky51 plants contained high levels of reactive oxygen species and exhibited enhanced cell death, the same as ssi2 plants. This suggested that high reactive oxygen species levels or increased cell death were not responsible for the enhanced susceptibility of ssi2 plants to B. cinerea. Exogenous SA inhibited JA-inducible PDF1.2 expression in the wild type but not in wrky50 or wrky51 mutant plants. These results show that the WRKY50 and WRKY51 proteins mediate both SA- and low-18:1-dependent repression of JA signaling.

Interaction between polygalacturonase-inhibiting protein and jasmonic acid during defense activation in tomato against Botrytis cinerea

Oligogalacturonic acids (OGAs) generated from in vitro interaction between fungal polygalacturonase (PG) and bean PG-inhibiting protein (PGIP) were shown to activate phytoalexin biosynthesis in soybean. Based on this observation, it was hypothesized that PGIP-dependent generation of OGAs activates plant defence responses in vivo. We tested the hypothesis that PGIP activates jasmonic acid-dependent responses to pathogens. For this purpose, a population of tomato plants segregating for a mutation in the jasmonate receptor CORONATINE INSENSITIVE1 (coi1) and for overexpression of pear PGIP (pPGIP) was challenged with Botrytis cinerea. The coi1 mutant was hypersensitive to B. cinerea, but overexpression of pPGIP in the coi1 mutant background reduced pathogen susceptibility, suggesting that these two genes independently alter defence responses. In addition, pPGIP overexpression suppressed pathogen induction of salicylic acid in the coi1 mutant and activated expression of acidic s-1,3-glucanase independently of the coi1 mutation. However, expression of proteinase inhibitor II (PIN II) in pPGIP overexpressing tomato plants was dependent on COI1. Effects of pPGIP overexpression on defence are therefore complex and only in the case of PIN II pPGIP acts through COI1.

Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth.

Plant drought stress response and resistance are complex biological processes that need to be analyzed at a systems level using genomics and physiological approaches to dissect experimental models that address drought stresses encountered by crops in the field. Toward this goal, a controlled, sublethal, moderate drought (mDr) treatment system was developed in Arabidopsis (Arabidopsis thaliana) as a reproducible assay for the dissection of plant responses to drought. The drought assay was validated using Arabidopsis mutants in abscisic acid (ABA) biosynthesis and signaling displaying drought sensitivity and in jasmonate response mutants showing drought resistance, indicating the crucial role of ABA and jasmonate signaling in drought response and acclimation. A comparative transcriptome analysis of soil water deficit drought stress treatments revealed the similarity of early-stage mDr to progressive drought, identifying common and specific stress-responsive genes and their promoter cis-regulatory elements. The dissection of mDr stress responses using a time-course analysis of biochemical, physiological, and molecular processes revealed early accumulation of ABA and induction of associated signaling genes, coinciding with a decrease in stomatal conductance as an early avoidance response to drought stress. This is accompanied by a peak in the expression of expansin genes involved in cell wall expansion, as a preparatory step toward drought acclimation by the adjustment of the cell wall. The time-course analysis of mDr provides a model with three stages of plant responses: an early priming and preconditioning stage, followed by an intermediate stage preparatory for acclimation, and a late stage of new homeostasis with reduced growth.

COI1, a jasmonate receptor, is involved in ethylene-induced inhibition of Arabidopsis root growth in the light

Plant response to stress is orchestrated by hormone signalling pathways including those activated by jasmonates (JAs) and by ethylene, both of which stunt root growth. COI1 is a JA receptor and is required for the known responses to this hormone. It was observed that the coi1 mutant, which is largely unresponsive to growth inhibition by JAs, was also partially unresponsive to growth inhibition by ethylene and by its immediate precursor, 1-aminocyclopropane-1-carboxylic acid (ACC), in the light but not in the dark. Although COI1 was required for this response to ACC, other components of the JA signal perception pathway were not. Mutants selected for insensitivity to ethylene, including etr1, ein2, and ein3, showed greater ACC-induced root growth inhibition in the light than in the dark. However, the double mutants etr1;coi1, ein2;coi1, and ein3;coi1, and coi1 seedlings treated with silver ions to block the ethylene receptors showed almost complete unresponsiveness to ACC-induced root growth inhibition in the light. The light requirement for the COI1-mediated growth inhibition by ACC was for long photoperiods, and the ACC response was not abolished by mutations in the known photoreceptors. The complementation assay indicated that SCF complex assembly was not required for COI1 function in the ACC response, in contrast to the JA response. It is concluded that COI1 is required for the light-dependent, JA-independent, root growth inhibition by ethylene.

Alternative splicing expands the repertoire of dominant JAZ repressors of jasmonate signaling

Jasmonates (JAs) are fatty acid-derived signaling compounds that control diverse aspects of plant growth, development and immunity. The F-box protein COI1 functions both as a receptor for jasmonoyl-l-isoleucine (JA-Ile) and as the component of an E3-ubiquitin ligase complex (SCF(COI1) ) that targets JAZ transcriptional regulators for degradation. A key feature of JAZ proteins is the C-terminal Jas motif that mediates the JA-Ile-dependent interaction with COI1. Here, we show that most JAZ genes from evolutionarily diverse plants contain a conserved intron that splits the Jas motif into 20 N-terminal and seven C-terminal (X(5) PY) amino acid submotifs. In most members of the Arabidopsis JAZ family, alternative splicing events involving retention of this intron generate proteins that are truncated before the X(5) PY sequence. In vitro pull-down and yeast two-hybrid assays indicate that these splice variants have reduced capacity to form stable complexes with COI1 in the presence of the bioactive stereoisomer of the hormone (3R,7S)-JA-Ile. cDNA overexpression studies showed that some, but not all, truncated splice variants are dominant repressors of JA signaling. We also show that strong constitutive expression of an intron-containing JAZ10 genomic clone is sufficient to repress JA responses. These findings provide evidence for functional differences between JAZ isoforms, and establish a direct link between the alternative splicing of JAZ pre-mRNA and the dominant repression of JA signal output. We propose that production of dominant JAZ repressors by alternative splicing reduces the negative consequences associated with inappropriate or hyperactivation of the JA response pathway.

Plant mediator

Jasmonate (JA) signaling plays an important role in regulating both plant defense and development. We have recently reported that the PHYTOCHROME AND FLOWERING TIME1 (PFT1) gene, which encodes the MEDIATOR25 subunit of the plant Mediator complex, is a key regulator of JA regulated transcription. We showed that the pft1 mutant had attenuated expression of a wide range of JA responsive genes and altered resistance to fungal pathogens. Here we examine the position of PFT1/MED25 within the JA pathway and discuss its role in “mediating” the JA response.

Cloning and characterization of HbJAZ1 from the laticifer cells in rubber tree (Hevea brasiliensis Muell. Arg.)

Although jasmonate (JA) signaling has recently been well elucidated in Arabidopsis thaliana, the JASMONATE ZIM domain proteins (JAZs) are suggested to have an important role in regulating specific JA responses in plants, not much is known about how the specific JA responses are regulated in plants. Laticifer is the sole site of natural rubber biosynthesis in rubber tree. Here, the full-length cDNA and promoter region of HbJAZ1 gene were cloned and characterized from the laticifer cells in rubber tree by a combination of molecular techniques and bioinformatic analyses. The cDNA was 1,442-bp long containing an 852-bp open reading frame (ORF) encoding a putative protein of 284 amino acids. The predicted HbJAZ1 protein possessed the conservative ZIM and Jas domains, and was homologous to the JAZ members from Arabidopsis and the JAZ homologs from other plant species. The 976-bp promoter region of HbJAZ1 was isolated using PCR-based DNA Walking. TATA box and other core configurations as well as some special cis-acting elements involving in gibberellin-, jasmonic acid- and wound-responsiveness were found within this region. Transcription pattern analysis revealed that HbJAZ expression was strongly up-regulated by tapping and mechanical wounding, but not by ethrel application. Characterization of HbJAZ1 will attribute to understand JA signaling in laticifers, a specialized tissue for natural rubber biosynthesis in rubber trees.

NINJA connects the co-repressor TOPLESS to jasmonate signalling

Jasmonoyl-isoleucine (JA-Ile) is a plant hormone that regulates a broad array of plant defence and developmental processes1–5. JA-Ile-responsive gene expression is regulated by the transcriptional activator MYC2 that interacts physically with the jasmonate ZIM-domain (JAZ) repressor proteins. Upon JA-Ile perception, JAZ proteins are degraded and JA-Ile-dependent gene expression is activated6,7. The molecular mechanisms by which JAZ proteins repress gene expression remain unknown. Here we show that the JAZ proteins recruit the Groucho/Tup1-type co-repressor TOPLESS (TPL)8 and TPL-related proteins (TPRs) through a previously uncharacterized adaptor protein, designated Novel INteractor of JAZ (NINJA). NINJA acts as a transcriptional repressor of which the activity is mediated by a functional TPL-binding EAR repression motif. Accordingly, both NINJA and TPL proteins function as negative regulators of jasmonate responses. Our results point to TPL proteins as general co-repressors that affect multiple signalling pathways through the interaction with specific adaptor proteins. This new insight reveals how stress- and growth-related signalling cascades use common molecular mechanisms to regulate gene expression in plants.

Manipulating the jasmonate response: How do methyl jasmonate additions mediate characteristics of aboveground and belowground mutualisms?

Summary1. Plants use a range of sophisticated strategies to protect themselves against herbivores and pathogens, such as the production of jasmonates, a group of plant hormones that prime the plant’s defense system upon attack. However, defense‐related mechanisms, such as the jasmonate response, play a more diverse role than previously appreciated. Jasmonates also regulate key mutualist relationships, leading to a suit of potential conflicting selection pressures as a single response is employed to mediate multiple species interactions.2. Here, we experimentally manipulate the host’s jasmonate response and document the impact on two key plant mutualisms: (i) changes to arbuscular mycorrhizal symbionts belowground (ii) modifications to floral traits affecting pollinator mutualists aboveground. By exogenously applying a range of methyl jasmonate solutions to cucumber plant roots grown with and without mycorrhizal fungi, we are able to examine the potential costs of the jasmonate response to both above and belowground mutualists.3. We demonstrate that the negative effect of jasmonates on floral traits depends on whether the plant is mycorrhizal or nonmycorrhizal. Mycorrhization had a positive effect on floral traits, but benefits were lost with jasmonate application. While low levels of jasmonate decreased floral traits, these same jasmonate levels increased colonization by the mycorrhizal symbiont three‐fold, but only under high phosphorus conditions.4. Our results highlight potential conflicts for the host in the regulation of their mutualists under different conditions and suggest that the overall impact of the jasmonate response depends on the plant mycorrhizal status and its nutrient context.5. These findings suggest that increasing the jasmonate response may lead to differential costs and benefits for plants and their mutualists, and highlight potential conflictin planta, with mycorrhizal symbionts benefiting from intermediate levels of jasmonates while certain floral traits can be depressed at this same level.

Ethylene Signaling Renders the Jasmonate Response of Arabidopsis Insensitive to Future Suppression by Salicylic Acid

Cross-talk between jasmonate (JA), ethylene (ET), and Salicylic acid (SA) signaling is thought to operate as a mechanism to fine-tune induced defenses that are activated in response to multiple attackers. Here, 43 Arabidopsis genotypes impaired in hormone signaling or defense-related processes were screened for their ability to express SA-mediated suppression of JA-responsive gene expression. Mutant cev1, which displays constitutive expression of JA and ET responses, appeared to be insensitive to SA-mediated suppression of the JA-responsive marker genes PDF1.2 and VSP2. Accordingly, strong activation of JA and ET responses by the necrotrophic pathogens Botrytis cinerea and Alternaria brassicicola prior to SA treatment counteracted the ability of SA to suppress the JA response. Pharmacological assays, mutant analysis, and studies with the ET-signaling inhibitor 1-methylcyclopropene revealed that ET signaling renders the JA response insensitive to subsequent suppression by SA. The APETALA2/ETHYLENE RESPONSE FACTOR transcription factor ORA59, which regulates JA/ET-responsive genes such as PDF1.2, emerged as a potential mediator in this process. Collectively, our results point to a model in which simultaneous induction of the JA and ET pathway renders the plant insensitive to future SA-mediated suppression of JA-dependent defenses, which may prioritize the JA/ET pathway over the SA pathway during multi-attacker interactions.

Velocity Estimates for Signal Propagation Leading to Systemic Jasmonic Acid Accumulation in Wounded Arabidopsis

The wound response prohormone jasmonic acid (JA) accumulates rapidly in tissues both proximal and distal to injury sites in plants. Using quantitative liquid chromatography-mass spectrometry after flash freezing of tissues, we found that JA accumulated within 30 s of injury in wounded Arabidopsis leaves (p = 3.5 e(-7)). JA augmentation distal to wounds was strongest in unwounded leaves with direct vascular connections to wounded leaves wherein JA levels increased significantly within 120 s of wounding (p = 0.00027). This gave conservative and statistically robust temporal boundaries for the average velocity of the long distance signal leading to distal JA accumulation in unwounded leaves of 3.4-4.5 cm min(-1). Like JA, transcripts of the JA synthesis gene LIPOXYGENASE2 (LOX2) and the jasmonate response gene JAZ10.3 also accumulated to higher levels in directly interconnected leaves than in indirectly connected leaves. JA accumulation in a lox2-1 mutant plant was initiated rapidly after wounding then slowed progressively compared with the wild type (WT). Despite this, JAZ10.3 expression in the two genotypes was similar. Free cyclopentenone jasmonate levels were similar in both resting WT and lox2-1. In contrast, bound cyclopentenone jasmonates (arabidopsides) were far lower in lox2-1 than in the WT. The major roles of LOX2 are to generate arabidopsides and the large levels of JA that accumulate proximal to the wound. LOX2 is not essential for some of the most rapid events elicited by wounding.

Possible function of isoleucine in the methyl jasmonate response of Arabidopsis to Phelipanche aegyptiaca

Resistance of Arabidopsis thaliana to Phelipanche aegyptiaca (syn. Orobanche aegyptiaca) can be induced by exposure of the host to low concentrations of gaseous methyl jasmonate, in a concentration-dependent fashion. Application of methyl jasmonate at marginal concentrations, 10−8 M, for 12 h reduced infection by 50%. However, if the host plants were supplied with isoleucine at 10−3 M, and the isoleucine removed prior to exposure to methyl jasmonate, infection was reduced to less than 20%. The presence of isoleucine throughout the experiment—before, during and after exposure to methyl jasmonate—reduced infection of the host to almost zero. These results suggest that when Arabidopsis is exposed to methyl jasmonate, full activation of the defense mechanisms, including formation of the isoleucine jasmonic acid conjugate, might be limited by the availability of isoleucine in the host. These findings add another factor to the complex interaction between infecting parasite, and evocation of host defense mechanisms.

A Leaky Mutation in DWARF4 Reveals an Antagonistic Role of Brassinosteroid in the Inhibition of Root Growth by Jasmonate in Arabidopsis

The F-box protein CORONATINE INSENSITIVE1 (COI1) plays a central role in jasmonate (JA) signaling and is required for all JA responses in Arabidopsis (Arabidopsis thaliana). To dissect JA signal transduction, we isolated the partially suppressing coi1 (psc1) mutant, which partially suppressed coi1 insensitivity to JA inhibition of root growth. The psc1 mutant partially restored JA sensitivity in coi1-2 background and displayed JA hypersensitivity in wild-type COI1 background. Genetic mapping, sequence analysis, and complementation tests revealed that psc1 is a leaky mutation of DWARF4 (DWF4) that encodes a key enzyme in brassinosteroid (BR) biosynthesis. Physiological analysis showed that an application of exogenous BR eliminated the partial restoration of JA sensitivity by psc1 in coi1-2 background and the JA hypersensitivity of psc1 in wild-type COI1 background. Exogenous BR also attenuated JA inhibition of root growth in the wild type. In addition, the expression of DWF4 was inhibited by JA, and this inhibition was dependent on COI1. These results indicate that (1) BR is involved in JA signaling and negatively regulates JA inhibition of root growth, and (2) the DWF4 is down-regulated by JA and is located downstream of COI1 in the JA-signaling pathway.

The Arabidopsis CORONATINE INSENSITIVE1 Protein Is a Jasmonate Receptor

Jasmonates play a number of diverse roles in plant defense and development. CORONATINE INSENSITIVE1 (COI1), an F-box protein essential for all the jasmonate responses, interacts with multiple proteins to form the SCF(COI1) E3 ubiquitin ligase complex and recruits jasmonate ZIM-domain (JAZ) proteins for degradation by the 26S proteasome. To determine which protein directly binds to jasmonoyl-isoleucine (JA-Ile)/coronatine (COR) and serves as a receptor for jasmonate, we built a high-quality structural model of COI1 and performed molecular modeling of COI1-jasmonate interactions. Our results imply that COI1 has the structural traits for binding JA-Ile or COR. The direct binding of these molecules with COI1 was further examined using a combination of molecular and biochemical approaches. First, we used the immobilized jasmonate approach to show that the COI1 protein in crude leaf extracts can bind to the jasmonate moiety of JA-Ile. Second, we employed surface plasmon resonance technology with purified COI1 and JAZ1 protein to reveal the interaction among COI1, JA-Ile, and JAZ1. Finally, we used the photoaffinity labeling technology to show the direct binding of COR with purified insect-expressed COI1. Taken together, these results demonstrate that COI1 directly binds to JA-Ile and COR and serves as a receptor for jasmonate.

The Mediator Complex Subunit PFT1 Is a Key Regulator of Jasmonate-Dependent Defense inArabidopsis

Jasmonate signaling plays an important role in both plant defense and development. Here, we have identified a subunit of the Mediator complex as a regulator of the jasmonate signaling pathway in Arabidopsis thaliana. The Mediator complex is a conserved multiprotein complex that acts as a universal adaptor between transcription factors and the RNA polymerase II transcriptional machinery. We report that the PHYTOCHROME AND FLOWERING TIME1 (PFT1) gene, which encodes the MEDIATOR25 subunit of Mediator, is required for jasmonate-dependent defense gene expression and resistance to leaf-infecting necrotrophic fungal pathogens. Conversely, PFT1 appears to confer susceptibility to Fusarium oxysporum, a root-infecting hemibiotrophic fungal pathogen known to hijack jasmonate responses for disease development. Consistent with this, jasmonate gene expression was suppressed in the pft1 mutant during infection with F. oxysporum. In addition, a wheat (Triticum aestivum) homolog of PFT1 complemented the defense and the developmental phenotypes of the pft1 mutant, suggesting that the jasmonate signaling functions of PFT1 may be conserved in higher plants. Overall, our results identify an important control point in the regulation of the jasmonate signaling pathway within the transcriptional machinery.

The ZIM domain mediates homo‐ and heteromeric interactions between Arabidopsis JAZ proteins

Discovery of the jasmonate ZIM-domain (JAZ) repressors defined the core jasmonate (JA) signalling module as COI1-JAZ-MYC2, and allowed a full view of the JA signalling pathway from hormone perception to transcriptional reprogramming. JAZ proteins are repressors of MYC2 and targets of SCF(COI1), which is the likely jasmonate receptor. Upon hormone perception, JAZ repressors are degraded by the proteasome releasing MYC2 and allowing the activation of JA responses. All members of the JAZ family share two conserved domains, the Jas motif, required for JAZ interactions with MYC2 and COI1, and the ZIM domain, the function of which is so far unknown. Here, we show that the ZIM domain acts as a protein-protein interaction domain mediating homo- and heteromeric interactions between JAZ proteins. These JAZ-JAZ interactions are independent of the presence of the hormone. The observation that only a few members of the JAZ family form homo- and heteromers may suggest the relevance of these proteins in the regulation of JA signalling. Interestingly, the JAZ3DeltaJas protein interacts with several JAZ proteins, providing new clues to understanding the dominant JA insensitivity promoted by truncated JAZDeltaJas proteins. We also provide evidence that the Jas motif mediates the hormone-dependent interaction between Arabidopsis JAZ3 and COI1, and further confirm that the Jas motif is required and sufficient for Arabidopsis JAZ3-MYC2 interaction. Finally, we show that interaction with MYC2 is a common feature of the JAZ family, as most JAZ proteins can bind MYC2 in pull-down and yeast two-hybrid assays.

Molecular diversity and gene expression of cotton ERF transcription factors reveal that group IXa members are responsive to jasmonate, ethylene and Xanthomonas.

Several ethylene-response factor (ERF) transcription factors are believed to play a crucial role in the activation of plant defence responses, but little is known about the relationships between the diversity of this family and the functions of groups or individual ERFs in this process. In this study, 200 ERF genes from the unigene cotton database were identified. Conserved amino acid residues and phylogeny reconstruction using the AP2 conserved domain suggest that the classification into 10 major groups used for Arabidopsis and rice is applicable to the cotton ERF family. Based on in silico studies, we predict that group IX ERF genes in cotton are involved in jasmonate (JA), ethylene (ET) and pathogen responses. To test this hypothesis, we analysed the transcript profiles of the group IXa subfamily in the regulation of specific resistance to Xanthomonas campestris pathovar malvacearum. The expression of four members of group IXa was induced on challenge with X. campestris pv. malvacearum. Furthermore, the expression of several ERF genes of group IXa was induced synergistically by JA in combination with ET, suggesting that the encoded ERF proteins may play key roles in the integration of both signals to activate JA- and ET-dependent responses.

The RHA2a-interacting proteins ANAC019 and ANAC055 may play a dual role in regulating ABA response and jasmonate response

Jasmonate- and ABA-mediated signalings are involved in the activation of defense responses of plants to biotic and abiotic stresses. Accumulating evidence has suggested the existence of comprehensive synergistic or antagonistic cross-talks between these two signaling pathways. However, relatively little is known about how these cross-talks are executed at the molecular level. Our recent works have implied that, ANAC019 and ANAC055, two highly related NAC family transcription factors in Arabidopsis, may play a dual role in regulating jasmonate response and ABA response.

Anatomical and Transcriptomic Studies of the Coleorhiza Reveal the Importance of This Tissue in Regulating Dormancy in Barley

The decay of seed dormancy during after-ripening is not well understood, but elucidation of the mechanisms involved may be important for developing strategies for modifying dormancy in crop species and, for example, addressing the problem of preharvest sprouting in cereals. We have studied the germination characteristics of barley (Hordeum vulgare 'Betzes') embryos, including a description of anatomical changes in the coleorhiza and the enclosed seminal roots. The changes that occur correlate with abscisic acid (ABA) contents of embryo tissues. To understand the molecular mechanisms involved in dormancy loss, we compared the transcriptome of dormant and after-ripened barley embryos using a tissue-specific microarray approach. Our results indicate that in the coleorhiza, ABA catabolism is promoted and ABA sensitivity is reduced and that this is associated with differential regulation by after-ripening of ABA 8'-hydroxylase and of the LIPID PHOSPHATE PHOSPHATASE gene family and ABI3-INTERACTING PROTEIN2, respectively. We also identified other processes, including jasmonate responses, cell wall modification, nitrate and nitrite reduction, mRNA stability, and blue light sensitivity, that were affected by after-ripening in the coleorhiza that may be downstream of ABA signaling. Based on these results, we propose that the coleorhiza plays a major role in causing dormancy by acting as a barrier to root emergence and that after-ripening potentiates molecular changes related to ABA metabolism and sensitivity that ultimately lead to degradation of the coleorhiza, root emergence, and germination.