Regulatory activity exerted by the SAUR-AC1 promoter region in transgenic plants

Identification of QTL underlying the leaf length and area of different leaves in barley

Leaf is the main organ of photosynthesis, which significantly impacts crop yield. A high-density linkage map containing 1894 single nucleotide polymorphism (SNP) and 68 simple sequence repeats (SSR) markers was used to identify quantitative trait locus (QTL) for flag leaf length (FLL), second leaf length (SLL), third leaf length (TLL), fourth leaf length (FOLL), flag leaf area (FLA), second leaf area (SLA), third leaf area (TLA) and fourth leaf area (FOLA). In total, 57 QTLs underlying the top four leaf length and area traits were identified and mapped on chromosome 2H, 3H, 4H and 7H. Individual QTL accounted for 5.17% to 37.11% of the phenotypic variation in 2015 and 2016. A major stable QTL qFLL2-2 close to the marker 2HL_25536047 was identified on the long arm of chromosome 2H. The most important QTL clustered region at M_256210_824 - 2HL_23335246 on chromosome 2H was associated with FLL, SLL, FLA and SLA and explained high phenotypic variation. These findings provide genetic basis for improving the leaf morphology of barley. In addition, our results suggested that the top four leaves were significantly positively correlated with plant height and some yield-related traits.

Identification of QTL underlying the leaf length and area of different leaves in barley

Leaf is the main organ of photosynthesis, which significantly impacts crop yield. A high-density linkage map containing 1894 single nucleotide polymorphism (SNP) and 68 simple sequence repeats (SSR) markers was used to identify quantitative trait locus (QTL) for flag leaf length (FLL), second leaf length (SLL), third leaf length (TLL), fourth leaf length (FOLL), flag leaf area (FLA), second leaf area (SLA), third leaf area (TLA) and fourth leaf area (FOLA). In total, 57 QTLs underlying the top four leaf length and area traits were identified and mapped on chromosome 2H, 3H, 4H and 7H. Individual QTL accounted for 5.17% to 37.11% of the phenotypic variation in 2015 and 2016. A major stable QTL qFLL2-2 close to the marker 2HL_25536047 was identified on the long arm of chromosome 2H. The most important QTL clustered region at M_256210_824 - 2HL_23335246 on chromosome 2H was associated with FLL, SLL, FLA and SLA and explained high phenotypic variation. These findings provide genetic basis for improving the leaf morphology of barley. In addition, our results suggested that the top four leaves were significantly positively correlated with plant height and some yield-related traits.

Small auxin upregulated RNA (SAUR) gene family in maize: identification, evolution, and its phylogenetic comparison with Arabidopsis, rice, and sorghum

Small auxin-up RNAs (SAURs) are the early auxin-responsive genes represented by a large multigene family in plants. Here, we identified 79 SAUR gene family members from maize (Zea mays subsp. mays) by a reiterative database search and manual annotation. Phylogenetic analysis indicated that the SAUR proteins from Arabidopsis, rice, sorghum, and maize had divided into 16 groups. These genes were non-randomly distributed across the maize chromosomes, and segmental duplication and tandem duplication contributed to the expansion of the maize SAUR gene family. Synteny analysis established orthology relationships and functional linkages between SAUR genes in maize and sorghum genomes. We also found that the auxin-responsive elements were conserved in the upstream sequences of maize SAUR members. Selection analyses identified some significant site-specific constraints acted on most SAUR paralogs. Expression profiles based on microarray data have provided insights into the possible functional divergence among members of the SAUR gene family. Quantitative real-time PCR analysis indicated that some of the 10 randomly selected ZmSAUR genes could be induced at least in maize shoot or root tissue tested. The results reveal a comprehensive overview of the maize SAUR gene family and may pave the way for deciphering their function during plant development.

A novel Arabidopsis MYB-like transcription factor, MYBH, regulates hypocotyl elongation by enhancing auxin accumulation

Critical responses to developmental or environmental stimuli are mediated by different transcription factors, including members of the ERF, bZIP, MYB, MYC, and WRKY families. Of these, MYB genes play roles in many developmental processes. The overexpression of one MYB gene, MYBH, significantly increased hypocotyl elongation in Arabidopsis thaliana plants grown in the light, and the expression of this gene increased markedly in the dark. The MYBH protein contains a conserved motif, R/KLFGV, which was implicated in transcriptional repression. Interestingly, the gibberellin biosynthesis inhibitor paclobutrazol blocked the increase in hypocotyl elongation in seedlings that overexpressed MYBH. Moreover, the function of MYBH was dependent on phytochrome-interacting factor (PIF) proteins. Taken together, these results suggest that hypocotyl elongation is regulated by a delicate and efficient mechanism in which MYBH expression is triggered by challenging environmental conditions such as darkness, leading to an increase in PIF accumulation and subsequent enhanced auxin biosynthesis. These results indicate that MYBH is one of the molecular components that regulate hypocotyl elongation in response to darkness.

Auxin and gibberellin responsive Arabidopsis SMALL AUXIN UP RNA36 regulates hypocotyl elongation in the light

The Arabidopsis SAUR36, renamed RAG1, integrates auxin and gibberellin signals to regulate apical hook maintenance in etiolated seedlings, hypocotyl elongation in the light and fertility. Phytohormone signalling intermediates integrate responses to developmental cues and the variety of environmental inputs thereby governing all aspects of plant growth and development. At the genetic level, interactions of different phytohormone signalling pathways lead to the regulation of overlapping sets of target genes. We have characterised SMALL AUXIN UP RNA 36 (SAUR36, At2g45210) whose expression is induced by auxins and repressed by gibberellins. Its expression appears to be restricted to elongating tissues. Germination responses to treatments with paclobutrazol and exogenous abscisic acid were affected in knock-out, knock-down as well as ectopic expression lines. At later stages of development, however, transgenic plants with reduced levels of SAUR36 expression appeared similar to wild-type plants, while ectopic expression of SAUR36 led to the absence of apical hooks in etiolated seedlings and longer hypocotyls in light-grown seedlings. Mature plants ectopically expressing SAUR36 further displayed strongly reduced fertility and wavy growth of inflorescence axes, the latter of which could be linked to defects in auxin transport. Taken together, our data suggest that SAUR36 plays a role in the regulation of seed germination by gibberellins and abscisic acid, light-dependent hypocotyl elongation as well as apical hook formation or maintenance. Therefore, we propose that it could act as one of the converging points of auxin and gibberellin signal integration in controlling key plant developmental events. Hence, we named the gene RESPONSE TO AUXINS AND GIBBERELLINS 1 (RAG1).

Arabidopsis SMALL AUXIN UP RNA63 promotes hypocotyl and stamen filament elongation

Auxin regulates plant growth and development in part by activating gene expression. Arabidopsis thaliana SMALL AUXIN UP RNAs (SAURs) are a family of early auxin-responsive genes with unknown functionality. Here, we show that transgenic plant lines expressing artificial microRNA constructs (aMIR-SAUR-A or -B) that target a SAUR subfamily (SAUR61-SAUR68 and SAUR75) had slightly reduced hypocotyl and stamen filament elongation. In contrast, transgenic plants expressing SAUR63:GFP or SAUR63:GUS fusions had long hypocotyls, petals and stamen filaments, suggesting that these protein fusions caused a gain of function. SAUR63:GFP and SAUR63:GUS seedlings also accumulated a higher level of basipetally transported auxin in the hypocotyl than did wild-type seedlings, and had wavy hypocotyls and twisted inflorescence stems. Mutations in auxin efflux carriers could partially suppress some SAUR63:GUS phenotypes. In contrast, SAUR63:HA plants had wild-type elongation and auxin transport. SAUR63:GFP protein had a longer half-life than SAUR63:HA. Fluorescence imaging and microsomal fractionation studies revealed that SAUR63:GFP was localized mainly in the plasma membrane, whereas SAUR63:HA was present in both soluble and membrane fractions. Low light conditions increased SAUR63:HA protein turnover rate. These results indicate that membrane-associated Arabidopsis SAUR63 promotes auxin-stimulated organ elongation.

Hypocotyl directional growth in Arabidopsis: a complex trait

The growth direction of the Arabidopsis (Arabidopsis thaliana) etiolated-seedling hypocotyl is a complex trait that is controlled by extrinsic signals such as gravity and touch as well as intrinsic signals such as hormones (brassinosteroid [BR], auxin, cytokinin, ethylene) and nutrient status (glucose [Glc], sucrose). We used a genetic approach to identify the signaling elements and their relationship underlying hypocotyl growth direction. BR randomizes etiolated-seedling growth by inhibiting negative gravitropism of the hypocotyls via modulating auxin homeostasis for which we designate as reset, not to be confused with the gravity set point angle. Cytokinin signaling antagonizes this BR reset of gravity sensing and/or tropism by affecting ethylene biosynthesis/signaling. Glc also antagonizes BR reset but acts independently of cytokinin and ethylene signaling pathways via inhibiting BR-regulated gene expression quantitatively and spatially, by altering protein degradation, and by antagonizing BR-induced changes in microtubule organization and cell patterning associated with hypocotyl agravitropism. This BR reset is reduced in the presence of the microtubule organization inhibitor oryzalin, suggesting a central role for cytoskeleton reorganization. A unifying and hierarchical model of Glc and hormone signaling interplay is proposed. The biological significance of BR-mediated changes in hypocotyl graviresponse lies in the fact that BR signaling sensitizes the dark-grown seedling hypocotyl to the presence of obstacles, overriding gravitropism, to enable efficient circumnavigation through soil.

Bipartite promoter element required for auxin response

Multiple mechanisms have been described for coordination of responses to the plant hormones auxin and brassinosteroids (Zhang et al., 2009). One unexplained phenomenon is the reliance of the auxin transcriptional response on a functional brassinosteroid pathway. In this study, we used luciferase reporters to interrogate the promoter of SMALL AUXIN-UP RNA15 (SAUR15), a well-characterized auxin and brassinosteroid early response gene in Arabidopsis (Arabidopsis thaliana). After identifying a minimal region sufficient for auxin response, we targeted predicted cis-regulatory elements contained within this sequence and found a critical subset required for hormone response. Specifically, reporter sensitivity to auxin treatment required two elements: a Hormone Up at Dawn (HUD)-type E-box and an AuxRE-related TGTCT element. Reporter response to brassinosteroid treatment relied on the same two elements. Consistent with these findings, the transcription factors BRASSINOSTEROID INSENSITIVE1-EMS SUPPESSOR1 and MONOPTEROS (MP)/ AUXIN RESPONSE FACTOR5 (ARF5) showed enhanced binding to the critical promoter region containing these elements. Treatment with auxin or brassinosteroids could enhance binding of either transcription factor, and brassinosteroid enhancement of MP/ARF5 binding required an intact HUD element. Conservation of clustered HUD elements and AuxRE-related sequences in promoters of putative SAUR15 orthologs in a number of flowering plant species, in combination with evidence for statistically significant clustering of these elements across all Arabidopsis promoters, provided further evidence of the functional importance of coordinated transcription factor binding.

Auxin-regulated cell polarity: an inside job?

Auxin is now known to be a key regulator of polar events in plant cells. The mechanism by which auxin conveys a polar signal to the cell is unknown, but one well-known hypothesis is that the auxin flux across the plasma membrane regulates vesicle trafficking. This hypothesis remains controversial because of its reliance on an as-yet-undiscovered membrane flux sensor. In this article I suggest instead that the polar signal is the auxin gradient within the cell cytoplasm. A computer model of vascular development is presented that demonstrates the plausibility of this scenario. The auxin-binding protein ABP1 might be the receptor for the auxin gradient.

GER1, a GDSL motif-encoding gene from rice is a novel early light- and jasmonate-induced gene

The reaction of the rice mutant HEBIBA differs from that of wild-type rice in that the mutant responds inversely to red light and is defective in the light-triggered biosynthesis of jasmonic acid (JA). Using the wild type and the HEBIBA mutant of rice in a differential display screen, we attempted to identify genes that act in or near the convergence point of light and JA signalling. We isolated specifically regulated DNA fragments from approximately 10 000 displayed bands, and identified a new early light- and JA-induced gene. This gene encodes an enzyme containing a GDSL motif, showing 38 % identity at the amino acid level to lipase Arab-1 in Arabidopsis thaliana. The GDSL CONTAINING ENZYME RICE 1 gene (GER1) is rapidly induced by both red (R) and far-red (FR) light and by JA. The results are discussed with respect to a possible role for GER1 as a negative regulator of coleoptile elongation in the context of recent findings on the impact of JA on light signalling.

The origin of the diversity of leaf venation pattern

The leaf venation pattern of plants shows remarkable diversity and species-specificity. However, the mechanism underlying the pattern formation and pattern diversity remains unclear. We developed a mathematical model that is based on the positive feedback regulation between plant hormone auxin and its efflux carrier. This system can generate auxin flow pathways by self-organization from an almost homogeneous state. This result explains a well-known experimental phenomenon referred as to "polar auxin transport." The model can produce diverse leaf venation patterns with spatial regularity under similar conditions to those of leaf development, that is, in the presence of leaf expansion and auxin sink. Final venation patterns are strikingly affected by leaf shape and leaf expansion. These results indicate that the positive feedback regulation between auxin and its efflux carrier is a central dynamic in leaf venation pattern formation. The diversity of leaf venation patterns in plant species is probably due to the differences of leaf shape and leaf expansion pattern.

Arabidopsis Aux/IAA genes are involved in brassinosteroid-mediated growth responses in a manner dependent on organ type

We examined whether auxin/indole-3-acetic acid (Aux/IAA) proteins, which are key players in auxin-signal transduction, are involved in brassinosteroid (BR) responses. iaa7/axr2-1 and iaa17/axr3-3 mutants showed aberrant BR sensitivity and aberrant BR-induced gene expression in an organ-dependent manner. Two auxin inhibitors were tested in terms of BR responses. Yokonolide B inhibited BR responses, whereas p-chlorophenoxyisobutyric acid did not inhibit BR responses. DNA microarray analysis revealed that 108 genes were up-regulated, while only eight genes were down-regulated in iaa7. Among the genes that were up- or down-regulated in axr2, 22% were brassinolide-inducible genes, 20% were auxin-inducible genes, and the majority were sensitive neither to BR nor to auxin. An inhibitor of BR biosynthesis, brassinazole, inhibited auxin induction of the DR5-GUS gene, which consists of a synthetic auxin-response element, a minimum promoter, and a beta-glucuronidase. These results suggest that Aux/IAA proteins function in auxin- and BR-signaling pathways, and that IAA proteins function as the signaling components modulating BR sensitivity in a manner dependent on organ type.

Arabidopsis constitutive photomorphogenic mutant, bls1, displays altered brassinosteroid response and sugar sensitivity

We have isolated an Arabidopsis mutant impaired in light- and brassinosteroid (BR) induced responses, as well as in sugar signalling. The bls1 (brassinosteroid, light and sugar1) mutant displays short hypocotyl, expanded cotyledons, and de-repression of light-regulated genes in young seedlings, and leaf differentiation and silique formation on prolonged growth in dark. In light, the bls1 mutant is dwarf and develops a short root, compact rosette, with reduced trichome number, and exhibits delayed bolting. The activity of the BR inducible TCH4 and auxin inducible SAUR promoters, fused with GUS gene, is also altered in seedlings harbouring bls1 mutant background. In addition, the bls1 mutant is hypersensitive to metabolizable sugars. The short hypocotyl phenotype in dark, short root phenotype in light and sugar hypersensitivity could be rescued with BR application. Moreover, the bls1 mutant also showed higher expression of a BR biosynthetic pathway gene CPD, which is known to be feedback-regulated by BR. Using a genome-wide AFLP mapping strategy, the bls1 mutant has been mapped to a 1.4 Mb region of chromosome 5. Since no other mutant with essentially a similar phenotype has been assigned to this region, we suggest that the bls1 mutant defines a novel locus involved in regulating endogenous BR levels, with possible ramifications in integrating light, hormone and sugar signalling.

AXR1 is involved in BR-mediated elongation and SAUR-AC1 gene expression in Arabidopsis

Limited information is available concerning the interactions between the brassinosteroid (BR) and auxin signaling pathways. The expression pattern of the SAUR-AC1 gene, an early auxin-inducible gene in Arabidopsis, was studied in response to brassinolide (BL), in the presence of a BR-biosynthesis inhibitor, in a BR-deficient mutant, and in combination with auxin. The results suggested that the SAUR-AC1 gene is regulated by BRs independently of auxin levels, and that it is important in BR-mediated elongation. The axr1 (auxin insensitive 1) mutant was less sensitive to BL-induced elongation and BL-induced SAUR-AC1 expression, suggesting that a ubiquitin ligase-mediated system is involved in BR-mediated elongation.

The Arabidopsis mutant alh1 illustrates a cross talk between ethylene and auxin

Ethylene or its precursor 1-aminocyclopropane-1-carboxylic acid (ACC) can stimulate hypocotyl elongation in light-grown Arabidopsis seedlings. A mutant, designated ACC-related long hypocotyl 1 (alh1), that displayed a long hypocotyl in the light in the absence of the hormone was characterized. Etiolated alh1 seedlings overproduced ethylene and had an exaggerated apical hook and a thicker hypocotyl, although no difference in hypocotyl length was observed when compared with wild type. Alh1 plants were less sensitive to ethylene, as reflected by reduction of ACC-mediated inhibition of hypocotyl growth in the dark and delay in flowering and leaf senescence. Alh1 also had an altered response to auxin, whereas auxin levels in whole alh1 seedlings remained unaffected. In contrast to wild type, alh1 seedlings showed a limited hypocotyl elongation when treated with indole-3-acetic acid. Alh1 roots had a faster response to gravity. Furthermore, the hypocotyl elongation of alh1 and of ACC-treated wild type was reverted by auxin transport inhibitors. In addition, auxin up-regulated genes were ectopically expressed in hypocotyls upon ACC treatment, suggesting that the ethylene response is mediated by auxins. Together, these data indicate that alh1 is altered in the cross talk between ethylene and auxins, probably at the level of auxin transport.

Phytochrome-hormonal signalling networks

Through time, plants have evolved an extraordinary ability to interpret environmental cues. One of the most reliable of these cues is light, and plants are particularly adept at sensing and translating environmental light signals. The phytochrome family of photoreceptors monitor cues such as daylength or vegetative shade and adjust development to reflect change in these parameters. Indeed, it is their ability to coordinate these complex developmental changes that underpins the remarkable success of plants. Evidence is mounting that hormones control many of these light-mediated changes. Therefore, if we are to understand how light manipulates development we need to explore the interplay between light and hormonal signalling. Toward this goal, this review highlights the known convergence points of the phytochrome and the hormonal networks and explores their interactions. Contents Summary 449 I. Introduction 449 II. The phytochrome protein 450 III. Bacteriophytochromes 450 IV. IBacteriophytochrome signalling 450 V. Plant phytochrome signalling 451 VI. Ethylene perception and signalling 451 VII. Cytokinin perception and signalling 452 VIII. Brassinosteroid perception and signalling 453 IX. Gibberellin signalling 455 X. Auxin signalling 456 XI. Proteolysis in light and hormonal signalling 458 XII. Conclusion 459 Acknowledgements 459 References 459.

Indole acetic acid distribution coincides with vascular differentiation pattern during Arabidopsis leaf ontogeny

We used an anti-indole acetic acid (IAA or auxin) monoclonal antibody-based immunocytochemical procedure to monitor IAA level in Arabidopsis tissues. Using immunocytochemistry and the IAA-driven beta-glucuronidase (GUS) activity of Aux/IAA promoter::GUS constructs to detect IAA distribution, we investigated the role of polar auxin transport in vascular differentiation during leaf development in Arabidopsis. We found that shoot apical cells contain high levels of IAA and that IAA decreases as leaf primordia expand. However, seedlings grown in the presence of IAA transport inhibitors showed very low IAA signal in the shoot apical meristem (SAM) and the youngest pair of leaf primordia. Older leaf primordia accumulate IAA in the leaf tip in the presence or absence of IAA transport inhibition. We propose that the IAA in the SAM and the youngest pair of leaf primordia is transported from outside sources, perhaps the cotyledons, which accumulate more IAA in the presence than in the absence of transport inhibition. The temporal and spatial pattern of IAA localization in the shoot apex indicates a change in IAA source during leaf ontogeny that would influence flow direction and, consequently, the direction of vascular differentiation. The IAA production and transport pattern suggested by our results could explain the venation pattern, and the vascular hypertrophy caused by IAA transport inhibition. An outside IAA source for the SAM supports the notion that IAA transport and procambium differentiation dictate phyllotaxy and organogenesis.

Expression of the AtGH3a gene, an Arabidopsis homologue of the soybean GH3 gene, is regulated by phytochrome B

Light is one of the most crucial environmental cues for plants. Phytochrome, one of the major photoreceptors of plants, regulates expression of many genes. We screened for Arabidopsis promoter trap lines that exhibited light-dependent reporter gene expression. Molecular analysis of one such line revealed that a reporter gene was inserted near an Arabidopsis homologue of the soybean GH3 gene, AtGH3a. We performed RNA gel blot analysis to further characterize the response of the AtGH3a gene to light. In response to the end-of-day far-red light treatment, the expression increased substantially. Analysis of the phyB-deficient mutant indicated that this light response is under the control of phytochrome B. The expression was also induced by exogenous auxin. Furthermore, the light response was substantially reduced in the auxin-related axr2 mutant. Taken together, it is suggested that phytochrome B regulates the expression of genes by altering the levels of auxin.

AXR2 encodes a member of the Aux/IAA protein family

The dominant gain-of-function axr2-1 mutation of Arabidopsis causes agravitropic root and shoot growth, a short hypocotyl and stem, and auxin-resistant root growth. We have cloned the AXR2 gene using a map-based approach, and find that it is the same as IAA7, a member of the IAA (indole-3-acetic acid) family of auxin-inducible genes. The axr2-1 mutation changes a single amino acid in conserved domain II of AXR2/IAA7. We isolated loss-of-function mutations in AXR2/IAA7 as intragenic suppressors of axr2-1 or in a screen for insertion mutations in IAA genes. A null mutant has a slightly longer hypocotyl than wild-type plants, indicating that AXR2/IAA7 controls development in light-grown seedlings, perhaps in concert with other gene products. Dark-grown axr2-1 mutant plants have short hypocotyls and make leaves, suggesting that activation of AXR2/IAA7 is sufficient to induce morphological responses normally elicited by light. Previously described semidominant mutations in two other Arabidopsis IAA genes cause some of the same phenotypes as axr2-1, but also cause distinct phenotypes. These results illustrate functional differences among members of the Arabidopsis IAA gene family.