An R2R3-type transcription factor gene AtMYB59 regulates root growth and cell cycle progression in Arabidopsis

Ectopic expression of the sesame MYB transcription factor SiMYB305 promotes root growth and modulates ABA-mediated tolerance to drought and salt stresses in Arabidopsis

An increasing number of candidate genes related to abiotic stress tolerance are being discovered and proposed to improve the existing cultivars of the high oil-bearing crop sesame (Sesamum indicum L.). However, the in planta functional validation of these genes is remarkably lacking. In this study, we cloned a novel sesame R2-R3 MYB gene SiMYB75 which is strongly induced by drought, sodium chloride (NaCl), abscisic acid (ABA) and mannitol. SiMYB75 is expressed in various sesame tissues, especially in root and its protein is predicted to be located in the nucleus. Ectopic over-expression of SiMYB75 in Arabidopsis notably promoted root growth and improved plant tolerance to drought, NaCl and mannitol treatments. Furthermore, SiMYB75 over-expressing lines accumulated higher content of ABA than wild-type plants under stresses and also increased sensitivity to ABA. Physiological analyses revealed that SiMYB75 confers abiotic stress tolerance by promoting stomatal closure to reduce water loss; inducing a strong reactive oxygen species scavenging activity to alleviate cell damage and apoptosis; and also, up-regulating the expression levels of various stress-marker genes in the ABA-dependent pathways. Our data suggested that SiMYB75 positively modulates drought, salt and osmotic stresses responses through ABA-mediated pathways. Thus, SiMYB75 could be a promising candidate gene for the improvement of abiotic stress tolerance in crop species including sesame.

The Heterologous Expression of a Chrysanthemum nankingense TCP Transcription Factor Blocks Cell Division in Yeast and Arabidopsis thaliana

Both the presence of, and the important contribution to growth and development made by TCP transcription factors, have been established in various plant species. Here, a TCP4 homolog isolated from Chrysanthemum nankingense was shown to be more strongly transcribed in the diploid than in the autotetraploid form of the species. CnTCP4 was shown to encode a member of the class II TCP family and to be transcribed most strongly in the leaf and ligulate flowers. Its transcription was found to be substantially inhibited by spraying the plant with the synthetic cytokinin 6-benzylaminopurine. The transient expression of CnTCP4 in onion epidermal cells showed that its product localized to the nucleus, and a yeast one hybrid assay suggested that its product had transcriptional activation ability. The constitutive expression of CnTCP4 in fission yeast suppressed cell proliferation, inducing the formation of longer and a higher frequency of multinuclated cells. Its constitutive expression in Arabidopsis thaliana reduced the size of the leaves. The presence of the transgene altered the transcription of a number of cell division-related genes. A yeast one hybrid assay identified a second TCP gene (CnTCP2) able to interact with the CnTCP4 promoter. A transient expression experiment in Nicotiana benthamiana leaves showed that CnTCP2 was able to activate the CnTCP4 promoter. Like CnTCP4, CnTCP2 was shown to encode a member of the class II TCP family, to be transcribed most strongly in the leaf and ligulate flowers, and to be suppressed by exogenous 6-benzylaminopurine treatment. The CnTCP2 protein also localized to the nucleus, but had no transcriptional activation ability. Its constitutive expression in A. thaliana had similar phenotypic consequences to those induced by CnTCP4.

Mining MYB transcription factors from the genomes of orchids (Phalaenopsis and Dendrobium) and characterization of an orchid R2R3-MYB gene involved in water-soluble polysaccharide biosynthesis

Members of the MYB superfamily act as regulators in a wide range of biological processes in plants. Despite this, the MYB superfamily from the Orchidaceae has not been identified, and MYB genes related to bioactive water-soluble polysaccharide (WSP) biosynthesis are relatively unknown. In this study, we identified 159 and 165 MYB genes from two orchids, Phalaenopsis equestris and Dendrobium officinale, respectively. The MYB proteins were classified into four MYB classes in both orchids: MYB-related (MYBR), R2R3-MYB, 3R-MYB and atypical MYB proteins. The MYBR proteins in both orchids were classified into five subfamilies and 12 genes were strongly up-regulated in response to cold stress in D. officinale. The R2R3-MYB proteins were both divided into 31 clades in P. equestris and D. officinale. Among these clades, nine contained MYB TFs related to secondary cell wall biosynthesis or testa mucilage biosynthesis in Arabidopsis thaliana. In D. officinale, 10 candidate genes showed an expression pattern corresponding to changes in the WSP content. Overexpression of one of these candidate genes (DoMYB75) in A. thaliana increased seed WSP content by about 14%. This study provides information about MYB genes in two orchids that will further help to understand the transcriptional regulation of WSP biosynthesis in these orchids as well as other plant species.

Mining MYB transcription factors from the genomes of orchids (Phalaenopsis and Dendrobium) and characterization of an orchid R2R3-MYB gene involved in water-soluble polysaccharide biosynthesis

Members of the MYB superfamily act as regulators in a wide range of biological processes in plants. Despite this, the MYB superfamily from the Orchidaceae has not been identified, and MYB genes related to bioactive water-soluble polysaccharide (WSP) biosynthesis are relatively unknown. In this study, we identified 159 and 165 MYB genes from two orchids, Phalaenopsis equestris and Dendrobium officinale, respectively. The MYB proteins were classified into four MYB classes in both orchids: MYB-related (MYBR), R2R3-MYB, 3R-MYB and atypical MYB proteins. The MYBR proteins in both orchids were classified into five subfamilies and 12 genes were strongly up-regulated in response to cold stress in D. officinale. The R2R3-MYB proteins were both divided into 31 clades in P. equestris and D. officinale. Among these clades, nine contained MYB TFs related to secondary cell wall biosynthesis or testa mucilage biosynthesis in Arabidopsis thaliana. In D. officinale, 10 candidate genes showed an expression pattern corresponding to changes in the WSP content. Overexpression of one of these candidate genes (DoMYB75) in A. thaliana increased seed WSP content by about 14%. This study provides information about MYB genes in two orchids that will further help to understand the transcriptional regulation of WSP biosynthesis in these orchids as well as other plant species.

The bHLH transcription factor gene AtUPB1 regulates growth by mediating cell cycle progression in Arabidopsis

Plant growth, development and interaction with the environment involve the action of transcription factor. bHLH proteins play an essential and often conserved role in the plant kingdom. However, bHLH proteins that participate in the cell division process are less well known. Here, we report that the bHLH transcription factor gene AtUPB1 is involved in mediating cell cycle progression and root development. In yeast cells, AtUPB1 inhibits cells proliferation and the cells had increased numbers of nuclei. UPB1 overexpression decreased the expression of the cell division marker CYCB1-1, and CDKA1 expression could overcome the defect of UPB1 overexpression. Moreover, UPB1 could directly bind to the promoter region of the SIM and SMR1 genes to regulate cell cycle. These results support a new role for AtUPB1 regulating root meristem development by mediating the expression of SIM/SMR1 genes.

The Arabidopsis thaliana transcription factor MYB59 regulates calcium signalling during plant growth and stress response

Transcription factor MYB59 is involved in plant growth and stress responses by acting as negative regulator of Ca signalling and homeostasis. The Arabidopsis thaliana transcription factor MYB59 is induced by cadmium (Cd) and plays a key role in the regulation of cell cycle progression and root elongation, but its mechanism of action is poorly understood. We investigated the expression of MYB59 and differences between wild-type plants, the myb59 mutant and MYB59-overexpressing lines (obtained by transformation in the mutant genotype) during plant growth and in response to various forms of stress. We also compared the transcriptomes of wild-type and myb59 mutant plants to determine putative MYB59 targets. The myb59 mutant has longer roots, smaller leaves and smaller cells than wild-type plants and responds differently to stress in germination assay. Transcriptomic analysis revealed the upregulation in the myb59 mutant of multiple genes involved in calcium (Ca) homeostasis and signalling, including those encoding calmodulin-like proteins and Ca transporters. Notably, MYB59 was strongly induced by Ca deficiency, and the myb59 mutant was characterized by higher levels of cytosolic Ca in root cells and showed a modest alteration of Ca transient frequency in guard cells, associated with the absence of Ca-induced stomatal closure. These results indicate that MYB59 negatively regulates Ca homeostasis and signalling during Ca deficiency, thus controlling plant growth and stress responses.

The CmTCP20 gene regulates petal elongation growth in Chrysanthemum morifolium

Chrysanthemum morifolium is one of the most popular ornamental species worldwide, with high ornamental and economic value. Petal size is an important factor that influences the ornamental value. CmTCP20 is a member of TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORs (TCPs) gene family, which is closely associated with the growth and development of plants. Our previous study found that the expression of CmTCP20 was obviously down-regulated during chrysanthemum petal elongation, but its function in petal elongation has not yet been revealed. We show here that the overexpression CmTCP20 in Arabidopsis and chrysanthemum leads to similar phenotypes, including larger flower buds (or inflorescences) and longer petals. Interestingly, ectopic expression in Schizosaccharomyces pombe yeast cells showed that CmTCP20 could repress cell division and promote cell elongation. Moreover, the yeast two-hybrid, BiFC and pull-down experimental results indicated that CmTCP20 may regulate petal size via interacting with CmJAZ1-like and inducing down-regulation of CmBPE2 gene expression. This study preliminarily clarifies the function of CmTCP20 on chrysanthemum petal elongation, providing the basic theory for improving the ornamental characteristic of chrysanthemum.

The developmental dynamics of the Populus stem transcriptome

The Populus shoot undergoes primary growth (longitudinal growth) followed by secondary growth (radial growth), which produces biomass that is an important source of energy worldwide. We adopted joint PacBio Iso-Seq and RNA-seq analysis to identify differentially expressed transcripts along a developmental gradient from the shoot apex to the fifth internode of Populus Nanlin895. We obtained 87 150 full-length transcripts, including 2081 new isoforms and 62 058 new alternatively spliced isoforms, most of which were produced by intron retention, that were used to update the Populus annotation. Among these novel isoforms, there are 1187 long non-coding RNAs and 356 fusion genes. Using this annotation, we found 15 838 differentially expressed transcripts along the shoot developmental gradient, of which 1216 were transcription factors (TFs). Only a few of these genes were reported previously. The differential expression of these TFs suggests that they may play important roles in primary and secondary growth. AP2, ARF, YABBY and GRF TFs are highly expressed in the apex, whereas NAC, bZIP, PLATZ and HSF TFs are likely to be important for secondary growth. Overall, our findings provide evidence that long-read sequencing can complement short-read sequencing for cataloguing and quantifying eukaryotic transcripts and increase our understanding of the vital and dynamic process of shoot development.

Overexpression of ScMYBAS1 alternative splicing transcripts differentially impacts biomass accumulation and drought tolerance in rice transgenic plants

Drought is the most significant environmental stress for agricultural production worldwide, and tremendous efforts have been made to improve crop yield under the increasing water scarcity. Transcription factors are major players in the regulation of water stress-related genes in plants. Recently, different MYB transcription factors were characterized for their involvement in drought response. A sugarcane R2R3-MYB gene (ScMYBAS1) and its four alternative forms of transcript (ScMYAS1-2, ScMYBAS1-3, ScMYBAS1-4 and ScMYBAS1-5) were identified in this study. The subcellular localization, in Nicotiniana benthamiana, of the TFs fused in frame with GFP revealed that ScMYBAS1-2-GFP and ScMYBAS1-3-GFP were observed in the nucleus. The overexpression of ScMYBAS1-2 and ScMYBAS1-3 spliced transcripts in rice promoted change in plant growth under both well-watered and drought conditions. The ScMYBAS1-2 and ScMYBAS1-3 transgenic lines revealed a higher relative water content (RWC) compared to the wild type before maximum stress under drought conditions. The ScMYBAS1-2 transgenic lines showed a reduction in biomass (total dry weight). Conversely, ScMYBAS1-3 showed an increased biomass (total dry weight) relative to the wild-type. The overexpression of ScMYBAS1-3 in rice transgenic lines showed involvement with drought tolerance and biomass and, for this reason, was considered a good target for plant transformation, particularly for use in developing genotypes with drought tolerance and biomass accumulation.

Biosynthesis of riccionidins and marchantins is regulated by R2R3-MYB transcription factors in Marchantia polymorpha

R2R3-MYB transcription factors constitute the largest gene family among plant transcription factor families. They became largely divergent during the evolution of land plants and regulate various biological processes. The functions of R2R3-MYBs are mostly characterized in seed plants but are poorly understood in non-seed plants. Here, we examined the function of two R2R3-MYB genes of Marchantia polymorpha (Mapoly0073s0038 and Mapoly0006s0226) that are closely related to subgroup 4 of the R2R3-MYB family. We performed LC/MS/MS metabolomics, RNA-seq analysis and expression analysis in overexpressors and knockout mutants of MpMYB14 and MpMYB02. Overexpression of MpMYB14 remarkably increased the amount of riccionidins, which are specific anthocyanins in liverworts and a few flowering plants. In contrast, overexpression of MpMYB02 increased the amount of several marchantins, which are characteristic cyclic bis (bibenzyl ether) compounds in M. polymorpha and related liverworts. Knockouts of MpMYB14 and MpMYB02 abolished the accumulation of riccionidins and marchantins, respectively. The expression of MpMYB14 was up-regulated by UV-B irradiation, N deficiency, and NaCl treatment, whereas the expression of MpMYB02 was down-regulated by NaCl treatment. Our results suggest that the regulatory framework of phenolic metabolism by R2R3-MYB was already established in early land plants.

Cholesterol accumulation by suppression of SMT1 leads to dwarfism and improved drought tolerance in herbaceous plants

Dwarfism and drought tolerance are 2 valuable traits in breeding of many crops. In this study, we report the novel physiological roles of cholesterol in regulation of plant growth and drought tolerance. Compared with the wild type, sterol-C24-methyltransferase 1 (SMT1) gene transcript was greatly reduced in a bermudagrass mutant with dwarfism and enhanced drought tolerance, accompanied with cholesterol accumulation, elevated transcript levels of a small group of genes including SAMDC, and increased concentrations of putrescine (Put), spermidine (Spd), and spermine (Spm). Knock-down of OsSMT1 expression by RNA interference resulted in similar phenotypic changes in transgenic rice. Moreover, exogenously applied cholesterol also led to elevated transcripts of a similar set of genes, higher levels of Put, Spd, and Spm, improved drought tolerance, and reduced plant height in both bermudagrass and rice. We revealed that it is Spm, but not Spd, that is responsible for the height reduction in bermudagrass and rice. In conclusion, we suggest that cholesterol induces expression of SAMDC and leads to dwarfism and elevated drought tolerance in plants as a result of the promoted Spd and Spm synthesis.

Functional Characterization of the Versatile MYB Gene Family Uncovered Their Important Roles in Plant Development and Responses to Drought and Waterlogging in Sesame

The MYB gene family constitutes one of the largest transcription factors (TFs) modulating various biological processes in plants. Although genome-wide analysis of this gene family has been carried out in some species, only three MYB members have been functionally characterized heretofore in sesame (Sesamum indicum L.). Here, we identified a relatively high number (287) of sesame MYB genes (SIMYBs) with an uncommon overrepresentation of the 1R-subfamily. A total of 95% of SIMYBs was mapped unevenly onto the 16 linkage groups of the sesame genome with 55 SIMYBs tandemly duplicated. In addition, molecular characterization, gene structure, and evolutionary relationships of SIMYBs were established. Based on the close relationship between sesame and Arabidopsis thaliana, we uncovered that the functions of SIMYBs are highly diverse. A total of 65% of SIMYBs were commonly detected in five tissues, suggesting that they represent key TFs modulating sesame growth and development. Moreover, we found that SIMYBs regulate sesame responses to drought and waterlogging, which highlights the potential of SIMYBs towards improving stress tolerance in sesame. This work presents a comprehensive picture of the MYB gene family in sesame and paves the way for further functional validation of the members of this versatile gene family.

PbrMYB21, a novel MYB protein of Pyrus betulaefolia, functions in drought tolerance and modulates polyamine levels by regulating arginine decarboxylase gene

MYB comprises a large family of transcription factors that play significant roles in plant development and stress response in plants. However, knowledge concerning the functions of MYBs and the target genes remains poorly understood. Here, we report the identification and functional characterization of a novel stress-responsive MYB gene from Pyrus betulaefolia. The MYB gene, designated as PbrMYB21, belongs to the R2R3-type and shares high degree of sequence similarity to MdMYB21. The transcript levels of PbrMYB21 were up-regulated under various abiotic stresses, particularly dehydration. PbrMYB21 was localized in the nucleus with transactivation activity. Overexpression of PbrMYB21 in tobacco conferred enhanced tolerance to dehydration and drought stresses, whereas down-regulation of PbrMYB21 in Pyrus betulaefolia by virus-induced gene silencing (VIGS) resulted in elevated drought sensitivity. Transgenic tobacco exhibited higher expression levels of ADC (arginine decarboxylase) and accumulated larger amount of polyamine in comparison with wild type (WT). VIGS of PbrMYB21 in Pyrus betulaefolia down-regulated ADC abundance and decreased polyamine level, accompanied by compromised drought tolerance. The promoter region of PbrADC contains one MYB-recognizing cis-element, which was shown to be interacted with PbrMYB21, indicating the ADC may be a target gene of PbrMYB21. Take together, these results demonstrated that PbrMYB21 plays a positive role in drought tolerance, which may be, at least in part, due to the modulation of polyamine synthesis by regulating the ADC expression.

Genome-wide analysis of specific alterations in transcript structure and accumulation caused by nutrient deficiencies in Arabidopsis thaliana

The alteration of transcript structure contributes to transcriptome plasticity. In this study, we analyzed the genome-wide response of exon combination patterns to deficiencies in 12 different nutrients in Arabidopsis thaliana roots. RNA sequencing analysis and bioinformatics using a simulation survey revealed more than 600 genes showing varying exon combinations. The overlap between genes showing differential expression (DE) and genes showing differential exon combination (DC) was notably low. Additionally, gene ontology analysis showed that gene functions were not shared between the DE and DC genes, suggesting that the genes showing DC had different roles than those showing DE. Most of the DC genes were nutrient specific. For example, two homologs of the MYB transcription factor genes MYB48 and MYB59 showed differential alternative splicing only in response to low levels of potassium. Alternative splicing of those MYB genes modulated DNA-binding motifs, and MYB59 is reportedly involved in the inhibition of root elongation. Therefore, the increased abundance of MYB isoforms with an intact DNA-binding motif under low potassium may be involved in the active inhibition of root elongation. Overall, we provide global and comprehensive data for DC genes affected by nutritional deficiencies, which contribute to elucidating an unknown mechanism involved in adaptation to nutrient deficiency.

Genome-wide organization and expression profiling of the R2R3-MYB transcription factor family in pineapple (Ananas comosus)

Background

The MYB proteins comprise one of the largest families of plant transcription factors, which are involved in various plant physiological and biochemical processes. Pineapple (Ananas comosus) is one of three most important tropical fruits worldwide. The completion of pineapple genome sequencing provides a great opportunity to investigate the organization and evolutionary traits of pineapple MYB genes at the genome-wide level.

Results

In the present study, a total of 94 pineapple R2R3-MYB genes were identified and further phylogenetically classified into 26 subfamilies, as supported by the conserved gene structures and motif composition. Collinearity analysis indicated that the segmental duplication events played a crucial role in the expansion of pineapple MYB gene family. Further comparative phylogenetic analysis suggested that there have been functional divergences of MYB gene family during plant evolution. RNA-seq data from different tissues and developmental stages revealed distinct temporal and spatial expression profiles of the AcMYB genes. Further quantitative expression analysis showed the specific expression patterns of the selected putative stress-related AcMYB genes in response to distinct abiotic stress and hormonal treatments. The comprehensive expression analysis of the pineapple MYB genes, especially the tissue-preferential and stress-responsive genes, could provide valuable clues for further function characterization.

Conclusions

In this work, we systematically identified AcMYB genes by analyzing the pineapple genome sequence using a set of bioinformatics approaches. Our findings provide a global insight into the organization, phylogeny and expression patterns of the pineapple R2R3-MYB genes, and hence contribute to the greater understanding of their biological roles in pineapple.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3896-y) contains supplementary material, which is available to authorized users.

Genome-Wide Identification, Evolution and Functional Divergence of MYB Transcription Factors in Chinese White Pear (Pyrus bretschneideri)

The MYB superfamily is large and functionally diverse in plants. To date, MYB family genes have not yet been identified in Chinese white pear (Pyrus bretschneideri), and their functions remain unclear. In this study, we identified 231 genes as candidate MYB genes and divided them into four subfamilies. The R2R3-MYB (PbrMYB) family shared an R2R3 domain with 104 amino acid residues, including five conserved tryptophan residues. The Pbr MYB family was divided into 37 functional subgroups including 33 subgroups which contained both MYB genes of Rosaceae plants and AtMYB genes, and four subgroups which included only Rosaceae MYB genes or AtMYB genes. PbrMYB genes with similar functions clustered into the same subgroup, indicating functional conservation. We also found that whole-genome duplication (WGD) and dispersed duplications played critical roles in the expansion of the MYB family. The 87 Pbr MYB duplicated gene pairs dated back to the two WGD events. Purifying selection was the primary force driving Pbr MYB gene evolution. The 15 gene pairs presented 1-7 codon sites under positive selection. A total of 147 expressed genes were identified from RNA-sequencing data of fruit, and six Pbr MYB members in subgroup C1 were identified as important candidate genes in the regulation of lignin synthesis by quantitative real-time PCR analysis. Further correlation analysis revealed that six PbrMYBs were significantly correlated with five structural gene families (F5H, HCT, CCR, POD and C3'H) in the lignin pathway. The phylogenetic, evolution and expression analyses of the MYB gene family in Chinese white pear establish a solid foundation for future comprehensive functional analysis of Pbr MYB genes.

Regulatory modules controlling early shade avoidance response in maize seedlings

Background

Optimization of shade avoidance response (SAR) is crucial for enhancing crop yield in high-density planting conditions in modern agriculture, but a comprehensive study of the regulatory network of SAR is still lacking in monocot crops.

Results

In this study, the genome-wide early responses in maize seedlings to the simulated shade (low red/far-red ratio) and also to far-red light treatment were transcriptionally profiled. The two processes were predominantly mediated by phytochrome B and phytochrome A, respectively. Clustering of differentially transcribed genes (DTGs) along with functional enrichment analysis identified important biological processes regulated in response to both treatments. Co-expression network analysis identified two transcription factor modules as potentially pivotal regulators of SAR and de-etiolation, respectively. A comprehensive cross-species comparison of orthologous DTG pairs between maize and Arabidopsis in SAR was also conducted, with emphasis on regulatory circuits controlling accelerated flowering and elongated growth, two physiological hallmarks of SAR. Moreover, it was found that the genome-wide distribution of DTGs in SAR and de-etiolation both biased toward the maize1 subgenome, and this was associated with differential retention of various cis-elements between the two subgenomes.

Conclusions

The results provide the first transcriptional picture for the early dynamics of maize phytochrome signaling. Candidate genes with regulatory functions involved in maize shade avoidance response have been identified, offering a starting point for further functional genomics investigation of maize adaptation to heavily shaded field conditions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2593-6) contains supplementary material, which is available to authorized users.

Comparative cell-specific transcriptomics reveals differentiation of C4 photosynthesis pathways in switchgrass and other C4 lineages

Almost all C4 plants require the co-ordination of the adjacent and fully differentiated cell types, mesophyll (M) and bundle sheath (BS). The C4 photosynthetic pathway operates through two distinct subtypes based on how malate is decarboxylated in BS cells; through NAD-malic enzyme (NAD-ME) or NADP-malic enzyme (NADP-ME). The diverse or unique cell-specific molecular features of M and BS cells from separate C4 subtypes of independent lineages remain to be determined. We here provide an M/BS cell type-specific transcriptome data set from the monocot NAD-ME subtype switchgrass (Panicum virgatum). A comparative transcriptomics approach was then applied to compare the M/BS mRNA profiles of switchgrass, monocot NADP-ME subtype C4 plants maize and Setaria viridis, and dicot NAD-ME subtype Cleome gynandra. We evaluated the convergence in the transcript abundance of core components in C4 photosynthesis and transcription factors to establish Kranz anatomy, as well as gene distribution of biological functions, in these four independent C4 lineages. We also estimated the divergence between NAD-ME and NADP-ME subtypes of C4 photosynthesis in the two cell types within C4 species, including differences in genes encoding decarboxylating enzymes, aminotransferases, and metabolite transporters, and differences in the cell-specific functional enrichment of RNA regulation and protein biogenesis/homeostasis. We suggest that C4 plants of independent lineages in both monocots and dicots underwent convergent evolution to establish C4 photosynthesis, while distinct C4 subtypes also underwent divergent processes for the optimization of M and BS cell co-ordination. The comprehensive data sets in our study provide a basis for further research on evolution of C4 species.

Transcriptome profiling of Kentucky bluegrass (Poa pratensis L.) accessions in response to salt stress

Background

Kentucky bluegrass (Poa pratensis L.) is a prominent turfgrass in the cool-season regions, but it is sensitive to salt stress. Previously, a relatively salt tolerant Kentucky bluegrass accession was identified that maintained green colour under consistent salt applications. In this study, a transcriptome study between the tolerant (PI 372742) accession and a salt susceptible (PI 368233) accession was conducted, under control and salt treatments, and in shoot and root tissues.

Results

Sample replicates grouped tightly by tissue and treatment, and fewer differentially expressed transcripts were detected in the tolerant PI 372742 samples compared to the susceptible PI 368233 samples, and in root tissues compared to shoot tissues. A de novo assembly resulted in 388,764 transcripts, with 36,587 detected as differentially expressed. Approximately 75 % of transcripts had homology based annotations, with several differences in GO terms enriched between the PI 368233 and PI 372742 samples. Gene expression profiling identified salt-responsive gene families that were consistently down-regulated in PI 372742 and unlikely to contribute to salt tolerance in Kentucky bluegrass. Gene expression profiling also identified sets of transcripts relating to transcription factors, ion and water transport genes, and oxidation-reduction process genes with likely roles in salt tolerance.

Conclusions

The transcript assembly represents the first such assembly in the highly polyploidy, facultative apomictic Kentucky bluegrass. The transcripts identified provide genetic information on how this plant responds to and tolerates salt stress in both shoot and root tissues, and can be used for further genetic testing and introgression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-2379-x) contains supplementary material, which is available to authorized users.

Rice responds to endophytic colonization which is independent of the common symbiotic signaling pathway

As molecular interactions of plants with N2 -fixing endophytes are largely uncharacterized, we investigated whether the common signaling pathway (CSP) shared by root nodule symbioses (RNS) and arbuscular mycorrhizal (AM) symbioses may have been recruited for the endophytic Azoarcus sp.-rice (Oryza sativa) interaction, and combined this investigation with global approaches to characterize rice root responses to endophytic colonization. Putative homologs of genes required for the CSP were analyzed for their putative role in endophytic colonization. Proteomic and suppressive subtractive hybridization (SSH) approaches were also applied, and a comparison of defense-related processes was carried out by setting up a pathosystem for flooded roots with Xanthomonas oryzae pv. oryzae strain PXO99 (Xoo). All tested genes were expressed in rice roots seedlings but not induced upon Azoarcus sp. inoculation, and the oscyclops and oscastor mutants were not impaired in endophytic colonization. Global approaches highlighted changes in rice metabolic activity and Ca(2+) -dependent signaling in roots colonized by endophytes, including some stress proteins. Marker genes for defense responses were induced to a lesser extent by the endophytes than by the pathogen, indicating a more compatible interaction. Our results thus suggest that rice roots respond to endophytic colonization by inducing metabolic shifts and signaling events, for which the CSP is not essential.

A Dynamic Gene Regulatory Network Model That Recovers the Cyclic Behavior of Arabidopsis thaliana Cell Cycle

Cell cycle control is fundamental in eukaryotic development. Several modeling efforts have been used to integrate the complex network of interacting molecular components involved in cell cycle dynamics. In this paper, we aimed at recovering the regulatory logic upstream of previously known components of cell cycle control, with the aim of understanding the mechanisms underlying the emergence of the cyclic behavior of such components. We focus on Arabidopsis thaliana, but given that many components of cell cycle regulation are conserved among eukaryotes, when experimental data for this system was not available, we considered experimental results from yeast and animal systems. We are proposing a Boolean gene regulatory network (GRN) that converges into only one robust limit cycle attractor that closely resembles the cyclic behavior of the key cell-cycle molecular components and other regulators considered here. We validate the model by comparing our in silico configurations with data from loss- and gain-of-function mutants, where the endocyclic behavior also was recovered. Additionally, we approximate a continuous model and recovered the temporal periodic expression profiles of the cell-cycle molecular components involved, thus suggesting that the single limit cycle attractor recovered with the Boolean model is not an artifact of its discrete and synchronous nature, but rather an emergent consequence of the inherent characteristics of the regulatory logic proposed here. This dynamical model, hence provides a novel theoretical framework to address cell cycle regulation in plants, and it can also be used to propose novel predictions regarding cell cycle regulation in other eukaryotes.

In multicellular organisms, cells undergo a cyclic behavior of DNA duplication and delivery of a copy to daughter cells during cell division. In each of the main cell-cycle (CC) stages different sets of proteins are active and genes are expressed. Understanding how such cycling cellular behavior emerges and is robustly maintained in the face of changing developmental and environmental conditions, remains a fundamental challenge of biology. The molecular components that cycle through DNA duplication and citokinesis are interconnected in a complex regulatory network. Several models of such network have been proposed, although the regulatory network that robustly recovers a limit-cycle steady state that resembles the behavior of CC molecular components has been recovered only in a few cases, and no comprehensive model exists for plants. In this paper we used the plant Arabidopsis thaliana, as a study system to propose a core regulatory network to recover a cyclic attractor that mimics the oscillatory behavior of the key CC components. Our analyses show that the proposed GRN model is robust to transient alterations, and is validated with the loss- and gain-of-function mutants of the CC components. The interactions proposed for Arabidopsis thaliana CC can inspire predictions for further uncovering regulatory motifs in the CC of other organisms including human.

High REDOX RESPONSIVE TRANSCRIPTION FACTOR1 Levels Result in Accumulation of Reactive Oxygen Species in Arabidopsis thaliana Shoots and Roots

Redox Responsive Transcription Factor1 (RRTF1) in Arabidopsis is rapidly and transiently upregulated by H2O2, as well as biotic- and abiotic-induced redox signals. RRTF1 is highly conserved in angiosperms, but its physiological role remains elusive. Here we show that inactivation of RRTF1 restricts and overexpression promotes reactive oxygen species (ROS) accumulation in response to stress. Transgenic lines overexpressing RRTF1 are impaired in root and shoot development, light sensitive, and susceptible to Alternaria brassicae infection. These symptoms are diminished by the beneficial root endophyte Piriformospora indica, which reduces ROS accumulation locally in roots and systemically in shoots, and by antioxidants and ROS inhibitors that scavenge ROS. More than 800 genes were detected in mature leaves and seedlings of transgenic lines overexpressing RRTF1; ∼ 40% of them have stress-, redox-, ROS-regulated-, ROS-scavenging-, defense-, cell death- and senescence-related functions. Bioinformatic analyses and in vitro DNA binding assays demonstrate that RRTF1 binds to GCC-box-like sequences in the promoter of RRTF1-responsive genes. Upregulation of RRTF1 by stress stimuli and H2O2 requires WRKY18/40/60. RRTF1 is co-regulated with the phylogenetically related RAP2.6, which contains a GCC-box-like sequence in its promoter, but transgenic lines overexpressing RAP2.6 do not accumulate higher ROS levels. RRTF1 also stimulates systemic ROS accumulation in distal non-stressed leaves. We conclude that the elevated levels of the highly conserved RRTF1 induce ROS accumulation in response to ROS and ROS-producing abiotic and biotic stress signals.

Identification and Characterization of 40 Isolated Rehmannia glutinosa MYB Family Genes and Their Expression Profiles in Response to Shading and Continuous Cropping

The v-myb avian myeloblastosis viral oncogene homolog (MYB) superfamily constitutes one of the most abundant groups of transcription factors (TFs) described in plants. To date, little is known about the MYB genes in Rehmannia glutinosa. Forty unique MYB genes with full-length cDNA sequences were isolated. These 40 genes were grouped into five categories, one R1R2R3-MYB, four TRFL MYBs, four SMH MYBs, 25 R2R3-MYBs, and six MYB-related members. The MYB DNA-binding domain (DBD) sequence composition was conserved among proteins of the same subgroup. As expected, most of the closely related members in the phylogenetic tree exhibited common motifs. Additionally, the gene structure and motifs of the R. glutinosa MYB genes were analyzed. MYB gene expression was analyzed in the leaf and the tuberous root under two abiotic stress conditions. Expression profiles showed that most R. glutinosa MYB genes were expressed in the leaf and the tuberous root, suggesting that MYB genes are involved in various physiological and developmental processes in R. glutinosa. Seven MYB genes were up-regulated in response to shading in at least one tissue. Two MYB genes showed increased expression and 13 MYB genes showed decreased expression in the tuberous root under continuous cropping. This investigation is the first comprehensive study of the MYB gene family in R. glutinosa.

Grafting triggers differential responses between scion and rootstock

Grafting is a well-established practice to facilitate asexual propagation in horticultural and agricultural crops. It has become a method for studying molecular aspects of root-to-shoot and/or shoot-to-root signaling events. The objective of this study was to investigate differences in gene expression between the organs of the scion and rootstock of a homograft (Arabidopsis thaliana). MapMan and Gene Ontology enrichment analysis revealed differentially expressed genes from numerous functional categories related to stress responses in the developing flower buds and leaves of scion and rootstock. Meta-analysis suggested induction of drought-type responses in flower buds and leaves of the scion. The flower buds of scion showed over-representation of the transcription factor genes, such as Homeobox, NAC, MYB, bHLH, B3, C3HC4, PLATZ etc. The scion leaves exhibited higher accumulation of the regulatory genes for flower development, such as SEPALLATA 1-4, Jumonji C and AHL16. Differential transcription of genes related to ethylene, gibberellic acid and other stimuli was observed between scion and rootstock. The study is useful in understanding the molecular basis of grafting and acclimation of scion on rootstock.

Arabidopsis ERF109 mediates cross-talk between jasmonic acid and auxin biosynthesis during lateral root formation

Jasmonic acid (JA) is well known to promote lateral root formation but the mechanisms by which JA signalling is integrated into the pathways responsible for lateral root formation, and how it interacts with auxin in this process remains poorly understood. Here, we report that the highly JA-responsive ethylene response factor 109 (ERF109) mediates cross-talk between JA signalling and auxin biosynthesis to regulate lateral root formation in Arabidopsis. erf109 mutants have fewer lateral roots under MeJA treatments compared with wild type whereas ERF109 overexpression causes a root phenotype that resembles those of auxin overproduction mutants. ERF109 binds directly to GCC-boxes in the promoters of ASA1 and YUC2, which encode two key enzymes in auxin biosynthesis. Thus, our study reveals a molecular mechanism for JA and auxin cross-talk during JA-induced lateral root formation.

Overexpression of a stress-responsive MYB transcription factor of Poncirus trifoliata confers enhanced dehydration tolerance and increases polyamine biosynthesis

MYBs are an important family of transcription factors that play significant roles in plant development and stress response in plants. However, knowledge concerning the functions of MYBs in the non-model plants and the target genes is still limited. In this study, we isolated a stress-responsive R2R3-type MYB gene from trifoliate orange (Poncirus trifoliata (L.) Raf.), designated as PtsrMYB. PtsrMYB shares the highest degree of identity with AtMYB109. Subcellular localization using onion epidermal cells indicates that PtsrMYB is localized in the nucleus. Transcript levels of PtsrMYB were up-regulated by abiotic stresses such as dehydration, salt, cold and ABA treatment. Overexpression of PtsrMYB in tobacco confers enhanced dehydration tolerance, as indicated by less water loss, lower levels of malondialdehyde and reactive oxygen species. The transgenic tobacco lines displayed higher mRNA levels of two arginine decarboxylase (ADC) genes before and after dehydration treatment when compared with the wild type, concurrent with the greater levels of polyamines. Several MYB-recognizing cis-acting elements exist on the promoters of PtADC gene. Yeast one-hybrid assay demonstrated that PtsrMYB predominantly interact with two regions of the promoter, indicating the PtADC may be a target gene of PtsrMYB. Take together, PtsrMYB plays a positive role in dehydration tolerance, which may be, at least in part, due to the modulation of polyamine synthesis by regulating the ADC gene.

Soybean GmMYB73 promotes lipid accumulation in transgenic plants

BACKGROUND

Soybean is one of the most important oil crops. The regulatory genes involved in oil accumulation are largely unclear. We initiated studies to identify genes that regulate this process.

RESULTS

One MYB-type gene GmMYB73 was found to display differential expression in soybean seeds of different developing stages by microarray analysis and was further investigated for its functions in lipid accumulation. GmMYB73 is a small protein with single MYB repeat and has similarity to CPC-like MYB proteins from Arabidopsis. GmMYB73 interacted with GL3 and EGL3, and then suppressed GL2, a negative regulator of oil accumulation. GmMYB73 overexpression enhanced lipid contents in both seeds and leaves of transgenic Arabidopsis plants. Seed length and thousand-seed weight were also promoted. GmMYB73 introduction into the Arabidopsis try cpc double mutant rescued the total lipids, seed size and thousand-seed weight. GmMYB73 also elevated lipid levels in seeds and leaves of transgenic Lotus, and in transgenic hairy roots of soybean plants. GmMYB73 promoted PLDα1 expression, whose promoter can be bound and inhibited by GL2. PLDα1 mutation reduced triacylglycerol levels mildly in seeds but significantly in leaves of Arabidopsis plants.

CONCLUSIONS

GmMYB73 may reduce GL2, and then release GL2-inhibited PLDα1 expression for lipid accumulation. Manipulation of GmMYB73 may potentially improve oil production in legume crop plants.

TaMYB13-1, a R2R3 MYB transcription factor, regulates the fructan synthetic pathway and contributes to enhanced fructan accumulation in bread wheat

Fructans are the major component of temporary carbon reserve in the stem of temperate cereals, which is used for grain filling. Three families of fructosyltransferases are directly involved in fructan synthesis in the vacuole of Triticum aestivum. The regulatory network of the fructan synthetic pathway is largely unknown. Recently, a sucrose-upregulated wheat MYB transcription factor (TaMYB13-1) was shown to be capable of activating the promoter activities of sucrose:sucrose 1-fructosyltransferase (1-SST) and sucrose:fructan 6-fructosyltransferase (6-SFT) in transient transactivation assays. This work investigated TaMYB13-1 target genes and their influence on fructan synthesis in transgenic wheat. TaMYB13-1 overexpression resulted in upregulation of all three families of fructosyltransferases including fructan:fructan 1-fructosyltransferase (1-FFT). A γ-vacuolar processing enzyme (γ-VPE1), potentially involved in processing the maturation of fructosyltransferases in the vacuole, was also upregulated by TaMYB13-1 overexpression. Multiple TaMYB13 DNA-binding motifs were identified in the Ta1-FFT1 and Taγ-VPE1 promoters and were bound strongly by TaMYB13-1. The expression profiles of these target genes and TaMYB13-1 were highly correlated in recombinant inbred lines and during stem development as well as the transgenic and non-transgenic wheat dataset, further supporting a direct regulation of these genes by TaMYB13-1. TaMYB13-1 overexpression in wheat led to enhanced fructan accumulation in the leaves and stems and also increased spike weight and grain weight per spike in transgenic plants under water-limited conditions. These data suggest that TaMYB13-1 plays an important role in coordinated upregulation of genes necessary for fructan synthesis and can be used as a molecular tool to improve the high fructan trait.

MYB transcription factor genes as regulators for plant responses: an overview

Regulation of gene expression at the level of transcription controls many crucial biological processes. Transcription factors (TFs) play a great role in controlling cellular processes and MYB TF family is large and involved in controlling various processes like responses to biotic and abiotic stresses, development, differentiation, metabolism, defense etc. Here, we review MYB TFs with particular emphasis on their role in controlling different biological processes. This will provide valuable insights in understanding regulatory networks and associated functions to develop strategies for crop improvement.

Transcriptome responses to combinations of stresses in Arabidopsis

Biotic and abiotic stresses limit agricultural yields, and plants are often simultaneously exposed to multiple stresses. Combinations of stresses such as heat and drought or cold and high light intensity have profound effects on crop performance and yields. Thus, delineation of the regulatory networks and metabolic pathways responding to single and multiple concurrent stresses is required for breeding and engineering crop stress tolerance. Many studies have described transcriptome changes in response to single stresses. However, exposure of plants to a combination of stress factors may require agonistic or antagonistic responses or responses potentially unrelated to responses to the corresponding single stresses. To analyze such responses, we initially compared transcriptome changes in 10 Arabidopsis (Arabidopsis thaliana) ecotypes using cold, heat, high-light, salt, and flagellin treatments as single stress factors as well as their double combinations. This revealed that some 61% of the transcriptome changes in response to double stresses were not predic from the responses to single stress treatments. It also showed that plants prioritized between potentially antagonistic responses for only 5% to 10% of the responding transcripts. This indicates that plants have evolved to cope with combinations of stresses and, therefore, may be bred to endure them. In addition, using a subset of this data from the Columbia and Landsberg erecta ecotypes, we have delineated coexpression network modules responding to single and combined stresses.

The rice R2R3-MYB transcription factor OsMYB55 is involved in the tolerance to high temperature and modulates amino acid metabolism

Temperatures higher than the optimum negatively affects plant growth and development. Tolerance to high temperature is a complex process that involves several pathways. Understanding this process, especially in crops such as rice, is essential to prepare for predicted climate changes due to global warming. Here, we show that OsMYB55 is induced by high temperature and overexpression of OsMYB55 resulted in improved plant growth under high temperature and decreased the negative effect of high temperature on grain yield. Transcriptome analysis revealed an increase in expression of several genes involved in amino acids metabolism. We demonstrate that OsMYB55 binds to the promoter regions of target genes and directly activates expression of some of those genes including glutamine synthetase (OsGS1;2) glutamine amidotransferase (GAT1) and glutamate decarboxylase 3 (GAD3). OsMYB55 overexpression resulted in an increase in total amino acid content and of the individual amino acids produced by the activation of the above mentioned genes and known for their roles in stress tolerance, namely L-glutamic acid, GABA and arginine especially under high temperature condition. In conclusion, overexpression of OsMYB55 improves rice plant tolerance to high temperature, and this high tolerance is associated with enhanced amino acid metabolism through transcription activation.

C2 from Beet curly top virus meddles with the cell cycle: a novel function for an old pathogenicity factor

Geminiviruses are ssDNA plant viruses that infect a wide range of crops. Since geminiviruses often infect terminally differentiated cells, they must induce cell cycle re-entry in order to replicate; until recently, only two viral proteins, the replication-associated protein Rep and the curtoviral pathogenicity factor C4, had been assigned a role in the restoration of cell competency. In a recent work, we demonstrated that C2 from Beet curly top virus activates the expression of host genes involved in DNA replication and/or control of the G2/M transition in a manner consistent with cell cycle re-entry. As expected, expression of BCTV C2 results in enhanced replication of DNA viruses. We conclude that BCTV C2 acts as a re-activator of the cell cycle in infected cells, enhancing the DNA replication competency and providing a cell environment favorable for replication of geminiviruses. Potential mechanisms for this novel function are discussed in light of our findings.

The R2R3-MYB, bHLH, WD40, and related transcription factors in flavonoid biosynthesis

R2R3-MYB, bHLH, and WD40 proteins have been shown to control multiple enzymatic steps in the biosynthetic pathway responsible for the production of flavonoids, important secondary metabolites in Camellia sinensis. Few related transcription factor genes have been documented. The presence of R2R3-MYB, bHLH, and WD40 were statistically and bioinformatically analyzed on 127,094 C. sinensis transcriptome unigenes, resulting in identification of 73, 49, and 134 genes, respectively. C. sinensis phylogenetic trees were constructed for R2R3-MYB and bHLH proteins using previous Arabidopsis data and further divided into 27 subgroups (Sg) and 32 subfamilies. Motifs in some R2R3-MYB subgroups were redefined. Furthermore, Sg26 and Sg27 were expanded compared to Arabidopsis data, and bHLH proteins in C. sinensis were grouped into nine subfamilies. According to the functional annotation of Arabidopsis, flavonoid biosynthesis in C. sinensis was predicted to include R2R3-MYB genes in Sg4 (6), Sg5 (2), and Sg7 (1), as well as bHLH genes in subfamily 2 (2) and subfamily 24 (5). The wide evolutionary gap prevented phylogenetic analysis of WD40s; however, a single gene, CsWD40-1, was observed to share 80.4 % sequence homogeny with AtTTG1. Analysis of CsMYB4-1, CsMYB4-2, CsMYB4-3, CsMYB4-4, CsMYB5-1, and CsMYB5-2 revealed the interaction motif [DE]Lx2[RK]x3Lx6Lx3R, potentially contributing to the specificity of the bHLH partner in the stable MYB-bHLH complex. Full-length end-to-end polymerase chain reaction (PCR) and quantitative reverse transcriptase (qRT)-PCR were used to validate selected genes and generate relative expression ratio profiles in C. sinensis leaves by developmental stage and treatment conditions, including hormone and wound treatments. Potential target binding sites were predicted.

CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses

Organisms have evolved endogenous biological clocks as internal timekeepers to coordinate metabolic processes with the external environment. Here, we seek to understand the mechanism of synchrony between the oscillator and products of metabolism known as Reactive Oxygen Species (ROS) in Arabidopsis thaliana. ROS-responsive genes exhibit a time-of-day-specific phase of expression under diurnal and circadian conditions, implying a role of the circadian clock in transcriptional regulation of these genes. Hydrogen peroxide production and scavenging also display time-of-day phases. Mutations in the core-clock regulator, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), affect the transcriptional regulation of ROS-responsive genes, ROS homeostasis, and tolerance to oxidative stress. Mis-expression of EARLY FLOWERING 3, LUX ARRHYTHMO, and TIMING OF CAB EXPRESSION 1 affect ROS production and transcription, indicating a global effect of the clock on the ROS network. We propose CCA1 as a master regulator of ROS homeostasis through association with the Evening Element in promoters of ROS genes in vivo to coordinate time-dependent responses to oxidative stress. We also find that ROS functions as an input signal that affects the transcriptional output of the clock, revealing an important link between ROS signaling and circadian output. Temporal coordination of ROS signaling by CCA1 and the reciprocal control of circadian output by ROS reveal a mechanistic link that allows plants to master oxidative stress responses.

Bioinformatic cis-element analyses performed in Arabidopsis and rice disclose bZIP- and MYB-related binding sites as potential AuxRE-coupling elements in auxin-mediated transcription

BACKGROUND

In higher plants, a diverse array of developmental and growth-related processes is regulated by the plant hormone auxin. Recent publications have proposed that besides the well-characterized Auxin Response Factors (ARFs) that bind Auxin Response Elements (AuxREs), also members of the bZIP- and MYB-transcription factor (TF) families participate in transcriptional control of auxin-regulated genes via bZIP Response Elements (ZREs) or Myb Response Elements (MREs), respectively.

RESULTS

Applying a novel bioinformatic algorithm, we demonstrate on a genome-wide scale that singular motifs or composite modules of AuxREs, ZREs, MREs but also of MYC2 related elements are significantly enriched in promoters of auxin-inducible genes. Despite considerable, species-specific differences in the genome structure in terms of the GC content, this enrichment is generally conserved in dicot (Arabidopsis thaliana) and monocot (Oryza sativa) model plants. Moreover, an enrichment of defined composite modules has been observed in selected auxin-related gene families. Consistently, a bipartite module, which encompasses a bZIP-associated G-box Related Element (GRE) and an AuxRE motif, has been found to be highly enriched. Making use of transient reporter studies in protoplasts, these findings were experimentally confirmed, demonstrating that GREs functionally interact with AuxREs in regulating auxin-mediated transcription.

CONCLUSIONS

Using genome-wide bioinformatic analyses, evolutionary conserved motifs have been defined which potentially function as AuxRE-dependent coupling elements to establish auxin-specific expression patterns. Based on these findings, experimental approaches can be designed to broaden our understanding of combinatorial, auxin-controlled gene regulation.

NIMA-related kinase NEK6 affects plant growth and stress response in Arabidopsis

The NIMA-related kinases (NEKs) are a family of serine/threonine kinases involved largely in cell cycle control in fungi, mammals and other eukaryotes. In Arabidopsis, NEK6 is involved in the regulation of epidermal cell morphogenesis. However, other roles of NEK6 in plants are less well understood. Here we report functions of NEK6 in plant growth, development and stress responses in Arabidopsis. NEK6 transcripts and proteins are induced by ethylene precursor ACC and salt stress. Expression of other NEK genes except NEK5 is also responsive to the two treatments. Overexpression and mutant analysis disclose that the NEK6 gene increases rosette growth, seed yield and lateral root formation. However, NEK6 appears to play a negative role in the control of seed size. The gene also promotes plant tolerance to salt stress and osmotic stress in its overexpressing plants. The NEK6 gene may achieve its function through suppression of ethylene biosynthesis and activation of CYCB1;1 and CYCA3;1 expression. Our present study reveals new functions of the NEK6 gene in plant growth and stress tolerance, and manipulation of NEK6 may improve important agronomic traits in crop plants.

TaMYB13 is a transcriptional activator of fructosyltransferase genes involved in β-2,6-linked fructan synthesis in wheat

Fructans are soluble fructosyl-oligosaccharides deposited in many cool-season grass species as a carbon reserve; they are synthesised by fructosyltransferases. In wheat and barley fructans can accumulate in mature stems at a very high level and serve as an important carbon source for grain filling. Fructan synthesis in temperate cereals is regulated by sucrose level and developmental signals, and functions as a metabolic adjustment for carbon balance between carbon supply and sink demand. In this study the expression levels of a highly homologous group of Triticum aestivumMYB genes (TaMYB13-1, TaMYB13-2 and TaMYB13-3) were found to be positively correlated with the mRNA levels of sucrose:sucrose 1-fructosyltransferase (1-SST) and sucrose:fructan 6-fructosyltransferase (6-SFT) in wheat stems among recombinant inbred lines with a wide range of fructan concentrations through Affymetrix array expression analysis. This expression correction extended to expression profiles during stem development. TaMYB13 contains an R2R3-type MYB domain. In vitro random DNA-binding site selection followed by base substitution mutagenesis revealed that TaMYB13 bound to a (A/G/T)TT(A/T/C)GGT core sequence, which was present in the promoters of wheat Ta1-SST and Ta6-SFT genes as well as a barley Hv6-SFT gene. Transactivation analysis showed that TaMYB13 was a transcriptional activator and could markedly enhance the expression of 1-SST and 6-SFT promoter-driven reporter genes in wheat. Elimination of TaMYB13-binding sites in Ta6-SFT and Ta1-SST promoters markedly reduced TaMYB13-mediated reporter gene transactivation. These data suggest that TaMYB13 and its orthologues are positive regulators for controlling the expression of major fructosyltransferases involved in the fructan synthetic pathway in temperate cereals.

Towards an understanding of the nature of resistance to Phytophthora root rot in red raspberry

A mapping population segregating for root rot resistance was screened under both field and glasshouse conditions over a number of seasons. Few correlations between field and glasshouse scores were significant. Final root rot scores were significantly negatively correlated with measures of root vigour. Two QTL associated with resistance were identified as were overlapping QTL for root vigour assessments. Markers significantly associated with the traits were used to identify BAC clones, which were subsequently sequenced to examine gene content. A number of genes were identified including those associated with stem cell identity, cell proliferation and elongation in the root zone, control of meristematic activity and organisation, cell signalling, stress response, sugar sensing and control of gene expression as well as a range of transcription factors including those known to be associated with defence. For marker-assisted breeding, the SSR marker Rub118b 110 bp allele from Latham was found in resistant germplasm but was not found in any of the susceptible germplasm tested.

Control of root hair development in Arabidopsis thaliana by an endoplasmic reticulum anchored member of the R2R3-MYB transcription factor family

The evolution of roots and root hairs was a crucial innovation that contributed to the adaptation of plants to a terrestrial environment. Initiation of root hairs involves transcriptional cues that in part determine cell patterning of the root epidermis. Once root hair initiation has occurred, elongation of the root hair takes place. Although many genes have been identified as being involved in root hair development, many contributors remain uncharacterized. In this study we report on the involvement of a member (here dubbed maMYB) of the plant-specific R2R3-MYB family of transcription factors in root hair elongation in Arabidopsis. We show that maMYB is associated with the endoplasmic reticulum membrane with the transcription factor domain exposed to the cytosol, suggesting that it may function as a membrane-tethered transcription factor. We demonstrate that a truncated form of maMYB (maMYB⁸⁴⁻³⁰⁹), which contains the R2R3-MYB transcription factor domain, is localized and retained in the nucleus, where it regulates gene expression. Silencing of maMyb resulted in plants with significantly shorter root hairs but similar root hair density compared with wild type, implying a role of the protein in root hair elongation. 2,4-D (2,4-dichlorophenoxyacetic acid), an exogenous auxin analog that promotes root hair elongation, rescued the short root hair phenotype and maMyb mRNA was induced in the presence of 2,4-D and IAA (indole-3-acetic acid). These results indicate a functional role of maMYB, which is integrated with auxin, in root hair elongation in Arabidopsis.

An arginine decarboxylase gene PtADC from Poncirus trifoliata confers abiotic stress tolerance and promotes primary root growth in Arabidopsis

Arginine decarboxylase (ADC) is an important enzyme responsible for polyamine synthesis under stress conditions. In this study, the gene encoding ADC in Poncirus trifoliata (PtADC) was isolated and it existed as a single-copy member. Transcript levels of PtADC were up-regulated by low temperature and dehydration. Overexpression of PtADC in an Arabidopsis thaliana ADC mutant adc1-1 promoted putrescine synthesis in the transgenic line and the stomatal density was reverted to that in the wild type. The transgenic line showed enhanced resistance to high osmoticum, dehydration, long-term drought, and cold stress compared with the wild type and the mutant. The accumulation of reactive oxygen species (ROS) in the transgenic line was appreciably decreased under the stresses, but ROS scavenging capacity was compromised when the transgenic plants were treated with the ADC inhibitor D-arginine prior to stress treatment. In addition, the transgenic line had longer roots than the wild type and the mutant under both normal and stressful conditions, consistent with larger cell number and length of the root meristematic zone. Taken together, these results demonstrated that PtADC is involved in tolerance to multiple stresses, and its function may be due, at least partly, to efficient ROS elimination and to its influence on root growth conducive to drought tolerance.

Germline specification and function in plants

The flowering plant germline is produced during the haploid gametophytic stage. Defining the germline is complicated by the extreme reduction of the male and female gametophytes, also referred to as pollen and embryo sac, respectively. Both male and female gamete progenitors are segregated by an asymmetric cell division, as is the case for the germline in animals. Genetic studies and access to the transcriptome of isolated gametes have provided a regulatory framework for the mechanisms that define the male germline. What specifies female germline identity remains unknown. Recent evidence indicates that an auxin gradient provides positional information and plays a role in defining the identity of the female gamete lineage. The animal germline is also marked by production of small RNAs, and recent evidence indicates that this trait might be shared with the plant gamete lineage.

Male gametogenesis and germline specification in flowering plants

During angiosperm male gametophyte development, the male germline is segregated by an asymmetric cell division of the haploid microspore. This review encompasses recent advances in understanding the genetic and molecular mechanisms involved in generating the male germline from this pluripotent germline initial and in specifying the production of the twin sperm cells required for double fertilization. Genetic studies and access to the transcriptome of isolated gametes have enabled remarkable progress in understanding some of the key regulators that control and integrate germ cell cycle progression with germline specification, and an emerging regulatory model is presented. Rapid advances have also been made in understanding epigenetic regulation and small RNA pathways in the male gametophyte and germline that impact on genome integrity and gamete development, traits that are shared with animal germlines. The review concludes with a perspective of the outstanding issues and directions of future research that will further our understanding of germline specification and the gametophytic control of pollen development.

Digital gene expression signatures for maize development

Genome-wide expression signatures detect specific perturbations in developmental programs and contribute to functional resolution of key regulatory networks. In maize (Zea mays) inflorescences, mutations in the RAMOSA (RA) genes affect the determinacy of axillary meristems and thus alter branching patterns, an important agronomic trait. In this work, we developed and tested a framework for analysis of tag-based, digital gene expression profiles using Illumina's high-throughput sequencing technology and the newly assembled B73 maize reference genome. We also used a mutation in the RA3 gene to identify putative expression signatures specific to stem cell fate in axillary meristem determinacy. The RA3 gene encodes a trehalose-6-phosphate phosphatase and may act at the interface between developmental and metabolic processes. Deep sequencing of digital gene expression libraries, representing three biological replicate ear samples from wild-type and ra3 plants, generated 27 million 20- to 21-nucleotide reads with frequencies spanning 4 orders of magnitude. Unique sequence tags were anchored to 3'-ends of individual transcripts by DpnII and NlaIII digests, which were multiplexed during sequencing. We mapped 86% of nonredundant signature tags to the maize genome, which associated with 37,117 gene models and unannotated regions of expression. In total, 66% of genes were detected by at least nine reads in immature maize ears. We used comparative genomics to leverage existing information from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) in functional analyses of differentially expressed maize genes. Results from this study provide a basis for the analysis of short-read expression data in maize and resolved specific expression signatures that will help define mechanisms of action for the RA3 gene.

MYB transcription factors in Arabidopsis

The MYB family of proteins is large, functionally diverse and represented in all eukaryotes. Most MYB proteins function as transcription factors with varying numbers of MYB domain repeats conferring their ability to bind DNA. In plants, the MYB family has selectively expanded, particularly through the large family of R2R3-MYB. Members of this family function in a variety of plant-specific processes, as evidenced by their extensive functional characterization in Arabidopsis (Arabidopsis thaliana). MYB proteins are key factors in regulatory networks controlling development, metabolism and responses to biotic and abiotic stresses. The elucidation of MYB protein function and regulation that is possible in Arabidopsis will provide the foundation for predicting the contributions of MYB proteins to the biology of plants in general.

Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.)

BACKGROUND

Quantitative real-time PCR (qRT-PCR) is currently the most accurate method for detecting differential gene expression. Such an approach depends on the identification of uniformly expressed 'housekeeping genes' (HKGs). Extensive transcriptomic data mining and experimental validation in different model plants have shown that the reliability of these endogenous controls can be influenced by the plant species, growth conditions and organs/tissues examined. It is therefore important to identify the best reference genes to use in each biological system before using qRT-PCR to investigate differential gene expression. In this paper we evaluate different candidate HKGs for developmental transcriptomic studies in the economically-important flax fiber- and oil-crop (Linum usitatissimum L).

RESULTS

Specific primers were designed in order to quantify the expression levels of 20 different potential housekeeping genes in flax roots, internal- and external-stem tissues, leaves and flowers at different developmental stages. After calculations of PCR efficiencies, 13 HKGs were retained and their expression stabilities evaluated by the computer algorithms geNorm and NormFinder. According to geNorm, 2 Transcriptional Elongation Factors (TEFs) and 1 Ubiquitin gene are necessary for normalizing gene expression when all studied samples are considered. However, only 2 TEFs are required for normalizing expression in stem tissues. In contrast, NormFinder identified glyceraldehyde-3-phosphate dehydrogenase (GADPH) as the most stably expressed gene when all samples were grouped together, as well as when samples were classed into different sub-groups.qRT-PCR was then used to investigate the relative expression levels of two splice variants of the flax LuMYB1 gene (homologue of AtMYB59). LuMYB1-1 and LuMYB1-2 were highly expressed in the internal stem tissues as compared to outer stem tissues and other samples. This result was confirmed with both geNorm-designated- and NormFinder-designated-reference genes.

CONCLUSIONS

The use of 2 different statistical algorithms results in the identification of different combinations of flax HKGs for expression data normalization. Despite such differences, the use of geNorm-designated- and NormFinder-designated-reference genes enabled us to accurately compare the expression levels of a flax MYB gene in different organs and tissues. Our identification and validation of suitable flax HKGs will facilitate future developmental transcriptomic studies in this economically-important plant.