Identification and Characterization of MIKCc-Type MADS-Box Genes in the Flower Organs of Adonis amurensis.

Adonis amurensis is a perennial herbaceous flower that blooms in early spring in northeast China, where the night temperature can drop to -15 °C. To understand flowering time regulation and floral organogenesis of A. amurensis, the MIKCc-type MADS (Mcm1/Agamous/ Deficiens/Srf)-box genes were identified and characterized from the transcriptomes of the flower organs. In this study, 43 non-redundant MADS-box genes (38 MIKCc, 3 MIKC*, and 2 Mα) were identified. Phylogenetic and conserved motif analysis divided the 38 MIKCc-type genes into three major classes: ABCDE model (including AP1/FUL, AP3/PI, AG, STK, and SEPs/AGL6), suppressor of overexpression of constans1 (SOC1), and short vegetative phase (SVP). qPCR analysis showed that the ABCDE model genes were highly expressed mainly in flowers and differentially expressed in the different tissues of flower organs, suggesting that they may be involved in the flower organ identity of A. amurensis. Subcellular localization revealed that 17 full-length MADSs were mainly localized in the nucleus: in Arabidopsis, the heterologous expression of three full-length SOC1-type genes caused early flowering and altered the expression of endogenous flowering time genes. Our analyses provide an overall insight into MIKCc genes in A. amurensis and their potential roles in floral organogenesis and flowering time regulation.

Identification and characterization of An-4, a potential quantitative trait locus for awn development in rice.

BACKGROUND: Awn of rice is an important domestication trait closely associated with yield traits. Therefore, the identification of genes for awn development is of great significance for the elucidation of molecular mechanism of awn development and the genetic improvement of yield traits in rice. RESULTS: In this study, using chromosome segment substitution lines (CSSLs) derived from a long-awned Guangxi common wild rice (GXCWR, Oryza rufipogon Griff.) and a short-awned indica cultivar 9311, we identified An-4, a potential quantitative trait locus (QTL) for awn development. Then, An-4 was fine mapped into a 56-kb region of chromosome 2, which contained four annotated genes. Among these four annotated genes, Os02g0594800 was concluded to be the potential candidate gene for An-4. An-4 exhibited pleiotropic effects on awn development and several yield traits. Scanning electron microscopy (SEM) analysis showed that An-4 significantly promoted awn development at Sp7 and Sp8 stage of spikelet development. Transcriptome analysis suggested that An-4 might influence the development of awn by regulating the expression of genes related to growth, developmental process, channel regulation and extracellular region. By contrast to those of 9311, the expression level of OsRR5 in CSSL128 was significantly down-regulated, whereas the expression levels of OsCKX2 and OsGA2ox5 in CSSL128 were significantly up-regulated. In addition, our study showed that An-4 had additive effects with other genes for awn development, such as An-1, An-2/LABA1 and An-3/GAD1/RAE2. CONCLUSIONS: The identification of An-4 lays a foundation for cloning of An-4 and further elucidation of the molecular mechanism of awn development. Moreover, the identification of favorable allelic variation of An-4 from 9311 will be useful to improve rice yield traits.

Understanding the Role of Populus ECERIFERUM2-Likes in the Biosynthesis of Very-Long-Chain Fatty Acids for Cuticular Waxes.

Cuticular waxes are derived from very-long-chain fatty acid (VLCFA) precursors made by the concerted action of four enzymes that form the fatty acid (FA) elongation complex. The condensing enzyme of the complex confers specificity to substrates of different chain lengths, yet on its own cannot account for the biosynthesis of VLCFAs longer than 28 carbons (C28). Recent evidence from Arabidopsis thaliana points to a synergistic role of clade II BAHD acyltransferases and condensing enzymes in the elongation of VLCFAs beyond C28. In Populus trichocarpa, clade II is composed of seven uncharacterized paralogous genes (PtCER2-like1-7). In the present study, five of these genes were heterologously expressed in yeast and their respective FA profiles were determined. PtCER2-likes differentially altered the accumulation of C28 and C30 FAs when expressed in the presence of the condensing enzyme AtCER6. Among these, PtCER2-like5 produced the highest levels of C28 FAs in yeast and its expression was localized to the epidermis in ß-glucuronidase-reporter poplar lines, consistent with a role in cuticular wax biosynthesis. Complementation of the A. thaliana cer2-5 mutant with PtCER2-like5 increased the levels of C28-derived cuticular waxes at the expense of C30-derived components. Together, these results demonstrate that the role of CER2-likes in cuticular wax biosynthesis is conserved in Populus clade II BAHD acyltransferases.

In-vitro cytotoxicity in relation to chemotypic diversity in diploid and tetraploid populations of Gentiana kurroo Royle.

ETHNOPHARMACOLOGICAL RELEVANCE: Gentiana kurroo is a multipurpose critically endangered medicinal herb prescribed as medicine in Ayurveda in India and exhibits various pharmacological properties including anti-cancer activity. The species is rich repository of pharmacologically active secondary metabolites together with secoiridoidal glycosides. AIM OF THE STUDY: The study aimed to investigate the chemical diversity in different populations/cytotypes prevailing in G. kurroo to identify elite genetic stocks in terms of optimum accumulation/biosynthesis of desired metabolites and having higher in-vitro cytotoxicity potential in relation to chemotypic diversity. MATERIAL AND METHODS: The wild plants of the species were collected from different ranges of altitudes from the Kashmir Himalayas. For cytological evaluation, the standard meiotic analysis was performed. The standard LC-MS/MS technique was employed for phytochemical analysis based on different marker compounds viz. sweroside, swertiamarin, and gentiopicroside. Different tissues such as root-stock, aerial parts, and flowers were used for chemo-profiling. Further, the methanolic extracts of diploid and tetraploid cytotypes were assessed for cytotoxic activity by using MTT assay against four different human cancer cell lines. RESULTS: The quantification of major bioactive compounds based on tissue- and location-specific comparison, as well as in-vitro cytotoxic potential among extant cytotypes, was evaluated. The comprehensive cytomorphological studies of the populations from NW Himalayas revealed the occurrence of different chromosomal races viz. n = 13, 26. The tetraploid cytotype was hitherto unreported. The tissue-specific chemo-profiling revealed relative dominance of different phytoconstituents in root-stock. There was a noticeable increase in the quantity of the analyzed compounds in relation to increasing ploidy status along the increasing altitudes. The MTT assay of methanolic extracts of diploid and tetraploid cytotypes displayed significant cytotoxicity potential in tetraploids. The root-stock extracts of tetraploids were highly active extracts with IC50 value ranges from 5.65 to 8.53 µg/mL against HCT-116 colon cancer. CONCLUSION: The chemical evaluation of major bioactive compounds in diverse cytotypes from different plant parts along different altitudes presented an appreciable variability in sweroside, swertiamarin, and gentiopicroside contents. Additionally, the concentrations of these phytoconstituents varied for cytotoxicity potential among different screened cytotypes. This quantitative difference of active bio-constituents was in correspondence with the growth inhibition percentage of different tested cancer cell lines. Thus, the present investigation strongly alludes towards a prognostic approach for the identification of elite cytotypes/chemotypes with significant pharmacological potential.

ZEITLUPE enhances expression of PIF4 and YUC8 in the upper aerial parts of Arabidopsis seedlings to positively regulate hypocotyl elongation.

KEY MESSAGE: Microarray and genetic analyses reveal that ZTL induces the expression of genes related to auxin synthesis, thereby promoting hypocotyl elongation. ZTL is a blue-light receptor that possesses a light-oxygen-voltage-sensing (LOV) domain, an F-box motif, and a kelch repeat domain. ZTL promotes hypocotyl elongation under high temperature (28 °C) in Arabidopsis thaliana; however, the mechanism of this regulation is unknown. Here, we divided seedlings into hypocotyls and upper aerial parts, and performed microarray analyses. In hypocotyl, 1062 genes were down-regulated in ztl mutants (ztl-3 and ztl-105) compared with wild type; some of these genes encoded enzymes involved in cell wall modification, consistent with reduced hypocotyl elongation. In upper aerial parts, 1038 genes were down-regulated in the ztl mutants compared with wild type; these included genes involved in auxin synthesis and auxin response. Furthermore, the expression of the PHYTOCHROME INTERACTING FACTOR 4 (PIF4) gene, which encodes a transcription factor known to positively regulate YUCCA genes (YUCs), was also decreased in the ztl mutants. Genetic analysis revealed that overexpression of PIF4 and YUC8 could restore the suppressed hypocotyl length in the ztl mutants. Our results suggest that ZTL induces expression of YUC8 via PIF4 in upper aerial parts and promotes hypocotyl elongation.

Molecular characterization and expression analysis of small heat shock protein 17.3 gene from Sorbus pohuashanensis (Hance) Hedl. in response to abiotic stress.

Sorbus pohuashanensis, a native tree species in China that is distributed at high altitudes. However, the problem of adaptability when introducing S. pohuashanensis to low altitude areas has not been solved. sHSPs can respond and play an essential role when exposing to abiotic stresses for plants. In this study, we aimed to investigate the expression patterns underlying the abiotic stress response of the small heat shock protein 17.3 gene from S. pohuashanensis (SpHSP17.3) at growing low altitude. 1 to 4 years old seedlings of S. pohuashanensis were used as materials for the gene cloning, the tissue-specific expression and the expression analysis underlying the response to abiotic stress using the transgentic methods and qPCR. We identified the open reading frame (ORF) sequence of SpHSP17.3 of 471 bp, which encodes a 17.3 kD protein of 156 amino acids that is located in cytoplasmic. We found that SpHSP17.3 had the highest expression in the stem, followed sequentially by fruit, root, and flower. The expression level of SpHSP17.3 in the leaves was significantly induced by the high temperature (42 °C), NaCl salt and drought stress of S. pohuashanensis. Notably, the same SpHSP17.3 expression trend was detected in the SpHSP17.3-overexpressing homozygous transgenic Arabidopsis underlying the high temperature, NaCl salt and drought stress, and the SpHSP17.3-overexpressing homozygous transgenic Arabidopsis also showed higher seed germination rates under the NaCl salt stress conditions. Our results suggested that SpHSP17.3 is involved in the response to high temperature, Nacl salt, and drought stress which would play a certain effect in the adaptability of introduction and domestication of S. pohuashanensis.

Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis.

BACKGROUND: Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness and remarkable anti-inflammatory activities. Triterpenoid saponins are the major bioactive compounds of Entada phaseoloides. However, genomic or transcriptomic technologies have not been used to study the triterpenoid saponin biosynthetic pathway in this plant. RESULTS: We performed comparative transcriptome analysis of the root, stem, and leaf tissues of Entada phaseoloides with three independent biological replicates and obtained a total of 53.26 Gb clean data and 116,910 unigenes, with an average N50 length of 1218 bp. Putative functions could be annotated to 42,191 unigenes (36.1%) based on BLASTx searches against the Non-redundant, Uniprot, KEGG, Pfam, GO, KEGG and COG databases. Most of the unigenes related to triterpenoid saponin backbone biosynthesis were specifically upregulated in the stem. A total of 26 cytochrome P450 and 17 uridine diphosphate glycosyltransferase candidate genes related to triterpenoid saponin biosynthesis were identified. The differential expressions of selected genes were further verified by qPT-PCR. CONCLUSIONS: The dataset reported here will facilitate the research about the functional genomics of triterpenoid saponin biosynthesis and genetic engineering of Entada phaseoloides.

Comparative sequence analysis across Brassicaceae, regulatory diversity in KCS5 and KCS6 homologs from Arabidopsis thaliana and Brassica juncea, and intronic fragment as a negative transcriptional regulator.

Intra- and epicuticular-waxes primarily comprising of very long chain aliphatic lipid (VLCFA), terpenoids and secondary metabolites such as sterol and flavonoids played a major role in successful colonization of terrestrial ecosystem by aquatic plants and are thus considered as a key evolutionary innovation. The key rate limiting step of Fatty Acid (FA) biosynthesis of condensation/elongation are catalyzed by the enzyme, ß-ketoacyl coenzyme A synthase (KCS), part of FAE (Fatty Acid Elongase) complex. KCS6 has been shown to be responsible for elongation using C22 fatty acid as substrate and is considered essential for synthesis of VLCFA for cuticular waxes. Earlier studies have established KCS5 as a close paralog of KCS6 in Arabidopsis thaliana, albeit with non-redundant function. We subsequently established segmental duplication responsible for origin of KCS6-KCS5 paralogy which is exclusive to Brassicaceae. In the present study, we aim to understand impact of duplication on regulatory diversification and evolution, through sequence and functional analysis of cis-regulatory element of KCS5 and KCS6. High level of sequence variation leading to conservation of only the proximal end of the promoter corresponding to the core promoter was observed among Brassicaceae members; such high diversity was also revealed when sliding window analysis revealed only two to three phylogenetic footprints. Profiling of transcription factor binding sites (TFBS) across Brassicaceae shows presence of light, hormone and stress responsive motifs; a few motifs involved in tissue specific expression (Skn-1; endosperm) were also detected. Functional characterization using transcriptional fusion constructs revealed regulatory diversification when promoter activity of homologs from A. thaliana and Brassica juncea were compared. When subjected to 5-Azacytidine, altered promoter activity was observed, implying role of DNA methylation in transcriptional regulation. Finally, investigation of the role of an 87 bp fragment from first intron that is retained in a splice variant, revealed it to be a transcriptional repressor. This is a first report on comparative sequence and functional analysis of transcriptional regulation of KCS5 and KCS6; further studies are required before manipulation of cuticular waxes as a strategy for mitigating stress.

A plant genetic network for preventing dysbiosis in the phyllosphere.

The aboveground parts of terrestrial plants, collectively called the phyllosphere, have a key role in the global balance of atmospheric carbon dioxide and oxygen. The phyllosphere represents one of the most abundant habitats for microbiota colonization. Whether and how plants control phyllosphere microbiota to ensure plant health is not well understood. Here we show that the Arabidopsis quadruple mutant (min7 fls2 efr cerk1; hereafter, mfec)1, simultaneously defective in pattern-triggered immunity and the MIN7 vesicle-trafficking pathway, or a constitutively activated cell death1 (cad1) mutant, carrying a S205F mutation in a membrane-attack-complex/perforin (MACPF)-domain protein, harbour altered endophytic phyllosphere microbiota and display leaf-tissue damage associated with dysbiosis. The Shannon diversity index and the relative abundance of Firmicutes were markedly reduced, whereas Proteobacteria were enriched in the mfec and cad1S205F mutants, bearing cross-kingdom resemblance to some aspects of the dysbiosis that occurs in human inflammatory bowel disease. Bacterial community transplantation experiments demonstrated a causal role of a properly assembled leaf bacterial community in phyllosphere health. Pattern-triggered immune signalling, MIN7 and CAD1 are found in major land plant lineages and are probably key components of a genetic network through which terrestrial plants control the level and nurture the diversity of endophytic phyllosphere microbiota for survival and health in a microorganism-rich environment.

Genetic localization of the SPC gene controlling pod coiling direction in Medicago truncatula.

BACKGROUND: Handedness in plants introduced by helical growth of organs is frequently observed, and it has fascinated plant scientists for decades. However, the genetic control of natural handedness has not been revealed. In the model legume Medicago truncatula, pods can be coiled in a clockwise or anti-clockwise manner, providing a model for genetic analysis of plant handedness. OBJECTIVE: We aimed to localize the Sense of Pod Coiling (SPC) gene controlling pod coiling direction in M. truncatula. METHODS: Linkage analysis was used with a biparental population for fine mapping of the SPC gene. The genome sequence of M. truncatula Mt4.0 was used for marker identification and physical mapping. Single nucleotide polymorphisms (SNPs) between the parental lines were converted to CAPS (cleaved amplified polymorphic sequences) markers. Genetic map was constructed using the software JoinMap version 3.0. Gene predication and annotation provided by the M. truncatula genome database (http://www.medicagogenome.org) was confirmed with the programs of FGENESH and Pfam 32.0, respectively. Quantitative reverse transcription PCR (qRT-PCR) was used to analyze the relative expression levels of candidate genes. RESULTS: The genetic analysis indicated that the anti-clockwise coiling is dominant to clockwise and is controlled by the single gene, SPC. The SPC gene was delimited to a 250 kb-region on Chromosome 7. Total of 15 protein-coding genes were identified in the SPC locus through gene annotation and sequence analysis. Of those, two genes, potentially encoding a receptor-like kinase and a vacuolar cation/proton exchanger respectively, were selected as candidates for the SPC gene. CONCLUSIONS: The result presented here lay a foundation for gene cloning of SPC, which will help us to understand the molecular mechanisms underlying helical growth in plant organs.

Integrated transcriptome and miRNA analysis uncovers molecular regulators of aerial stem-to-rhizome transition in the medical herb Gynostemma pentaphyllum.

BACKGROUND: Gynostemma pentaphyllum is an important perennial medicinal herb belonging to the family Cucurbitaceae. Aerial stem-to-rhizome transition before entering the winter is an adaptive regenerative strategy in G. pentaphyllum that enables it to survive during winter. However, the molecular regulation of aerial stem-to-rhizome transition is unknown in plants. Here, integrated transcriptome and miRNA analysis was conducted to investigate the regulatory network of stem-to-rhizome transition. RESULTS: Nine transcriptome libraries prepared from stem/rhizome samples collected at three stages of developmental stem-to-rhizome transition were sequenced and a total of 5428 differentially expressed genes (DEGs) were identified. DEGs associated with gravitropism, cell wall biosynthesis, photoperiod, hormone signaling, and carbohydrate metabolism were found to regulate stem-to-rhizome transition. Nine small RNA libraries were parallelly sequenced, and seven significantly differentially expressed miRNAs (DEMs) were identified, including four known and three novel miRNAs. The seven DEMs targeted 123 mRNAs, and six pairs of miRNA-target showed significantly opposite expression trends. The GpmiR166b-GpECH2 module involved in stem-to-rhizome transition probably promotes cell expansion by IBA-to-IAA conversion, and the GpmiR166e-GpSGT-like module probably protects IAA from degradation, thereby promoting rhizome formation. GpmiR156a was found to be involved in stem-to-rhizome transition by inhibiting the expression of GpSPL13A/GpSPL6, which are believed to negatively regulate vegetative phase transition. GpmiR156a and a novel miRNA Co.47071 co-repressed the expression of growth inhibitor GpRAV-like during stem-to-rhizome transition. These miRNAs and their targets were first reported to be involved in the formation of rhizomes. In this study, the expression patterns of DEGs, DEMs and their targets were further validated by quantitative real-time PCR, supporting the reliability of sequencing data. CONCLUSIONS: Our study revealed a comprehensive molecular network regulating the transition of aerial stem to rhizome in G. pentaphyllum. These results broaden our understanding of developmental phase transitions in plants.

Identification and validation of reference genes for real-time quantitative RT-PCR analysis in jute.

BACKGROUND: With the availability of genome sequences, gene expression analysis of jute has drawn considerable attention for understanding the regulatory mechanisms of fiber development and improving fiber quality. Gene expression profiles of a target gene can provide valuable clues towards the understanding of its biological function. Reverse transcription quantitative real-time PCR (qRT-PCR) is the best method for targeted gene expression analysis due to its sensitivity and reproducibility. However, calculating relative expression requires reference genes, which must be stable across various biological conditions. For this purposes, 11 prospective genes namely, 28S RNA, ACT7, CYP, EF1A, EF2, ETIF3E, GAPDH, PP2Ac, PTB, UBC2 and UBI1 were evaluated for their potential use as reference genes in jute. RESULTS: The expression stabilities of eleven prospective genes were analyzed in various jute plant tissues, such as the root, stick, bark, leaf, flower, seed and fiber, as well as under abiotic (waterlogged, drought and salinity) and biotic stress (infestation with Macrophomina phaseolina) conditions with different time points. All 11 genes were variably expressed in different tissues and stress conditions. To find suitable reference genes in different sample sets, a comprehensive approach based on four statistical algorithms such as GeNorm, BestKeeper, NormFinder the ΔCt was used. The PP2Ac and EF2 genes were the most stably expressed across the different tissues. ACT7 and UBC2 were suitable reference genes under drought stress, and CYP and PP2Ac were the most appropriate after inoculation with Macrophomina phaseolina. Under salinity stress, PP2Ac and UBC2 were the best genes, and ACT7 and PP2Ac were the most suitable under waterlogged conditions. CONCLUSION: Expression stability of reference genes from jute varied in different tissues and selected experimental conditions. Our results provide a valuable resource for the accurate normalization of gene expression experiments in fiber research for important bast fiber crops.

Manglietia pubipedunculata (Magnoliaceae), a new species from Yunnan, China.

A new species, Manglietia pubipedunculata Q. W. Zeng & X. M. Hu (Magnoliaceae) is described and illustrated from Yunnan, China. In addition to macromorphological examination, we comparatively studied on micromorphology of leaf epidermis, leaf structure, and epidermal cell on the sclerotesta. This new species is similar to M. kwangtungensis in terms of having dense pubescence, however, their pubescence are quite different. Manglietia pubipedunculata has appressed, compressed, shorter and sparser pubescence consisting of single or two cells. Moreover, it differs from M. kwangtungensis by showing shorter and thicker peduncles, longer styles, basal carpels covered with sparsely brown appressed pubescence, and more ovules per carpel. Furthermore, the new species has thinner leaves, brown and rugged surfaces on sclerotesta, and the alveolate cell pattern consisting of pentagon or hexagon cells with papilla on secondary cell wall under the observation by SEM. The phylogenetic analysis from two nuclear PHYA and LEAFY and chloroplast trnH-psbA sequences of 11 taxa reveals that M. pubipedunculata is a distinct species.

Overexpression of the RNA binding protein MhYTP1 in transgenic apple enhances drought tolerance and WUE by improving ABA level under drought condition.

MhYTP1 is involved in post-transcriptional regulation as a member of YT521-homology (YTH) domain-containing RNA-binding proteins. We previously cloned MhYTP1 and found it participated in various biotic and abiotic stress responses. However, its function in long-term moderate drought has not been verified. Thus, we explored its biological role in response to drought. Under drought condition, the net photosynthesis rate (Pn) and water use efficiency (WUE) were significantly elevated in MhYTP1-overexpressing (OE) apple plants when compared with the non-transgenic (NT) controls. Further analysis indicated MhYTP1 expression was associated with elevated ABA content, increased stomatal density and reduced stomatal aperture. In addition, to gain insight into the function of stem-specific expression of MhYTP1, grafting experiments were performed. Interestingly, lower transpiration rate (Tr) and higher WUE were observed when transgenic plants were used as scions as opposed to rootstocks and when transgenic rather than NT plants were used as rootstocks, indicating MhYTP1 plays crucial roles in grafted plants. These results define a function for MhYTP1 in promoting tolerance to drought conditions, and suggest that MhYTP1 can serve as a candidate gene for future apple drought resistance breeding with the help of biotechnology.

Phosphoglycerate Kinases Are Co-Regulated to Adjust Metabolism and to Optimize Growth.

In plants, phosphoglycerate kinase (PGK) converts 1,3-bisphosphoglycerate into 3-phosphoglycerate in glycolysis but also participates in the reverse reaction in gluconeogenesis and the Calvin-Benson cycle. In the databases, we found three genes that encode putative PGKs. Arabidopsis (Arabidopsis thaliana) PGK1 was localized exclusively in the chloroplasts of photosynthetic tissues, while PGK2 was expressed in the chloroplast/plastid of photosynthetic and nonphotosynthetic cells. PGK3 was expressed ubiquitously in the cytosol of all studied cell types. Measurements of carbohydrate content and photosynthetic activities in PGK mutants and silenced lines corroborated that PGK1 was the photosynthetic isoform, while PGK2 and PGK3 were the plastidial and cytosolic glycolytic isoforms, respectively. The pgk1.1 knockdown mutant displayed reduced growth, lower photosynthetic capacity, and starch content. The pgk3.2 knockout mutant was characterized by reduced growth but higher starch levels than the wild type. The pgk1.1 pgk3.2 double mutant was bigger than pgk3.2 and displayed an intermediate phenotype between the two single mutants in all measured biochemical and physiological parameters. Expression studies in PGK mutants showed that PGK1 and PGK3 were down-regulated in pgk3.2 and pgk1.1, respectively. These results indicate that the down-regulation of photosynthetic activity could be a plant strategy when glycolysis is impaired to achieve metabolic adjustment and optimize growth. The double mutants of PGK3 and the triose-phosphate transporter (pgk3.2 tpt3) displayed a drastic growth phenotype, but they were viable. This implies that other enzymes or nonspecific chloroplast transporters could provide 3-phosphoglycerate to the cytosol. Our results highlight both the complexity and the plasticity of the plant primary metabolic network.

The miR156-SPL4 module predominantly regulates aerial axillary bud formation and controls shoot architecture.

Grasses possess basal and aerial axillary buds. Previous studies have largely focused on basal bud (tiller) formation but scarcely touched on aerial buds, which may lead to aerial branch development. Genotypes with and without aerial buds were identified in switchgrass (Panicum virgatum), a dedicated bioenergy crop. Bud development was characterized using scanning electron microscopy. Microarray, RNA-seq and quantitative reverse transcription polymerase chain reaction (RT-qPCR) were used to identify regulators of bud formation. Gene function was characterized by down-regulation and overexpression. Overexpression of miR156 induced aerial bud formation in switchgrass. Various analyses revealed that SQUAMOSA PROMOTER BINDING PROTEIN LIKE4 (SPL4), one of the miR156 targets, directly regulated aerial axillary bud initiation. Down-regulation of SPL4 promoted aerial bud formation and increased basal buds, while overexpression of SPL4 seriously suppressed bud formation and tillering. RNA-seq and RT-qPCR identified potential downstream genes of SPL4. Unlike all previously reported genes acting as activators of basal bud initiation, SPL4 acts as a suppressor for the formation of both aerial and basal buds. The miR156-SPL4 module predominantly regulates aerial bud initiation and partially controls basal bud formation. Genetic manipulation of SPL4 led to altered plant architecture with increased branching, enhanced regrowth after cutting and improved biomass yield.

A pivotal role of the jasmonic acid signal pathway in mediating radiation-induced bystander effects in Arabidopsis thaliana.

Although radiation-induced bystander effects (RIBE) in Arabidopsis thaliana have been well demonstrated in vivo, little is known about their underlying mechanisms, particularly with regard to the participating signaling molecules and signaling pathways. In higher plants, jasmonic acid (JA) and its bioactive derivatives are well accepted as systemic signal transducers that are produced in response to various environmental stresses. It is therefore speculated that the JA signal pathway might play a potential role in mediating radiation-induced bystander signaling of root-to-shoot. In the present study, pretreatment of seedlings with Salicylhydroxamic acid, an inhibitor of lipoxigenase (LOX) in JA biosynthesis, significantly suppressed RIBE-mediated expression of the AtRAD54 gene. After root irradiation, the aerial parts of A. thaliana mutants deficient in JA biosynthesis (aos) and signaling cascades (jar1-1) showed suppressed induction of the AtRAD54 and AtRAD51 genes and TSI and 180-bp repeats, which have been extensively used as endpoints of bystander genetic and epigenetic effects in plants. These results suggest an involvement of the JA signal pathway in the RIBE of plants. Using the root micro-grafting technique, the JA signal pathway was shown to participate in both the generation of bystander signals in irradiated root cells and radiation responses in the bystander aerial parts of plants. The over-accumulation of endogenous JA in mutant fatty acid oxygenation up-regulated 2 (fou2), in which mutation of the Two Pore Channel 1 (TPC1) gene up-regulates expression of the LOX and allene oxide synthase (AOS) genes, inhibited RIBE-mediated expression of the AtRAD54 gene, but up-regulated expression of the AtKU70 and AtLIG4 genes in the non-homologous end joining (NHEJ) pathway. Considering that NHEJ is employed by plants with increased DNA damage, the switch from HR to NHEJ suggests that over-accumulation of endogenous JA might enhance the radiosensitivity of plants in terms of RIBE.

Vesicles Are Persistent Features of Different Plastids.

Peripheral vesicles in plastids have been observed repeatedly, primarily in proplastids and developing chloroplasts, in which they are suggested to function in thylakoid biogenesis. Previous observations of vesicles in mature chloroplasts have mainly concerned low temperature pretreated plants occasionally treated with inhibitors blocking vesicle fusion. Here, we show that such vesicle-like structures occur not only in chloroplasts and proplastids, but also in etioplasts, etio-chloroplasts, leucoplasts, chromoplasts and even transforming desiccoplasts without any specific pretreatment. Observations are made both in C3 and C4 species, in different cell types (meristematic, epidermis, mesophyll, bundle sheath and secretory cells) and different organs (roots, stems, leaves, floral parts and fruits). Until recently not much focus has been given to the idea that vesicle transport in chloroplasts could be mediated by proteins, but recent data suggest that the vesicle system of chloroplasts has similarities with the cytosolic coat protein complex II system. All current data taken together support the idea of an ongoing, active and protein-mediated vesicle transport not only in chloroplasts but also in other plastids, obviously occurring regardless of chemical modifications, temperature and plastid developmental stage.

Interactive effect of water and nitrogen regimes on plant growth, root traits and water status of old and modern durum wheat genotypes.

MAIN CONCLUSIONS: The selection of the ideal root drought adaptive traits should take into account the production and maintenance of root tissues alongside the capacity to capture soil resources. Ten old and modern Spanish durum wheat (Triticum turgidum L. var durum) genotypes were grown in lysimeters under two contrasting water and nitrogen regimes to study the effect of such growth conditions on: (1) the aerial biomass, (2) the growth and structure of the roots and (3) the relationships of the root structure with aerial biomass, photosynthetic and transpirative characteristics and water use efficiency. Both high water and nitrogen regimes significantly increased aerial biomass. Root dry biomass and root length increased and decreased in response to improved water supply and nitrogen regimes, respectively. No significant correlations were detected between aerial biomass and any root trait under well-watered conditions. Under water stress aerial biomass was negatively correlated with root dry biomass, root length and root weight density and positively correlated with the specific root length, particularly for the subset of old genotypes. The high nitrogen regime significantly enriched the carbon isotope composition of the flag leaf (δ (13)CFL) and hindered the effect of the high water regime on decreasing δ (13)CFL enrichment. Thus, positive correlations of aerial biomass with δ (13)CFL were detected regardless of the water regime. The study revealed: (1) the importance of root traits for higher aerial biomass under the low water regime; (2) that the interaction between nitrogen and the water regime may affect the predictive nature of the δ (13)C in drought breeding programs; and (3) the selection of the ideal root system structure should take into account the metabolic costs of the production and maintenance of root tissues alongside the capacity of capturing resources.

Cloning and characterization of SPL-family genes in the peanut (Arachis hypogaea L.).

SQUAMOSA promoter-binding protein-like (SPL) proteins play crucial roles in plant growth, development, and responses to environmental stressors. The peanut (Arachis hypogaea L.) is a globally important oil crop. In this study, we cloned the full-length cDNA of 15 SPLs in the peanut by transcriptome sequencing and rapid amplification of cDNA ends, and analyzed their genomic DNA sequences. cDNA lengths varied significantly, from 369 to 3102 bp. The SBP domain of the peanut SPL proteins was highly conserved compared to SPLs in other plant species. Based on their sequence similarity to SPLs from other plant species, the peanut SPLs could be grouped into five subgroups. In each subgroup, lengths of individual genes, conserved motif numbers, and distribution patterns were similar. Seven of the SPLs were predicted to be targets of miR156. The SPLs were ubiquitously expressed in the roots, leaves, flowers, gynophores, and seeds, with different expression levels and accumulation patterns. Significant differences in the expression of most of the SPLs were observed between juvenile and adult leaves, suggesting that they are involved in developmental regulation. Dynamic changes occurred in transcript levels at stage 1 (aerial grown green gynophores), stage 2 (gynophores buried in soil for about three days), and stage 3 (gynophores buried in soil for about nine days with enlarged pods). Possible roles that these genes play in peanut pod initiation are discussed.