Microsatellite markers were developed for Dicksonia sellowiana (Dicksoniaceae), an overexploited and endangered tree-fern species native to Brazil. From an enriched genomic library, 11 primer pairs were selected and used to characterize 36 D. sellowiana individuals from six Brazilian populations. Eight primer pairs amplified dinucleotide and hexanucleotide repeats with two to ten alleles per locus; three primer pairs were monomorphic. For the set of polymorphic markers, the mean observed and expected heterozygosity ranged from 0.29 to 0.44 and from 0.27 to 0.56, respectively. Eight of the primer pairs were also successfully amplified for Cyathea vestita (Cyatheaceae). These molecular markers can be useful tools for genetic studies aiming to analyze the impact of deforestation and overexploitation on the population structure and genetic diversity of fern species from various botanical families.

Abscisic acid (ABA) regulates plant responses to various environmental stresses. Oxidative cleavage of cis-epoxycarotenoids catalyzed by 9-cis-epoxycarotenoid dioxygenase (NCED) is the critical step in the biosynthesis of ABA in higher plants. Using a homologous cloning approach, a NCED-like gene (designated as TaNCED1) was isolated from wheat (Triticum aestivum). It contained an open reading frame of 1 848 bp and encodes a peptide of 615 amino acids. Multiple sequence alignments showed that TaNCED1 shared high identity with NCEDs from other plants. Phylogenetic analysis revealed that TaNCED1 was most closely related to a barley HvNCED1 gene. The predicted 3D structure of TaNCED1 showed high similarity with other homologues. Southern blot analysis indicated that TaNCED1 was a single copy in the genome of wheat. TaNCED1 was differentially expressed in various organs and the expression was up-regulated by low temperature, drought, NaCl, and ABA. Heterologous expression of TaNCED1 in tobacco (Nicotiana tabacum) significantly improved its drought tolerance. Under drought treatment, TaNCED1-overexpressing transgenic tobacco plants exhibited higher germination rate, higher relative water content, content of soluble sugars and of ABA when compared with the wild type plants.

Lipase class 3 is part of the triacylglycerol lipase family involved in lipid degradation, esterification, and transesterification processes in plants. In this study, a lipase class 3 gene and promoter from oil palm (Elaeis guineensis Jacq.) were isolated and characterized by Northern blot, Southern blot, oil palm genome sequence, and transient expression GUS assay. The full-length lipase class 3 (FLL1) deduced polypeptide encoded 483 amino acids and was identical to that deduced from lipase (EgLip1) cDNA (GI: 409994625). It contained the lipase consensus sequence, GxSxG motif, and a putative catalytic triad and had a 3-dimensional protein model similar to that of a lipase from Giberella zeae with a 50 % identity. The Northern blot and reverse transcription polymerase chain reaction (RT-PCR) show that FLL1 was predominantly expressed in the mesocarp and the expression increased as fruits reached maturity. A lower expression was detected in germinated seedlings and especially in roots. The expression of FLL1 was also enhanced in the mesocarp of cold treated fruits. A high oil accumulation in the mesocarp during fruit development makes this tissue a suitable target for a genetic modification, hence the isolation of the FLL1 promoter. The transient expression of the β-glucuronidase (GUS) gene driven by the FLL1 promoter detected the GUS expression in mesocarp slices, especially in vascular bundles. This suggests the potential role of using the promoter as tool to direct the expression of a transgene to the mesocarp of transgenic oil palm.

Transcription factors play vital roles in stress signal transduction and gene expression modulation. The sequence analysis shows that MdCBF1 from Malus domestica Borkh. cv. Fuji contained an AP2 core domain of 56 amino acids. By comparison of deduced amino acid sequences of CBF related proteins, we deduced that MdCBF1 is a CBF transcription factor gene which belongs to AP2/EREBP family, DREB-A1 subfamily. Further, we reported that transgenic Arabidopsis thaliana plants expressing the MdCBF1 gene exhibited stronger growth than wild type plants under freezing stress. The analysis of RT-PCR for stress-responsive genes implied that MdCBF1 over-expressing plants had a higher expression of COR15a, RD29A, and RD29B genes than wild type plants. Collectively, our results indicate that MdCBF1 might play an important role in the response of transgenic Arabidopsis plants to freezing stress.

In Arabidopsis, EXPORTIN1A (HIT2/XPO1A) and EXPORTIN1B (XPO1B) mediate the translocation of nuclear export sequence (NES)-bearing proteins from nucleus to cytoplasm. However, a mutation in HIT2/XPO1A but not in XPO1B induces sensitivity to high irradiance (HI). Arabidopsis thaliana heat stress elements A4a and A5 (AtHsfA4a and AtHsfA5) are involved in plant responses to HI and possess NESs; therefore, their nucleo-cytoplasmic partitioning was analyzed. In wild-type and xpo1b mutant cells, AtHsfA4a normally remained in the cytoplasm but became concentrated in the nucleus following exposure to HI, whereas AtHsfA5 was constitutively distributed in both cytoplasm and nucleus. However, in hit2/xpo1a mutant, AtHsfA4a and AtHsfA5 were always confined to the nucleus, regardless of the irradiance. Although AtHsfA4a can enhance the ability of plants to scavenge H₂O₂, and AtHsfA5 is a repressor of AtHsfA4a, athsfa5 but not athsfa4a mutant plants exhibited HI sensitivity. Additionally, athsfa4a plants expressing AtHsfA4aΔNES were sensitive to HI, but athsfa5 plants expressing AtHsfA5ΔNES were not. Meanwhile, hit2/athsfa4a double mutant was more tolerant to HI than hit2. These results indicate that both AtHsfA4a and AtHsfA5 were HIT2/XPO1A-specific substrates. Long-term accumulation of AtHsfA4a contributed to the hit2 HI-sensitive phenotype independent of the scavenging ability of H₂O₂, and the presence of AtHsfA5 could mitigate this adverse effect.

The Arabidopsis heme oxygenase 1 (HY1) plays a significant role in the signal transduction of abiotic stimuli and hormonal response. To characterize the HY1 promoter, an approximately 1.8 kb of it (pHY1, -1666 to +132) and its deletion fragments (5D1, -1528 to +132; 5D2, -1109 to +132; 5D3, -688 to +132; 5D4, -169 to +132; 3D1, -1666 to +100; 3D2, -1666 to -1; and 3D3, -1666 to -170), were fused to the β-glucuronidase (GUS) reporter gene and transformed into Arabidopsis. The transgenic plants were subjected to several environmental stimuli (especially to mild salinity, iron deficiency, and mercury exposure). The results show that the region from +1 to +100 in the 5'-untranslated region were essential for HY1 basal promoter activity. The induced GUS activities under NaCl and H₂O₂ treatments were slowed down by the progressive 5' deletion (from -1666 to -688) and correlated with the reduced numbers of myeloblastosis (MYB) binding sites (MBSs; -1542, -1333, -1078, and -177). The MBS-free promoter construct 5D4 (-169 to +132), however, fully lost the inducibility. Therefore, we propose that the MBS elements existing in the HY1 promoter might be crucial for salinity-induced HY1 up-regulation in an H₂O₂-dependent fashion. Moreover, the regions from -169 to -1 and -688 to -169 were presumed as the regulatory regions of HY1 promoter in response to iron deficiency and mercury exposure, respectively.

Forty one simple sequence repeats were isolated from two microsatellite enriched libraries of date palm (Phoenix dactylifera L.). After screening, 17 selected microsatellite loci were characterized and evaluated on a set of 31 cultivars and clones from Algerian and Californian germplasm. All primer pairs produced an amplification product of the expected size and detected high polymorphism among the analysed samples. These nuclear simple sequence repeat (SSR) markers are expected to be a very effective tool for evaluating genetic diversity in date palm germplasm. Acrosstaxa amplification showed the usefulness of most SSR markers in 14 other species across the genus Phoenix.

Viral resistance can be effectively induced in transgenic plants through their silencing machinery. Thus, we designed nine short hairpin RNAs (shRNA) constructs to target nuclear inclusion protein b (NIb), helper component proteinase (HC-Pro), cylindrical inclusion protein (CI) and viral protein genome linked (VPg) genes of Potato virus Y (PVY^N) and Tobacco etch virus (TEV-SD1). The shRNAs were completely complementary to the genes of PVY^N, and contained 1-3 nt mismatches to the genes of TEV-SD1. To study the specificity of gene silencing in shRNA-mediated viral resistance, the constructs were introduced into tobacco plants. The results of viral resistance assay revealed that these nine kinds of transgenic tobacco plants can effectively induce viral resistance against both PVY^N and TEV-SD1, and the shRNA construct targeting the NIb gene showed higher silencing efficiency. Northern blot and short interfering RNA (siRNA) analyses demonstrated that the viral resistance can be attributed to the degradation of the target RNA through the RNA silencing system. Correlation analysis of siRNA sequence characteristics with its activity suggested that the secondary structure stability of the antisense strand did not influence siRNA activity; 1 to 3 nt 5' end of the sense strand caused a significant effect on siRNA activity where the first base such as U was favourable for silencing; the base mismatch between the siRNA and the target gene may be more tolerated in the 5' end.

Heterotrimeric guanine-nucleotide-binding proteins (G-proteins) play important roles in signal transduction and regulate responses to various stresses. Although G-protein signaling pathways have been extensively identified and characterized in model plants, there is little knowledge in non-model and especially in woody plants. Mulberry is an economically and ecologically important perennial tree, which is adaptable to many environmental stresses. In this study, we identified and cloned six G-protein genes including one Gα, one Gβ, two Gγ, one RGS (regulator of G-protein signaling protein) and one RACK1 (receptor for activated C kinase 1) involved in G-protein signaling. Sequence and phylogenetic analysis revealed that Morus G-proteins are evolutionarily conserved compared with those of other plants. A real-time quantitative reverse transcription polymerase chain reaction analysis showed that Morus G-protein signaling genes were ubiquitously but differentially expressed in various tissues. The expression of all of these genes was affected by abiotic stresses and signal molecules, which indicated that Morus G-protein signaling may be involved in environmental stress and defense responses.

Mapping of quantitative trait genes (QTGs) associated with drought related traits is essential for improving drought tolerance in crop species. In silico identification of candidate genes relies on annotation of critical QTGs to a variety of web resource-based datasets. The barley reference sequence was employed to map QTGs significantly associated with the proline accumulation and osmotic potential. Annotation of the critical QTGs contigs to the NCBI protein database identified 72 gene orthologs located on chromosomes 1H, 2H, and 7H, from which seven genes were identified as candidates. Expression analysis of all seven candidate genes revealed differential expression pattern between plants grown under well-watered conditions and drought-stress. The results represent a successful and highly powerful implementation of genome-wide scanning approach based on in silico mapping of QTGs to identify gene clusters having a common transcript pattern with similar function.

Protein phosphorylation/dephosphorylation is a major signalling event induced by abiotic stresses in plants. Sucrose nonfermenting 1-related protein kinase 2 (SnRK2) plays important roles in response to osmotic stress. In the present study, four SnRK2s, TpSnRK2.1/3/7/8, were cloned and characterized from Triticum polonicum L. (dwarf Polish wheat, DPW, AABB). All of these were individually located on 2AL, 1AL, 2AL, and 5BL. Two spliced isoforms of TpSnRK2.8 (TpSnRK2.8a and TpSnRK2.8b) were observed. TpSnRK2.1 and TpSnRK2.3 were classified into the group II; TpSnRK2.7 was classified into the group I; and TpSnRK2.8a/b were classified into the group III. Expression patterns revealed that TpSnRK2.1 responded to cold, NaCl, polyethylene glycol (PEG), and abscisic acid (ABA) in both roots and leaves; TpSnRK2.3 was strongly regulated by cold, NaCl, and ABA in both roots and leaves, and by PEG in roots; TpSnRK2.7 was induced by NaCl and PEG in roots, but was not activated by ABA; and TpSnRK2.8s were significantly activated by cold, NaCl, PEG, and ABA in both roots and leaves. From the above results, we inferred that TpSnRK2.1/3/8 may participate in the responses to environmental stresses in ABA-dependent signal transduction pathway but TpSnRK2.7 is possibly involved in responses to environmental stresses in a non-ABA-dependent manner. They play important roles in specific tissues under different stresses.

In this study we examined the genetic diversity and geographic scale of genotype distribution within the model legume species Medicago truncatula widely distributed in pasture and marginal agricultural lands in Greece and other Mediterranean countries. Thirty one Medicago truncatula and Medicago littorialis accessions were chosen on the basis of their geographical distributions and studied using 9 polymorphic simple sequence repeats (SSR) markers. The number of alleles per locus varied between 3 and 7. A total of 42 alleles were detected with a mean value of 4.66 alleles per locus. Geographic origin was not related with genotypic similarity among accessions. However, there were instances of close genetic relatedness between accessions from neighboring locations in a geographic compartment. In conclusion, the presented data revealed extensive M. truncatula genotype dispersal in Greece pointing to the significance of preserving local genetic resources in their natural environment.

Gibberellin 2-oxidases (GA2oxs) irreversibly convert bioactive gibberellins (GAs) and their immediate precursors into inactive GAs via 2-β hydroxylation and so regulate gibberellin content in plants. However, to the best of our knowledge, little has been known about the GA2oxs and its function in cool season turfgrass Poa pratensis. In this study, rapid amplification of cDNA end (RACE) was employed to isolate PpGA2ox from P. pratensis. The open reading frame of PpGA2ox was 1 047 bp in length, corresponding to 348 amino acids. PpGA2ox was localized in both nucleus and cytoplasm. The expression of PpGA2ox could be up-regulated by 10 μM gibberellic acid, 5 μM methyl jasmonate, or 10 μM indole-3-acetic acid. In addition, its native promoter could drive GUS expression in both leaf apex and shoot apical region. Moreover, overexpression of PpGA2ox in Arabidopsis led to GA-deficiency leading to dwarf phenotype, delayed flowering time, and increased chlorophyll content. Our study suggests that PpGA2ox could be a candidate gene for breeding new cultivars of P. pratensis.

An efficient in vitro regeneration protocol through somatic embryogenesis was established from stem transverse thin cell layers (tTCLs) of Dendrobium aqueum Lindley, an imperiled orchid. This study outlines the induction and successive maturation stages of D. aqueum somatic embryos (SEs). The tTCLs (~ 0.5 mm thick) cultured on halfstrength Murashige and Skoog (MS) medium containing cytokinins and auxins, either individually or in combination, produced embryogenic callus (EC). Treatment with 0.5 mg dm^-3 zeatin induced EC in 41.42 % of tTCLs. As many as 42.66 globular SEs per tTCL were formed in the presence of 1.5 mg dm^-3N⁶-(2-isopentyl) adenine (2iP) but only on 10.33 % of explants. The combined treatment of 2iP (1.5 mg dm^-3) and 0.5 mg dm^-3 6-benzyladenine resulted in 34 globular SEs on 14.7 % of tTCLs whereas the combination of 2iP and 1.0 mg dm^-3 indole-3-butyric acid (IBA) induced 7.4 globular SEs on 52.33 % of tTCLs. Supplementation of activated charcoal, amino acids, and antioxidants alleviated browning at all the concentrations tested, but the EC response declined. The addition of 0.5 mg dm^-3 polyvinylpyrrolidone to 1.5 mg dm^-3 2iP and 1.0 mg dm^-3 IBA produced 24 SEs on 19.89 % of tTCLs suggesting that the EC and SEs can be effectively induced by individual cytokinins whereas the synergistic treatments with other compounds can only enhance the induction of EC. Histological observations of EC showed the formation of globular SEs from sub-epidermal regions. Successive developmental stages of globular SEs and the intermediate stage of protocorm like bodies until the formation of plantlets were observed. The plantlets obtained through SEs showed no morphological variations, and inter simple sequence repeat profiles also confirmed the genetic fidelity of in vitro-derived progeny with high monomorphism (97.78 %). In conclusion, the use of stem tTCLs is an effective method to produce SEs through indirect somatic embryogenesis in D. aqueum.

5-Methyltryptophan (5MT), a tryptophan analog, resistant M4 rice mutants with high free amino acid contents were obtained through in vitro mutagenesis. To evaluate the 5MT resistance mechanism, a cDNA library was constructed by using the leaves and roots of the 5MT resistant mutant plants. Expressed sequenced tags (ESTs) of 1 019 randomly selected clones were analyzed and then assembled 588 unigens. A total of 389 unigenes had significant homologies with known protein sequences at the NCBI database and the remaining 199 unigenes were designated unidentified genes. These unigens were grouped into 13 categories according to their putative functions. Of the 233 randomly selected clones, 25 were identified as differentially expressed genes between 5MT resistant and 5MT sensitive wild type plants. For further study of the differential expression of the genes, expression patterns of 12 genes related to various biological functions were evaluated in response to 5MT treatment in both the resistant plants and sensitive plants. All of the tested 12 genes exhibited higher expression levels in mutant plants than wild type plants under the 5MT inhibition. These expression patterns of the 12 genes suggested that the genes related to 5MT resistance in the rice mutants have a variety of functions, and yield remarkably diverse expression patterns upon 5MT treatment. Many genes that were identified tend to be related to defense and stress responses, suggesting "cross-talking" between biotic/abiotic stresses including the 5MT treatment. Therefore, 5MT resistant mutants might be of value for identifying genes related to plant defenses and stresses.

Virus-induced gene silencing (VIGS) is a post-transcriptional gene silencing method used for unraveling gene functions. As an attractive alternative to mutant collections or stable transgenic plants, it has been widely used in reverse-genetics studies owing to its ease use and quick turnaround time. Turnip yellow mosaic virus (TYMV) has the ability to induce VIGS in Arabidopsis thaliana. However, the conventional vector construction is difficult and the efficiencies of the infection methods are low. Here, we improved the vector construction and viral infection methods, inserted an inverted-repeat fragment of the phytoene desaturase gene into a TYMV-derived vector by homologous recombination and transformed Brassica rapa with plasmid DNA harboring a cDNA copy of the TYMV genome through particle bombardment. An apparent photobleaching phenotype was detected and efficient VIGS was induced. An 80-bp fragment was sufficient to produce VIGS in leaves, stems, roots, flowers, siliques, and stalks of B. rapa. Because TYMV has a wide host range in Brassica, the VIGS system described here will contribute to the improvement of high-throughput technology and efficient functional research in B. rapa and other Brassicaceae crops.

The gene NCED1 encodes 9-cis-epoxycarotenoid dioxygenase, which catalyzes oxidative cleavage of 9-cis-epoxycarotenoids neoxanthin and violaxanthin to xanthoxin, a key step in the biosynthesis of abscisic acid in higher plants. In the present study, the complete NCED1 of 1 917 bp was cloned and characterized from rice (Oryza sativa L. cv. N22) as no earlier reports were available for its characterization from indica cultivar. The NCED1 had no intron and encoded a protein of 639 amino acids with a predicted molecular mass of 68.62 kD and pI of 6.07. The aliphatic index and grand average of hydropathicity were found to be 77.04 and -0.148, respectively. Multiple alignment analysis revealed that the sequence shared a high identity with the Oryza sativa japonica group (100 %) followed by Triticum aestivum (90 %), Hordeum vulgare (90 %), and Zea mays (89 %). The enzyme had a RPE65 domain of 476 amino acid residues. The RPE65 domain requires Fe(II) as a cofactor coordinated with 4 histidine residues and 3 glutamic acid residues. The phylogenic tree shows that NCED1 of japonica rice and NCED1 of indica rice were in the same group. They might have been evolved from a common ancestor. Analysis with a PSORT III tool shows that NCED is a chloroplastic protein. The real-time quantitative PCR and RNA-sequencing studies show that the expression of NCED1 was progressively reduced with increasing water stress, and a negative correlation between expression of OsNCED1 and severity of stress was established. Further, NCED1 expression negatively correlated with abscisic acid (ABA) accumulation under water stress whereas in some other species its expression increased along with ABA accumulation. This might be due to feedback inhibition of the ABA biosynthesis in rice.

Transcription factors are involved in lipid metabolism, and in present study, the transcription factor WRINKLED 1 (GhWRI1) was cloned from Gossypium hirsutum L. cv. Coker 201 by reverse transcription (RT)-PCR and rapid amplification of cDNA ends. The Pro35S:WRI1 vector was constructed and transformed into upland cotton cv. Sumian 20 using the pollen tube pathway method. After PCR and Southern blot verification of the positive transgenic plants, T₂ transgenic lines derived from T₁ individuals with the insertion gene in a single copy were chosen for further dissection. Semi-quantitative and quantitative RT-PCR analyses indicated that GhWRI1 gene expression increased in transgenic plants compared with that in the wild-type. Seed lipid content increased at most transgenic plants, and at the same time, protein content decreased. Compared to the control, major agronomical traits were not affected by overexpression of GhWRI1 in transgenic plants.

Sugars are important molecules that function not only as primary metabolites, but also as nutrients and signal molecules in plants. The sugar transport protein genes family SWEET has been recently identified. The availability of the Dendrobium officinale and Phalaenopsis equestris genome sequences offered the opportunity to study the SWEET gene family in this two orchid species. We identified 22 and 16 putative SWEET genes, respectively, in the genomes of D. officinale and P. equestris using comprehensive bioinformatics analysis. Based on phylogenetic comparisons with SWEET proteins from Arabidopsis and rice, the DoSWEET and PeSWEET proteins could be divided into four clades; among these, clade II specifically lacked PeSWEETs and clade IV specifically lacked DoSWEETs, and there were orthologs present between D. officinale and P. equestris. Protein sequence alignments suggest that there is a predicted serine phosphorylation site in each of the highly conserved MtN3/saliva domain regions. Gene expression analysis in four tissues showed that three PeSWEET genes were most highly expressed in the flower, leaf, stem, and root, suggesting that these genes might play important roles in growth and development in P. equestris. Analysis of gene expression in different floral organs showed that five PeSWEET genes were highly expressed in the column (gynostemium), implying their possible involvement in reproductive development in this species. The expression patterns of seven PeSWEETs in response to different abiotic stresses showed that three genes were upregulated significantly in response to high temperature and two genes were differently expressed at low temperature. The results of this study lay the foundation for further functional analysis of SWEET genes in orchids.

Root hairs play important roles in plant nutrient and water acquisition. To better understand the genetic mechanism controlling root hair development in rice (Oryza sativa L.), a rice mutant with root hair defects was isolated and characterized. Cryo-scanning electron microscope (SEM) showed that the density and length of root hairs in the mutant were significantly reduced compared to wild type (WT). Map-based cloning and complementation test revealed that the mutation occurred in a NADPH oxidase gene OsNOX3 (LOC_Os01g61880). The OsNOX3 displays high sequence similarity with the previously characterized NOX genes RTH5 in maize and RHD2 in Arabidopsis, which play critical roles in root hair development. Expression pattern analysis indicated that OsNOX3 is expressed in various tissues throughout the plant with high expression in roots and root hairs. Subcellular localization analysis confirmed that OsNOX3 is located on the plasma membrane. Staining assays showed that the content of superoxide and hydrogen peroxide are significantly reduced in root hair tips of Osnox3 when compared to WT. Our results showed critical roles of OsNOX3 in regulating both root hair initiation and elongation in rice, which is similar to RTH5 but different from RHD2, confirming the difference of genetic mechanisms regulating root hair morphogenesis in monocot and dicot plants.

A study was conducted to generate fingerprints of thirty-two Indian potato cultivars using capillary electrophoresis based semi-automated simple sequence repeat analysis. Five fluorescent-tagged primer pairs (STPOACUTR, LEGAST1, STPOAC58, STM0030 and STM0031) used in this study yielded 43 alleles at 16 different loci, showing multi-loci resolving character. The estimated similarity between the cultivars was in the range of 0.72 to 0.98 indicating narrow genetic relationship. None of the primer set alone could differentiate all 32 cultivars included in this study. However, two primer sets STM-0031 and STPOAC58 amplifying 12 and 9 polymorphic alleles, respectively, could together distinguish all of them. The results indicated usefulness of semi-automated capillary electrophoresis in quick and reproducible SSR genotyping of potato cultivars.

Leek is an economically important vegetable. In model plants, the CONSTANS (CO) and CONSTANS-like (COL) genes play central roles in plant flowering modulation. However, none of leek CO homolog has been identified, because of limited gene resources obtained in this crop. Here, we reported the transcriptome analysis of leek, along with the identification of putative leek CONSTANS-like (COL) (ApCOL) genes. A total of 189 713 non-redundant transcripts were de novo assembled by using about 128.9 million clean sequence reads, of which, 48 621 were achieved for functional annotation. Thereafter, the search for putative ApCOL genes against the assembled transcripts was performed, and 17 genes were identified. The 17 putative ApCOL proteins, together with 16 function-known COL proteins published for other species, were subjected to phylogenetic analysis and divided into four groups. Some putative ApCOL members showed high sequence similarity with published COL proteins involved in flowering regulation. Expression analysis revealed that, among the 17 putative ApCOL genes, eight, two, and three genes showed higher expression in leaves, cauloids, and roots, respectively. The discovery of putative ApCOL genes and the characterization of their expression patterns will provide a basis for future clarification of their functions in leek growth and development.

The Arabidopsis thaliana (L.) Heynh. atExt1 extensin gene is expressed in a cell and tissue-specific manner, in response to developmental cues, and is inducible by a wide range of biotic and abiotic stresses. Over-expression of this gene has been shown to alter stem morphology and to limit the invasiveness of virulent bacterial pathogens, indicating that this cell wall protein gene plays an important role in plant development and defense. A detailed sequence analysis of 3.2 kb of the atExt1 gene promoter region has identified a large number of putative 5'cis-acting elements. Based on the location of clusters of putative promoter control elements, seven atExt1 5' promoter truncations were constructed, fused upstream of the β-glucuronidase (GUS) reporter gene, and transformed into A. thaliana. Transgenic plants carrying the various promoter constructs were challenged by wounding and pathogen attack and analysed for GUS expression - this analysis revealed a complex pattern of regulation, involving positive and negative control regions. Northern analysis using wounded tissues from transgenic Arabidopsis plants carrying the 3.2 kb-promoter::GUS construct confirmed the transcriptional activation of the transgene.

Low temperature is the main limiting factor for cultivation expansion, fast growth, and high yield of Eucalyptus species. To investigate the mechanism of their cold tolerance, a cDNA subtraction library representing the cold-induced genes of Eucalyptus dunnii was constructed using suppression subtractive hybridization (SSH) technique. A gene encoding a calmodulin-binding protein (CaMBP) was identified from the SSH library, and the expression pattern of CaMBP under cold stress was further evaluated through reverse transcription - quantitative polymerase chain reaction (RT-qPCR). The expressions of EguCBF1a and EdCaMBP increased already after 4 h of the cold stress, supporting the idea that the CaMBP gene may have a function in the survival of Eucalyptus during winter. A full-length mRNA sequence of 1 808 bp was obtained via a rapid amplification of cDNA ends method, and the sequence was subsequently deposited to GenBank (accession No. JX401571). The CaMBP cDNA of E. dunnii contained a single open reading frame of 1 362 bp, a 5t' untranslated region of 175 bp, and a 3t' untranslated region of 268 bp. Multiple sequence alignment and phylogenetic analysis indicated that CaMBP of E. dunnii shared 56 to 84 % identities with the CaMBPs of other plants and was similar to that of Ricinus communis, Medicago truncatula, and Gossypium hirsutum.

Chili pepper (Capsicum annuum L.) cv. Árbol and Uvilla fruits differing in anthocyanin contents were analyzed to characterize the accumulation patterns. The maximum accumulation of the aglycon delphinidin occurred 20 days postanthesis (DPA) with higher content in Uvilla than in Árbol fruits. Regarding the cDNA library, 9 186 cDNA clones were selected. The clones with high homology to genes concerning anthocyanin biosynthesis, such as encoding chalcone synthase (CHS), chalcone isomerase (CHI), flavanone 3-hydroxylase (F3H), flavonoid 3',5'-hydroxylase (F3'5'H), dihydroflavonol 4-reductase (DFR), anthocyanidin synthase (ANS), UDP Glc-flavonoid 3-O-gluco-syl transferase (UFGT), and also those possibly involved in anthocyanin transport into the vacuoles, an anthocyanin permease (ANP) and a glutathione S-transferase (GST) were used for gene expression analysis. In general, the expression of all investigated genes was developmentally regulated in both Árbol and Uvilla. CHS and CHI transcripts were expressed at the maximal level at 10 DPA, and then consistently declined throughout fruit development. F3'5'H, DFR, UFGT and GST expression exhibited a positive correlation with anthocyanin accumulation, and the highest transcript levels were detected prior to or by the time of maximum anthocyanin accumulation, depending on the chili pepper type. Pericarp fruit tissues from cv. Tampiqueño 74, an anthocyanin non-accumulator, also showed CHS, CHI, F3H, ANS and ANP expression at some developmental stages.

DNA methylation is known to play a crucial role in regulating plant development and organ or tissue differentiation. Here, we focused on the DNA methylation dynamics during the germination of wheat seeds using the adapted AFLP technique so called methylation-sensitive amplified polymorphism (MSAP). The MSAP profiles of genomic DNA in embryo and endosperm tissues of germinating seeds, as well as dry seeds were characterized and notable changes of cytosine methylation were detected. Comparisons of MSAP profiles in different tissues tested showed that the methylation level in dry seeds is the highest. The alteration analysis of cytosine methylation displayed that the number of demethylation events were three times higher than that of de novo methylation, which indicated that the demethylation was predominant in germinating wheat seeds, though the methylation events occurred as well. Sixteen differentially displayed DNA fragments in MSAP profiles were cloned and the sequencing analysis confirmed that nine of them contained CCGG sites. The further BLAST search showed that four of the cloned sequences were located in coding regions. Interestingly, three of the sixteen candidates were homologous to retrotransposons, which indicated that switches between DNA methylation and demethylation occurred in retrotransposon elements along with the germination of wheat seeds.

MYB transcription factors (TFs) are known to have important functions in regulating the biosynthesis of secondary metabolites in plants. In this study, LeMYB1, a member of the MYB gene family of Lithospermum erythrorhizon, was cloned via the rapid amplification of cDNA ends. The alignment of the predicted translations of LeMYB1 with other MYB proteins revealed that LeMYB1 contained an N-terminal R2R3 repeat and a high degree of amino acid identity to NtMYBJS1 which is involved in jasmonic acid signalling and phenylpropanoid biosynthetic pathway regulation. To determine the expression pattern of LeMYB1, its promoter was cloned and the sequence analysis was performed. The results revealed a number of potential regulatory motifs related to tissue-specific gene expression and abiotic and biotic stress responses. Real-time PCR results suggest that LeMYB1 was induced transiently during the early stage when L. erythrorhizon cells were transferred from a B5 growth medium to a M9 production medium for shikonin formation. Exogenous methyl jasmonate (MeJA), an effective inducer of shikonin biosynthesis, induced the rapid LeMYB1 expression. In contrast, a treatment with ibuprofen (IBU), an inhibitor of jasmonate biosynthesis, significantly inhibited the LeMYB1 expression. Another inhibitor of shikonin formation, 2,4-dichlorophenoxyacetic acid (2,4-D), also markedly repressed the expression of LeMYB1. Tissue-specific expression analysis showed that LeMYB1 mRNA was predominantly accumulated in roots where shikonin was synthesized. Thus, the LeMYB1 gene may be a valuable member of the R2R3-MYB family in L. erythrorhizon and is possibly involved in the regulation of shikonin biosynthesis.

High summer temperature negatively affects cotton yield, and better understanding of genetic mechanisms of heat stress responses in cotton may facilitate development of new heat tolerant cultivars. We attempted to determine heat responsive genes in cotton using tolerant (Stoneville 453, BA 119) and susceptible (Nazilli 84S) cultivars. Twenty five expressed sequence tags (ESTs) were sequenced and studied for gene homology. Sixteen ESTs were significantly similar to known genes, whereas eight ESTs were similar to not annotated cDNA clones and 1 EST did not show homology to any known gene. Expression of some ESTs was analyzed by quantitative real-time PCR and IAA-ala hydrolase (IAR3), folylpolyglutamate synthase (FPGS3), and two not annotated ESTs (GhHS126 and GhHS128) were consistently up-regulated under both short- and long-term heat stress. Since cotton is considered relatively more heat tolerant than most of the other crops, it can be suggested that these genes and ESTs could play a significant role in heat tolerance. In addition, GhHS126 and GhHS128 might be parts of the new candidate genes for heat tolerance.

Pathogenesis-related (PR) proteins play key roles in plant disease resistance. Here, we isolated and characterized pathogenesis-related PR2 gene encoding β-1,3-glucanase from Brassica juncea and named it BjPR2 (GenBank accession number DQ359125). The amino acid sequence of BjPR2 showed ~99 % similarity with β-1,3-glucanase of Brassica rapa, B. napus, and B. oleracea. BjPR2 transcription was rapidly increased after Alternaria brassicae infection, salicylic acid application, and wounding, but the induction was delayed in response to jasmonic acid. To investigate the transcriptional regulation of BjPR2 gene, its promoter was isolated. In silico analysis of BjPR2 promoter showed cis-regulatory elements upstream of TATA and CAAT boxes responsive to defense, hormones, wounding, and plant developmental stage. Homozygous Arabidopsis thaliana lines were developed with plasmid construct having β-glucuronidase (GUS) reporter gene driven by BjPR2 promoter. The analysis of GUS protein in Arabidopsis lines showed that BjPR2 promoter drived distinct pattern of pathogen inducible expression after fungal infection (Alternaria brassicae, Erysiphe orontii), phytohormones, and wounding. It also showed age dependent and organ specific expressions. BjPR2 promoter drove strong GUS activity in Arabidopsis seedlings and showed organ specific expression at the later growth stages (lateral organ junctions, leaf serrate, base of siliques, and receptacle). Due to stress-inducible and tissue specific nature, the BjPR2 promoter can serve as a potential candidate in genetic engineering.

In this study, seven cDNA fragments of genes, differentially expressed in ovaries after pollination in Cymbidium hybridium, were identified and characterized by mRNA differential display reverse transcription polymerase chain reaction (DDRT-PCR). Four (CDD-313, CDD-272, CDD-265, CDD-243) among these seven cDNA fragments showed no significant homology with ESTs or genes in the databases of NCBI; another three (CDD-193, CDD-218, CDD-470) showed significant homologies with sequences encoding components of an ABC-type transporter, a GTPase and 40S ribosomal S3 proteins (RPS3), respectively. The differential expression patterns of them were confirmed by reverse Northern dot blot analysis. More interestingly, CDD-470 appeared to be present and highly expressed in the pollinated ovaries and encoded a new factor of RPS3 participating in cell growth and proliferation. We deduced that this 40s ribosomal S3 like protein was involved in ovary development of orchids.