Expression profiles of putative defence-related proteins in oil palm (Elaeis guineensis) colonized by Ganoderma boninense.

Basal stem rot (BSR) is a major disease of oil palm caused by a pathogenic fungus, Ganoderma boninense. However, the interaction between the host plant and its pathogen is not well characterized. To better understand the response of oil palm to G. boninense, transcript profiles of eleven putative defence-related genes from oil palm were measured by quantitative reverse-transcription (qRT)-PCR in the roots of oil palms treated with G. boninense from 3 to 12 weeks post infection (wpi). These transcripts encode putative Bowman-Birk serine protease inhibitors (EgBBI1 and 2), defensin (EgDFS), dehydrin (EgDHN), early methionine-labeled polypeptides (EgEMLP1 and 2), glycine-rich RNA binding protein (EgGRRBP), isoflavone reductase (EgIFR), metallothionein-like protein (EgMT), pathogenesis-related-1 protein (EgPRP), and type 2 ribosome-inactivating protein (EgT2RIP). The transcript abundance of EgBBI2 increased in G. boninense-treated roots at 3 and 6. wpi compared to those of controls; while the transcript abundance of EgBBI1, EgDFS, EgEMLP1, EgMT, and EgT2RIP increased in G. boninense-treated roots at 6 or 12. wpi. Meanwhile, the gene expression of EgDHN was up-regulated at all three time points in G. boninense-treated roots. The expression profiles of the eleven transcripts were also studied in leaf samples upon inoculation of G. boninense and Trichoderma harzianum to identify potential biomarkers for early detection of BSR. Two candidate genes (EgEMLP1 and EgMT) that have different profiles in G. boninense-treated leaves compared to those infected by T. harzianum may have the potential to be developed as biomarkers for early detection of G. boninense infection

Sequence analysis and gene expression of putative oil palm chitinase and chitinase-like proteins in response to colonization of Ganoderma boninense and Trichoderma harzianum

Chitinases are glycosyl hydrolases that cleave the β-1,4-glycosidic linkages between N-acetylglucosamine residues in chitin which is a major component of fungal cell wall. Plant chitinases hydrolyze fungal chitin to chitin oligosaccharides that serve as elicitors of plant defense system against fungal pathogens. However, plants synthesize many chitinase isozymes and some of them are not pathogenesis-related. In this study, three full-length cDNA sequences encoding a putative chitinase (EgChit3-1) and two chitinase-like proteins (EgChit1-1 and EgChit5-1) have been cloned from oil palm (Elaeis guineensis) by polymerase chain reaction (PCR). The abundance of these transcripts in the roots and leaves of oil palm seedlings treated with Ganoderma boninense (a fungal pathogen) or Trichoderma harzianum (an avirulent symbiont), and a combination of both fungi at 3, 6 and 12 weeks post infection were profiled by real time quantitative reverse-transcription (qRT)-PCR. Our findings showed that the gene expression of EgChit3-1 increased significantly in the roots of oil palm seedlings treated with either G. boninense or T. harzianum and a combination of both; whereas the gene expression of EgChit1-1 in the treated roots of oil palm seedlings was not significantly higher compared to those of the untreated oil palm roots. The gene expression of EgChit5-1 was only higher in the roots of oil palm seedlings treated with T. harzianum compared to those of the untreated oil palm roots. In addition, the gene expression of EgChit1-1 and EgChit3-1 showed a significantly higher gene expression in the leaf samples of oil palm seedlings treated with either G. boninense or T. harzianum

Profiling the differentially expressed genes in two rice varieties during rapid grain-filling stages

Grain filling is an important agronomic trait, which directly affects the final yield of rice. Partially filled and empty rice grains are among the factors that limit the yield of MR219, one of the highest yielding rice varieties in Malaysia. In this study, the NSF 20 K rice oligonucleotide array, which contains 20,000 70-mer oligonucleotide probes, was used for direct comparison of the transcriptomes of MR219 and MR84 (a rice variety that has higher percentage of filled grains compared to MR219), during rapid grain-filling period at 5 and 10 days after fertilization (DAF). A total of 155 and 233 genes were differentially expressed in MR219 compared to MR84 at 5 and 10 DAF, respectively; and 9 of these expression ratios were tested using quantitative real-time RT PCR. Among the differentially expressed genes identified were those encoding hexokinase, various sugar transporters, GSDL-like lipase/acylhydrolase, brassinosteroid-insensitive 1-associated receptor kinase 1 precursor and homeobox protein GLABRA2, which were analyzed by real-time RT PCR in this study. The differences demonstrated by these genes in their transcript levels and profiles, between the two rice varieties understudied at different stages of grain filling may contribute to the formulation of hypotheses toward the understanding of poor percentage of filled grains in MR219

Transcriptional response of oil palm (Elaeis guineensis Jacq.) inoculated simultaneously with both Ganoderma boninense and Trichoderma harzianum

Application of beneficial microbes offers an environmentally friendly alternative for mitigation of basal stem rot (BSR) disease in oil palm. However, the biocontrol mechanisms of Trichoderma against the pathogenic Ganoderma spp. which cause BSR are largely unknown at the molecular level. To identify the transcripts involved during induced systemic resistance (ISR), we analyzed the root transcriptomes of oil palm seedlings inoculated simultaneously with both G. boninense and T. harzianum, and un-inoculated oil palm seedlings, as well as those that were inoculated with either pathogenic or beneficial fungi. Our analyses revealed that the biocontrol mechanisms of T. harzianum against G. boninense involve modulation of genes related to biosynthesis of phytohormones (ethylene, MeJA and MeSA), antioxidant (l-ascorbate and myo-inositol) and unique secondary metabolites such as momilactone, cell wall metabolisms, and detoxification of phytotoxic compounds; in addition to its role as a biofertilizer which improves nutritional status of host plant. The outcomes of this study have fueled our understanding on the biocontrol mechanisms involving T. harizianum against G. boninense infection in oil palm roots

Isolation and characterization of floral transcripts from mangosteen (Garcinia mangostana L.)

The understanding of flower initiation, development, and maturation in mangosteen is of paramount importance to shorten its long juvenile phase and to synchronize its flowering or fruiting time. In this study, we have identified 97 tentative unique genes with higher expression levels in young flower buds compared to young shoots by using suppressive subtraction hybridization and reverse northern analysis. Sequence analysis showed that 63.9% of these transcripts had non-significant matches to sequences in the non-redundant protein database in Gen- Bank, 19.6% had significant matches to unknown proteins while the remaining 16.5% had putative functions in transcription, stress, signal transduction, cell wall biogen-esis, photosynthesis and miscellaneous. The full-length cDNA of GmAGMBP encoding AG-motif binding protein(a zinc finger transcriptional factor), and 3 0 termini cDNA sequences of GmHSA32 and GmBZIP, encoding heat-stress-associated 32 (HSA32) and bZIP transcription factor,respectively; were cloned and further analysed. Real-time PCR analysis revealed that these three genes have different transcript profiles in flowers of different developmental stages and young shoots. The highest abundance of transcripts was achieved in flowers with diameters ranging from 0.5 to 0.9 cm for GmAGMBP and GmBZIP and in flowers with diameters less than 0.5 cm for GmHSA32. Southern analysis suggested that GmAGMBP might be single copy gene while GmHSA3A could possibly belong to a small gene family in the mangosteen genome

Leaf transcriptome of oil palm (Elaeis guineensis Jacq.) infected by Ganoderma boninense

Oil palm is susceptible to Ganoderma infection which causes basal stem rot (BSR). Induced defense gene profiles in oil palm leaves will assist the identification of markers for detection of infected oil palms. In this study, we have sequenced the mRNA samples from the leaves of G. boninense infected oil palm seedlings (LG) and in control treatment (LC). Differential gene expression analysis showed 711 and 482 genes that were up-and down-regulated more than fourfold in LG, respectively, compared to the LC. Differential gene expression analyses revealed the modulation of oil palm genes involved in defense response such as chitinases, glucanases, and thaumatin-like proteins that showed up-regulation in LG. In addition, genes for enzymes related to the biosynthesis of flavonoids, alkaloids, and terpenes were up-regulated, while many genes involved in photosynthesis were found to be suppressed in LG. Our findings provided information on how infected oil palm leaves diverting their resources into defense at the cost of other biological processes, contributing towards identification of candidate markers for the detection of infected oil palms

Expression of Chitinases and Glucanases in Oil Palm in Response to Ganoderma and Trichoderma Treatments

Cell wall degrading enzymes (CWDEs) such as chitinases and glucanases are produced by plants during the infection of pathogens as part of their defense mechanism. In this study, the full length complementary DNA (cDNA) sequences encoding two chitinases (EgChit3-1 and EgChit5-1) and one (EgGlc5-2) glucanase from the oil palm root have been isolated by Rapid Amplification of cDNA Ends – Polymerase Chain Reaction (RACE-PCR). Meanwhile the 5’- terminal cDNA sequence encoding a chitinase (EgChit1-1) was successfully isolated. Sequence analysis was performed on the three full-length cDNA sequences obtained from this study and two full-length cDNA sequences encoding glucanases (EgGlc1-1 and EgGlc5-1) obtained from the expressed sequence tags (ESTs) of oil palm root cDNA library. Analyses of the cDNA sequences revealed that EgGlc1-1 is related to the glycosyl hydrolase (GH) family 3 while EgGlc5-1 and EgGlc5-2 are related to the GH family 17. EgChit1-1 was categorized in the GH family 19 whereas EgChit3-1 and EgChit5-1 are related to the GH family 18. Real time reverse transcription polymerase chain reaction (RT-PCR) was performed to detect the transcript levels of the isolated glucanases and chitinases using oil palm seedlings treated with Ganoderma boninense PER71, Trichoderma harzianum T32 singly and in a combination of Ganoderma and Trichoderma at 3, 6 and 12 weeks post infection (wpi). Lesions caused by Ganoderma infection were only observed at 6 wpi and 12 wpi in Ganoderma-treated seedlings. The Trichoderma colony forming unit (CFU) estimation in Ganoderma-Trichoderma- and Trichoderma-treated seedlings increased gradually from 3-12 wpi. The expression of EgGlc1-1 was induced by Trichoderma in Trichoderma-treated seedlings at 3, 6 and 12 wpi. The expression of EgGlc5-1 and EgGlc5-2 was elevated in the roots of control seedlings while suppressed treated seedlings at 3, 6 and 12 wpi. The transcript encoding EgChit1-1 increased in respond to Ganoderma infection at early stage (3 wpi). The transcript of EgChit3-1 and EgChit5-1 were increased at later stages of infection in roots of Ganoderma- and Trichoderma-treated seedlings. The findings of this study provide an insight to the gene expression of a few glucanases and chitinases during colonization of Ganoderma and Trichoderma on oil palm seedlings. Not all glucanases and chitinases in this study played a role in oil palm defense. Different glucanases and chitinases were regulated differently in oil palm seedlings when they were exposed to Ganoderma, Trichoderma singly and in a combination of Ganoderma-Trichoderma

Weibull-Fréchet random path length model for avalanche gain and noise in photodiodes

A four-parameter Weibull-Fréchet (WF) distribution function has been introduced in the random path length (RPL) model for nonlocal modelling of soft-threshold ionisation in semiconductors. The WF function has been demonstrated to be capable of reproducing the realistic probability distribution function (PDF) of electron and hole ionisation path lengths extracted from full band Monte Carlo (FBMC) transport simulations of bulk GaAs. The electron-initiated multiplication in GaAs avalanche photodiodes (APDs) calculated by the WF-RPL model is in excellent agreement with the results from FBMC. The predicted excess noise factor is closer to that of FBMC as compared to the hard threshold RPL model. The advantage of this improved RPL model as a tool for predicting the PDF of electron and hole ionisation path lengths in AlAs0.56Sb0.44 from the experimentally measured avalanche gain and noise has been analysed. The electron ionisation path length PDF of AlAs0.56Sb0.44 has a unique feature of two decay rates with a narrow full width at half maximum and a long tail. The extremely low hole ionisation coefficient in AlAs0.56Sb0.44 is found with a PDF of ionisation path length spanning over 50 µm at an electric field of 600 kVcm−1, supporting the very low hole feedback ionisation in AlAs0.56Sb0.44 APDs. The combination of the detailed and peaked electron's ionisation path length PDF and of the broad hole's ionisation path length PDF is responsible for the extremely low avalanche noise in the 1.55 µm thick AlAs0.56Sb0.44 APDs

De novo transcriptome analyses of hostfungal interactions in oil palm (Elaeis guineensis Jacq.)

Background: Basal stem rot (BSR) is a fungal disease in oil palm (Elaeis guineensis Jacq.) which is caused by hemibiotrophic white rot fungi belonging to the Ganoderma genus. Molecular responses of oil palm to these pathogens are not well known although this information is crucial to strategize effective measures to eradicate BSR. In order to elucidate the molecular interactions between oil palm and G. boninense and its biocontrol fungus Trichoderma harzianum, we compared the root transcriptomes of untreated oil palm seedlings with those inoculated with G. boninense and T. harzianum, respectively. Results: Differential gene expression analyses revealed that jasmonate (JA) and salicylate (SA) may act in an antagonistic manner in affecting the hormone biosynthesis, signaling, and downstream defense responses in G. boninense-treated oil palm roots. In addition, G. boninense may compete with the host to control disease symptom through the transcriptional regulation of ethylene (ET) biosynthesis, reactive oxygen species (ROS) production and scavenging. The strengthening of host cell walls and production of pathogenesis-related proteins as well as antifungal secondary metabolites in host plants, are among the important defense mechanisms deployed by oil palm against G. boninense. Meanwhile, endophytic T. harzianum was shown to improve the of nutrition status and nutrient transportation in host plants. Conclusion: The findings of this analysis have enhanced our understanding on the molecular interactions of G. boninense and oil palm, and also the biocontrol mechanisms involving T. harzianum, thus contributing to future formulations of better strategies for prevention and treatment of BSR