Draft genome sequence of the rubber tree Hevea brasiliensis 7thSpace Interactive (press release) Conclusions: The knowledge gained from this genome sequence will aid in the future development of high-yielding clones to keep up with the ever...
We developed a novel Designed Primer-based RNA-sequencing strategy (DP-seq) that uses a defined set of heptamer primers to amplify the majority of expressed transcripts from limiting amounts of mRNA, while preserving their relative abundance.
Biswapriya Biswavas Misra's insight:
We developed a novel Designed Primer-based RNA-sequencing strategy (DP-seq) that uses a defined set of heptamer primers to amplify the majority of expressed transcripts from limiting amounts of mRNA, while preserving their relative abundance. Our strategy reproducibly yielded high levels of amplification from as low as 50 picograms of mRNA while offering a dynamic range of over five orders of magnitude in RNA concentrations. We also demonstrated the potential of DP-seq to selectively suppress the amplification of the highly expressing ribosomal transcripts by more than 70% in our sequencing library. Using lineage segregation in embryonic stem cell cultures as a model of early mammalian embryogenesis, DP-seq revealed novel sets of low abundant transcripts, some corresponding to the identity of cellular progeny before they arise, reflecting the specification of cell fate prior to actual germ layer segregation.
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Biswapriya Biswavas Misra's insight:
The rubber tree (Hevea spp.), cultivated in equatorial and tropical countries, is the primary plant used in natural rubber production. Due to genetic and physiological constraints, inbred lines of this species are not available. Therefore, alternative approaches are required for the characterization of this species, such as the genetic mapping of full-sib crosses derived from outbred parents. In the present study, an integrated genetic map was obtained for a full-sib cross family with simple sequence repeats (SSRs) and expressed sequence tag (EST-SSR) markers, which can display different segregation patterns. To study the genetic architecture of the traits related to growth in two different conditions (winter and summer), quantitative trait loci (QTL) mapping was also performed using the integrated map. Traits evaluated were height and girth growth, and the statistical model was based in an extension of composite interval mapping. The obtained molecular genetic map has 284 markers distributed among 23 linkage groups with a total length of 2688.8 cM. A total of 18 QTLs for growth traits during the summer and winter seasons were detected. A comparison between the different seasons was also conducted. For height, QTLs detected during the summer season were different from the ones detected during winter season. This type of difference was also observed for girth. Integrated maps are important for genetics studies in outbred species because they represent more accurately the polymorphisms observed in the genitors. QTL mapping revealed several interesting findings, such as a dominance effect and unique segregation patterns that each QTL could exhibit, which were independent of the flanking markers. The QTLs identified in this study, especially those related to phenotypic variation associated with winter could help studies of marker-assisted selection that are particularly important when the objective of a breeding program is to obtain phenotypes that are adapted to sub-optimal regions.
Tapping panel dryness (TPD) syndrome affecting rubber tree (Hevea brasiliensis) is known to reduce natural latex production. Its aetiology remains ambiguous despite long years of research. A low molecular weight RNA similar to viroid RNA was isolated from TPD-affected samples of rubber trees. In the present study, a modified return-polyacrylamide gel electrophoresis procedure was standardised. The viroid-like low molecular weight (LMW) RNA was found associated with leaf, bark and root tissues and rubber seedlings. The technique was employed to detect LMW RNA in different clones of rubber planted in different locations and in bud-grafted plants. The LMW RNA isolated from TPD-affected trees was found infectious on seedlings of tomato cv Pusa Ruby. The LMW RNA was reisolated from symptomatic tomato leaves but not from control plants. This is for the first time that a biotic agent, a viroid RNA, is found consistently associated with the syndrome. The technology developed can be useful to demonstrate the onset of TPD in untapped trees in the absence of other methods such as nucleic acid hybridisation.
To gain more insight into the molecular mechanisms of Colletotrichum gloeosporioides pathogenesis, Agrobacterium tumefaciens-mediated transformation (ATMT) was used to identify mutants of C. gloeosporioides impaired in pathogenicity. An ATMT library of 4128 C. gloeosporioides transformants was generated. Transformants were screened for defects in pathogenicity with a detached copper brown leaf assay. 32 mutants showing reproducible pathogenicity defects were obtained. Southern blot analysis showed 60.4% of the transformants had single-site T-DNA integrations. 16 Genomic sequences flanking T-DNA were recovered from mutants by thermal asymmetric interlaced PCR, and were used to isolate the tagged genes from the genome sequence of wild-type C. gloeosporioides by Basic Local Alignment Search Tool searches against the local genome database of the wild-type C. gloeosporioides. One potential pathogenicity genes encoded calcium-translocating P-type ATPase. Six potential pathogenicity genes had no known homologs in filamentous fungi and were likely to be novel fungal virulence factors. Two putative genes encoded Glycosyltransferase family 28 domain-containing protein and Mov34/MPN/PAD-1 family protein, respectively. Five potential pathogenicity genes had putative function matched with putative protein of other Colletotrichum species. Two known C. gloeosporioides pathogenicity genes were also identified, the encoding Glomerella cingulata hard-surface induced protein and C. gloeosporioides regulatory subunit of protein kinase A gene involved in cAMP-dependent PKA signal transduction pathway.
The present invention relates to an isolated polypeptide for catalyzing plastidial biosynthesis of isopentenyl diphosphate, dimethylallyl diphosphate or the combination thereof in the plant of Hevea brasiliensis, comprising amino acid sequence set forth in SEQ ID NO. 2, SEQ ID NO. 4, SEQ ID NO. 6, SEQ ID NO. 8, SEQ ID NO. 10 or SEQ ID NO. 12; and a method for catalyzing the biosynthesis of isopentenyl diphosphate, dimethylallyl diphosphate or the combination thereof for enhancing the biosynthesis of natural rubber from its precursors. The present invention also relates to an isolated polynucleotide encoding the polypeptide, a recombinant gene construct comprising the polynucleotide, a transformant and a transgenic plant comprising the recombinant gene construct.
Material behaviors and anti-algal performances of PVC and wood PVC composites (WPVC) were examined after adding commercial algaecides of different types and contents. Three different wood types commonly found in tropical climates – namely, Xylia kerrii Craib & Hutch.; Hevea brasiliensis Muell.; and Mangifera indica Linn. – were of interest. Isoproturon (3-(4-isopropylphenyl)-1,1-dimethylurea), a urea-based algaecide, and Terbutryn (N2-tert-butyl-N4-ethyl-6-methylthio-1,3,5-triazine-2,4-diamine), a triazine-based algaecide, were used as anti-algal agents in this study; concentrations in the specimens varied from 0–1,500 ppm. Surface color, thermal properties, chemical structure and mechanical properties of the materials were also monitored. The results revealed that addition of Isoproturon tended to considerably change the surface color of the materials, particularly for PVC which had the highest ΔE∗ value, whereas addition of Terbutryn did not. The effect of wood types was found to influence the initial surface color of the materials. Evidence based on DSC, FT-IR and contact angle testing indicated that Isoproturon had a strong molecular interaction with PVC and could induce PVC degradation. The mechanical properties of PVC and WPVC were affected by the addition of wood, but not by algaecide addition. The results of the growth inhibition zone and chlorophyll-a content in Chlorella vulgaris TISTR 8580 suggested that Terbutryn exhibited better anti-algal performance than Isoproturon with a recommended dosage of 1,000 ppm while Isoproturon at 1,500 ppm could act as an effective coupling agent in WPVC composites.
Este estudo descreve a distribuição e determina a taxa anual de crescimento e a idade das árvores de Garcinia brasiliensis e de Hevea spruceana em uma floresta inundável na região de Manaus. Oito parcelas contíguas de 25 x 25 metros foram instaladas, onde todos os indivíduos das duas espécies com altura ≥ 1,0 m foram mapeados. O diâmetro, a altura das árvores e os níveis de inundação foram registrados para todos os indivíduos. A radiação fotossinteticamente ativa (RFA) foi medida em indivíduos da regeneração (≤ 10 cm diâmetro a altura do peito –dap). Foram calculadas a área basal e o volume para cada indivíduo, e determinados o padrão de crescimento e a idade das árvores utilizando métodos dendrocronológicos. Um total de 105 indivíduos foi amostrado, a maioria na classe de regeneração. Hevea spruceana apresentou o maior número de indivíduos (n=80), as maiores taxas de crescimento em dap e em altura. Garcinia brasiliensis (n=25) apresentou idade, dap e altura maiores do que Hevea spruceana. Ambas as espécies foram sujeitas a diferentes níveis de inundação e de radiação. A estrutura populacional e a distribuição dos indivíduos dessas espécies mostram ser, aparentemente, influenciadas pelas variações na topografia local em pequena escala. Os diferentes requerimentos por radiação destas espécies sugerem ocupação de diferentes nichos ecológicos.
Abstract Bacterial endophytes offer control against many diseases of crop plants as potential biocontrol agents. Antagonistic bacterial endophytes acting against Phytophthora meadii have been screened from leaf, petiole and root tissues of Hevea brasiliensis. Six bacterial endophytes could exhibit more than 50 % inhibition of P. meadii, among which EIL-2, from disease-free zones showed a maximum of 62.5 % inhibition. The isolate EIL-2 was characterized as Alcaligenes sp. and the other isolates were identified as Pseudomonas aeruginosa. 16S rDNA sequence analysis showed that there existed genetic variation among the five isolates of P. aeruginosa from different tissues of the plant indicating the tissue type adaptation of the isolates. Dual culture technique with endophyte EIL-2 completely arrested the growth of P. meadii when inoculated prior to pathogen. The bioassay with EIL-2 in H. brasiliensis clones, RRII 105 showed 43 % reduction of lesion size on infected leaves whereas in RRIM 600 it was only 30 %.
PENENTUAN pH DAN SUHU OPTIMUM UNTUK AKTIVITAS EKSTRAK KASAR ENZIM LIPASE DARI KECAMBAH BIJI KARET (Hevea brasiliensis) TERHADAP HIDROLISIS PKO (Palm Kernel Oil)
Biswapriya Biswavas Misra's insight:
Determination of optimum pH and temperature for crude lipase enzyme activity from rubber seeds germination had been conducted. Rubber seed germination made by soaking time process, seed separation with shell’s and seed germination in temperature 27-30oC during 6 days. Crude lipase enzyme was obtained by two times centrifugations with the speed of rotation at 5000 rpm and 10000 rpm during 30 minutes by additing aceton 70%. The crude enzyme is diluted with phosfat buffer pH 7,0. The activity test of crude lipase enzyme is done by measurement of free fatty acid levels is obtained from hydrolisis process of PKO as subtrate by titrimetric method at temperature variation 40; 45; 50; 55; 60oC and pH 6,0; 6,5; 7,0; 7,5; 8,0. The result shower that the highest activity is 2,432 U/mL at pH optimum 7,0 and temperature optimum 40oC.
Natural rubber is a high-molecular-mass biopolymer found in the latex of >2,500 plant species, including Hevea brasiliensis, Parthenium argentatum and Taraxacum spp. The active sites of rubber biosynthesis are rubber particles, which comprise a hydrophobic rubber core surrounded by a phospholipid monolayer membrane containing species-dependent lipids and associated proteins. Small rubber particle proteins are the most abundant rubber particle-associated proteins in Taraxacum brevicorniculatum (TbSRPPs) and may promote rubber biosynthesis by stabilizing the rubber particle architecture. We investigated the transcriptional regulation of genes encoding SRPPs and identified a bZIP transcription factor (TbbZIP.1) similar to the Arabidopsis thaliana ABI5–ABF–AREB subfamily, which is thought to include downstream targets of ABA and/or abiotic stress-inducible protein kinases. The TbbZIP.1 gene was predominantly expressed in laticifers and regulates the expression of TbSRPP genes in an ABA-dependent manner. The individual TbSRPP genes showed distinct induction profiles, suggesting diverse roles in rubber biosynthesis and stress adaptation. The potential involvement of TbSRPPs in the adaptation of T. brevicorniculatum plants to environmental stress is discussed based on our current knowledge of the stress-response roles of SRPPs and their homologs, and the protective function of latex and rubber against pathogens. Our data suggest that TbSRPPs contribute to stress tolerance in T. brevicorniculatum and that their effects are mediated by TbbZIP.1.
HIGH LATEX YIELDING AND DISEASE RESISTANCE OF RUBBER CLONES IRR 200 SERIES
Biswapriya Biswavas Misra's insight:
Rubber clones of Indonesian Rubber Research (IRR) 200 series have been produced from intensive breeding program started in 1985. Some clones showed superior characteristics such as high latex yielding, vigorous, and disease resistant. This study aimed to test their performances in a field trial conducted since 1999 at Sungei Putih Experimental Garden, North Sumatra. The experiment was designed in a randomized block, using twelve IRR clones as treatment and PB 260 clone as control, three replications. Planting distance was 5 m x 4 m and plot size was 10 rows x 50 trees. Observations were made on girth size of the 2, 3 and 4 year-old trees, dry rubber yield following the 1/2S d/2 and 1/2S d/3.ET2.5% tapping systems, bark thickness, rings number and diameter of latex vessels, as well as leaf fall diseases intensities of 3-5 year-old trees. The results showed four IRR 200 clones, i.e. IRR 207, IRR 208, IRR 211 and IRR 220 produced high latex. Using the 1/2S d/2 tapping system, three clones with highest dry rubber yield were obtained, namely IRR 208 (49.8 g tree-1 tapping-1 or g t-1 t-1), IRR 211 (48.8 g t-1 t-1) and IRR 220 (52.0 g t-1 t-1), whereas that using the 1/2S d/3. ET2.5% tapping system, their yields were 63.2 g, 64.3 g, and 66.2 g t-1 t-1, respectively. At four year-old, these clones had girth size of 41.4-51.0 cm, girth increment 9.7-11.6 cm year-1, bark thickness 6.3-7.2 mm, latex vessel rings number 6.8-7.0, and diameter of latex vessels 23.75-26.57 mm. All of the clones were moderately resistant to Colletotrichum, Oidium and Corynespora leaf fall diseases. This study suggests that IRR 207, IRR 208, IRR 211 and IRR 220 rubber clones are suitable for commercial stake holders and the recommended tapping system is 1/2S d/3.ET2.5%.
Using cultivars which are genetically resistant to South American leaf blight (SALB) caused by the fungus Microcyclus ulei is the only way to plant rubber trees in disease-affected areas. Numerous field observations led to the hypothesis that the resistance of the cultivar Fx2784 to SALB is likely to be monogenic. In this study, we investigated this hypothesis by examining the distribution of the trait in a cross between the resistant cultivar and a susceptible one. The individuals resulting from this cross were planted in field trials in French Guiana and Brazil. The resistance of all the trees was assessed by field observations. Bulk segregant analysis (BSA) using microsatellite markers was performed in French Guiana to determine which markers were genetically linked to resistance, and the results were validated by field observations in Brazil. In both locations, a 1:1 segregation of the resistance trait was observed, thus reinforcing the monogenic hypothesis. BSA showed tight linkage between resistance and the microsatellite markers located in linkage group 2 in the Hevea genome and enabled to pinpoint the resistance locus. The location was confirmed by observations on the trees planted in Brazil. This result should facilitate the use of Fx2784 resistance in future breeding programs for SALB resistance. This is the third major locus conferring resistance to SALB identified in rubber tree (Hevea spp.). These three loci are genetically independent, a favorable situation for genetic improvement of SALB resistance.
The present invention discloses an isolated polynucleotide encoding an enzyme for catalyzing cytosolic biosynthesis of isopentenyl diphosphate, dimefhylallyl diphosphate or the combination thereof in the plant of Hevea brasiliensis, comprising nucleotide sequence set forth in SEQ ID NO. 1, SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ' ID NO. 9 or any complementary sequence thereof; and a method for enhancing cytoplasmic availability and functionality of the enzyme, comprising the steps of predicting catalytic domain, signal peptide or membrane-spanning domain of the enzyme; introducing a point mutation to the predicted catalytic domain, signal peptide or membrane-spanning transmembrane domain; and expressing the mutated catalytic domain, signal peptide or membrane-spanning transmembrane domain in a plant cell, tissue or organ of Hevea brasiliensis. The present invention also relates to an isolated polypeptide encoded by the polynucleotide, a recombinant gene construct comprising the polynucleotide, a transformant and a transgenic plant comprising the recombinant gene construct, with enhanced production of cytosolic isoprenoid towards rubber production.
The present invention relates to an isolated polynucleotide encoding an enzyme for catalyzing biosynthesis, conversion or utilization of prenyl-pyrophosphate for rubber biosynthesis in the plant of Hevea brasiliensis, comprising nucleotide sequence set forth in SEQ ED NO. 1, SEQ ID NO. 3, SEQ ID NO. 5, SEQ ID NO. 7, SEQ ID NO. 9 or any complementary sequence thereof. The present invention also relates to an isolated polypeptide encoded by the polynucleotide; a recombinant gene construct comprising the polynucleotide; a transformant; and a transgenic plant comprising the recombinant gene construct, with enhanced biosynthesis and accumulation of polyisoprenoids; as well as a method for enhancing biosynthesis and accumulation of polyisoprenoids comprising the steps of cloning the gene construct comprising the polynucleotide and expressing the gene construct in a host cell.
Abstract: The aim of this work was studying nitrogen compounds and enzyme assimilation activity pattern distribution under influence of different nitrogen sources as well as to analyze lipids alterations in seeds submitted to storage, from an experiment conducted in greenhouse. Ammonium and nitrate were supplied as nitrogen form in the concentration of 8mM and no nitrogen as a control. Plants were growth in plastic vases contained wash sand and nitrogen solution renewed in the seven days interval. From 0 to 27 days were evaluated total nitrogen concentration, amino acids, soluble protein, nitrate and ammonium from roots, enzyme assimilation activity nitrogen from stem and leaves. The treatments were obtained by the combination among three sources (nitrogen absence, ammonium and nitrate) and two times of exposition (from 0 to 27 days) as factorial 3X2 in randomized design with four repetitions and the average tested by Tukey test to 5%. The results permitted conclude that the plants growth in ammonium presence showed high nitrogen incorporation what meant high amino acids and protein accumulation. The nitrogen forms promoted different answers in relation to enzyme activity pattern from nitrogen metabolism. Therefore, the assimilation both nitrate and ammonium occur by GS/GOGAT; however, there is strong dependence between the GS activity and the cellular nitrate pool as well between GDH activity and the ammonium cellular pool. In relation to nitrogen assimilation at different parts of the plant it could conclude that the nitric nitrogen is in part assimilated by roots preferentially via GS/GOGAT, with little GDH participation and the other part is translocated to meristematic tissue of stem where is storage or assimilated; ammonium nitrogen is assimilated totally at the roots by GS/GOGAT with significant participation of GDH; the high enzyme activity in the leaves demonstrate its participation both primary assimilation as ammonium re-assimilation. GDH leaves was detected, despite in secondary, independent paper of the sources or time of exposition. RN activity in vitro was higher in the plants that had received nitrate, being detected in the roots and stems and not detected in leaves, even so all the indications points with respect to its participation in the metabolism, suggesting that a more sensible assays. The lipid modification in seeds storage from 0, 60 and 105 days to evaluate the chemistry oil composition by GC/MS by continuous extraction with ethyl ether in soxhlet aparatus. It can be observed by results that the rubber tree seeds oil to 0 day of storage has as constituents palmitic, steariac, oleic, linoleic and linolenic acids, being the latter more abundant. At 60 days is observed the oleic acid appearance and at 105 days the total disappearance of linolenic acid and oleic acid in this period is the most abundant compound. Thus, it can be conclude that during storage the number of unsaturated fatty acids is a reduced in function of lipid peroxidation.
The most effective control of a weed flora consisting mainly of Digitaria sanguinalis, Cassia tora, Ipomoea spp., Richardia brasiliensis and Sida spp. was obtained with 5 kg napropamide + 0.8 kg simazine/ha.
Biswapriya Biswavas Misra's insight:
The most effective control of a weed flora consisting mainly of Digitaria sanguinalis, Cassia tora, Ipomoea spp., Richardia brasiliensis and Sida spp. was obtained with 5 kg napropamide + 0.8 kg simazine/ha. Control was long lasting and no injury to rubber trees was observed.
The rubber particle is a special organelle in which natural rubber is synthesised and stored in the laticifers of Hevea brasiliensis. To better understand the biological functions of rubber particles and to identify the candidate rubber biosynthesis-related proteins, a comprehensive proteome analysis was performed on H. brasiliensis rubber particles using shotgun tandem mass spectrometry profiling approaches—resulting in a thorough report on the rubber particle proteins. A total of 186 rubber particle proteins were identified, with a range in relative molecular mass of 3.9–194.2 kDa and in isoelectric point values of 4.0–11.2. The rubber particle proteins were analysed for gene ontology and could be categorised into eight major groups according to their functions: including rubber biosynthesis, stress- or defence-related responses, protein processing and folding, signal transduction and cellular transport. In addition to well-known rubber biosynthesis-related proteins such as rubber elongation factor (REF), small rubber particle protein (SRPP) and cis-prenyl transferase (CPT), many proteins were firstly identified to be on the rubber particles, including cyclophilin, phospholipase D, cytochrome P450, small GTP-binding protein, clathrin, eukaryotic translation initiation factor, annexin, ABC transporter, translationally controlled tumour protein, ubiquitin-conjugating enzymes, and several homologues of REF, SRPP and CPT. A procedure of multiple reaction monitoring was established for further protein validation. This comprehensive proteome data of rubber particles would facilitate investigation into molecular mechanisms of biogenesis, self-homeostasis and rubber biosynthesis of the rubber particle, and might serve as valuable biomarkers in molecular breeding studies of H. brasiliensis and other alternative rubber-producing species.
ABSTRACT: In national rubber plantation as well as private, one of the activities that has been done annually is estimate production for the following year based on certain block of rubber plantation. Establishing the estimation of the production according to land and plants potential is important because the estimation of production which is not appropriate will cause the production of following year disturbed even the economical life of the plant will be reduced. The modeling estimation of rubber tree production based on satelit, genetic potential and field unit data aimed to (1) examining the ability of remote sensing and geographical information system to identification of rubber tree and manage the production in the rubber plantation (2) examining the relationship the variation of the spectral reflection value (band VNIR), vegetation index, leaf area indexs (LAI) toward rubber plant production (3) making estimation of rubber tree production model, based on satelit data, plant genetic potential (clone variety and physiological quality), and environment conditions (climate and soil). Determining production method are divided into two, those are qualitative and quantitative. Qualitative is done by ranging the crown density based on NDVI with map of land capability. The quantitative models is done based on raster spatially model with the smallest unit is 15 x15 meter. The factor which can be used as a model is the crown density level, spectral reflection value that sourced from Satelit data (ASTER), genetic potential (clone variety and physiological quality), and field unit data (soil and climate). Rubber identification using satelit data based on visual interpretation and NDVI classification showed 75,52 % and 99,90 %. The regression result showed that the highest determination coefficient (r2) is the red wave length with the age of percent of age off rubber tree coefficient about 5-15 years is 79,3% and the age of 6-25 years is 97,6%. The production models with the percentage of highest accuracy is model based the red wave length, genetic potential, and field unit data with percentage accuracy 74,00% ( first model ), 68,73% ( second model) and 64,81% (third model ).