Functional genomics of rice

Rice functional genomic research at the post-genomic era has been accelerated by the developmental of technical and resource platforms, focusing on construction of mutant libraries, isolation of full-length cDNAs, global gene expression, data mining and rice bioinformatics. Taking advantage of the high quality genome sequence and global gene expression profiles available in the public domain, our group have predicted: 1) biologically significant cis-acting regulatory elements (CREs), which help to prioritize candidate rice CREs for genetic and biochemical analyses; and 2) protein-protein interactions that extend known pathways and improve functional annotation of many unknown rice proteins and networks in rice. In addition, we studied the global gene expression profiles of two Malaysian rice cultivars, MR219 and MR84 of indica subspecies, which have different percentage of filled grains using the NSF 20 K rice oligonucleotide array developed from the rice sequences of japonica subspecies. Direct comparison of the transcriptomes of MR219 and MR84 during rapid grain-filling period at 5 and 10 days after fertilization (DAF) enhanced our understanding on poor grain filling (partially filled and empty rice grains) which affects the final yield of MR219. Following that, we also elucidated the functions of unknown rice genes by overexpressing or silencing them in MR219. Meanwhile, we used rice as a model for functional genomic research for other plant species such as mangrove and oil palm

HnRNP-like proteins as post-transcriptional regulators

Plant cells contain a diverse repertoire of RNA-binding proteins (RBPs) that coordinate a network of post-transcriptional regulation. RBPs govern diverse developmental processes by modulating the gene expression of specific transcripts. Recent gene annotation and RNA sequencing clearly showed that heterogeneous nuclear ribonucleoprotein (hnRNP)-like proteins which form a family of RBPs, are also expressed in higher plants and serve specific plant functions. In addition to their involvement in post-transcriptional regulation from mRNA capping to translation, they are also involved in telomere regulation, gene silencing and regulation in chloroplast. Here, we review the involvement of plant hnRNP-like proteins in post-transcription regulation of RNA processes and their functional roles in control of plant developmental processes especially plant-specific functions including flowering, chloroplastic-specific mRNA regulation, long-distance phloem transportation and plant responses to environmental stresses

Transcriptomic changes in the root of oil palm (Elaeis guineensis Jacq.) upon inoculation with Bacillus sphaericus UPMB10

Plant growth-promoting bacteria (PGPB) promote plant growth through a combination of mechanisms which affect mineral nutrition and root development. In this study, we profiled the transcripts in oil palm roots inoculated with a PGPB, Bacillus sphaericus UPMB10, upon the establishment of a stable inoculum on the root surface by cDNA microarray analysis. A total of 70 from more than 3,700 transcripts examined were found to be significantly upregulated in the roots of oil palm inoculated with B. sphaericus UPMB10 compared to those from un-inoculated oil palm roots. Majority of these genes were related to protein synthesis and processing, stress, primary metabolism, and membrane transport. Many ribosomal proteins were upregulated in the roots of B. sphaericus-inoculated oil palm plantlets. In addition, B. sphaericus UPMB10 were able to upregulate the expression of a gene encoding low affinity nitrate transporter, independent of root morphogenesis. These rhizosphere bacteria were also demonstrated to induce stress-related proteins that may lead to tolerance to biotic and abiotic stresses

Unraveling the nuclear and chloroplast genomes of an agar producing red macroalga, Gracilaria changii (Rhodophyta, Gracilariales)

Agar and agarose have wide applications in food and pharmaceutical industries. Knowledge on the genome of red seaweeds that produce them is still lacking. To fill the gap in genome analyses of these red algae, we have sequenced the nuclear and organellar genomes of an agarophyte, Gracilaria changii. The partial nuclear genome sequence of G. changii has a total length of 35.8 Mb with 10,912 predicted protein coding sequences. Only 39.4% predicted proteins were found to have significant matches to protein sequences in SwissProt. The chloroplast genome of G. changii is 183,855 bp with a total of 201 open reading frames (ORFs), 29 tRNAs and 3 rRNAs predicted. Five genes: ssrA, leuC and leuD CP76_p173 (orf139) and pbsA were absent in the chloroplast genome of G. changii. The genome information is valuable in accelerating functional studies of individual genes and resolving evolutionary relationship of red seaweeds

Effects of herbicides on fungal phytopathogens

Herbicides are inevitable inputs to control excessive weed in crop land, particularly where modern agricultural practices such as conservation tillage, are opted. Intensive farming has increased the market value of herbicides among the other pesticides. Although herbicides are effective in controlling weed population, administration of this synthetic chemicals may alter the soil microbial community causing potential increase of plant pathogens. Moreover, herbicides may also have nontarget effects on the cultivated crops making them more susceptible to diseases. Actions of herbicides in soil that either stimulate microbial growth or wipe out some microbial population may create space for the thrivial of opportunistic fungi. Previous studies showed that white rot fungi are more tolerant to herbicides as they produce lignin degrading enzymes that are highly oxidative, non-specific and are able to transform a wide range of herbicides. Besides that, this group of fungi can grow on agricultural waste substrates. Influence of these herbicides on soil microbial ecosystem and interactions of plants and pathogenic white rot fungi modulate disease development in plant hosts

Molecular cloning of a putative Acanthus ebracteatus- 9-cis-epoxycarotenoid deoxygenase (AeNCED) and its overexpression in rice

9-Cis-epoxycarotenoid dioxygenase (NCED) is an important enzyme which catalyzes the oxidative cleavage of abscisic acid (ABA), a plant growth regulator which plays a vital role in stress tolerance. In this study, a cDNA sequence encoding NCED from a mangrove plant (Acanthus ebracteatus) was analyzed and overexpressed in rice. Analysis of the deduced amino acid sequence of AeNCED revealed an open reading frame of 1,638 bp encoding a protein of 545 amino acids, with a 123 bp 5’-untranslated region (UTR) and a 259 bp 3’-UTR. The deduced amino acid sequence of AeNCED is more than 80% identical to the amino acid sequences of carotenoid cleavage dioxygenase from carrot, tomato, and coffee. The RNA encoding AeNCED was detected in transgenic rice (Oryza sativa cv. BRRI dhan29) plants overexpressing this cDNA. These plants only showed significantly higher tolerance to salinity at germination and better performance at seedling stages. The levels of ABA in transgenic rice seedlings overexpressing AeNCED treated with 100 mM NaCl for 24 hours were higher than those of untransformed plants. However, a higher level of dihydrophaseic acid (DPA) and ABA glucose ester (ABA-GE) were also observed in these transgenic plants suggesting that rapid degradation of ABA through a self-regulation mechanism

Selection of reference genes for quantitative real-time PCR normalization in Ganoderma-infected oil palm (Elaies guineensis) seedlings

African oil palm (Elaeis guineensis) is an important oil bearing tree commercially cultivated in Malaysia. Palm oil is an important product for local consumption, provides enormous socio-economic benefits of trade and employment opportunities, and fulfilling the growing global demand for vegetable oils. The monoculture system has fostered the outbreak of basal stem rot (BSR) disease caused by the fungus Ganoderma boninense. Quantitative real-time PCR (qRT-PCR) is a widely used molecular technique to examine the infection effect on gene expression in oil palm. The selection of appropriate reference genes is vital for accurate data normalization. In this study, the expression stability of six housekeeping genes- β-actin, cyclophilin, GAPDH, MSD, NAD and ubiquitin were validated in oil palm root tissue after fungal infection. NormFinder and BestKeeper algorithms were used to cross-validate the expression stability of the candidate reference genes. MSD, NAD and ubiquitin were shown to exhibit the highest expression stability. These genes were recommended as reference genes for gene expression studies of oil palm root tissue at early fungal infection stage

Transgenic plants producing polyhydroxyalkanoates

Currently, the polyhydroxybutyrate (PHB) copolymer, polyhydroxy-co-valerate (PHBV) is being produced commercially using a two-stage glucose / propionate fed batch fermentation process using Ralstonia eutropha. The economics of the manufacturing process are still a major barrier to the widespread use of polyhydroxyalkanoates (PHAs) and intensive efforts are being made to reduce the cost of production by means of bioprocess design and metabolic engineering of production strains. However, despite these improvements, the production costs are still high compared to petroleum-derived commodity plastics. An alternative strategy for lowering production costs that has been proposed is to develop transgenic plants that produce PHAs. This strategy is considerably cheaper because the PHAs production from plants does not require expensive fermentation equipment and processing facilities

Exogenous application of glycine betaine alleviates salt induced damages more efficiently than ascorbic acid in in vitro rice shoots

Considerable amount of research have indicated that exogenous application various compounds such as compatible solutes, plant hormones and antioxidants could enhanced salt stress tolerance in plants. However, the salt stress alleviating effect of these compounds on Malaysian rice varieties has not been investigated. Therefore, this study was undertaken with the objective to examine the salt stress mitigating effect of glycine betaine and ascorbic acid on rice shoot apices of two Malaysian rice varieties under NaCl stress. Results clearly indicated that supplementation of glycine betaine at 5 and 10 mM effectively ameliorates salt stress induced damages resulted in improved plant height, root length, biomass and total chlorophyll in both varieties tested, MR220 and MR253 as compared to salt stress condition. However, further increased of glycine betaine to 15 and 20 mM did not showed further enhancement on the overall plant growth. Supplementation of 5 mM glycine betaine increased the plant height of MR220 and MR253 to 17.0 cm and 13.3 cm as compared to 9.8 cm and 10.3 cm in salt stress media. It was noted that supplementation of of glycine betaine successfully increase the total chlorophyll content from 7.0 mg/mL FW to 13.4 and 9.1 mg/mL FW for MR220 and 8.7 and 13.8 mg/mL FW for MR253 at 5 and 10 mM respectively. Conversely, supplementation of ascorbic acidat all concentrations tested did not showed salt stress mitigating effect on the growth of rice shoot. Furthermore, ascorbic acid supplemented at 10, 15 and 20 mM was found exerted negative impact on plant growth with reduction in all growth parameters measured. In short, results from the study clearly indicated the potential of glycine betaine in mitigating salt-stress induced damages. However, more studies need to be carry out in the near future based on glasshouse and field scale trials to study the changes in the rice agronomic traits, especially the yield component should be evaluated because tolerance in stress could not represent the final yield

Ecological and evolutionary diversification of sulphated polysaccharides in diverse photosynthetic lineages: a review

Sulphated polysaccharides (SPs) are carbohydrate macromolecules with sulphate esters that are found among marine algae, seagrasses, mangroves and some terrestrial plants. The sulphate concentration in the ocean (28 mM) since ancient time could have driven the production of SPs in marine algae. SPs have a gelatinous property that can protect marine algae against desiccation and salinity stress. Agar and carrageenan are red algal SPs that are widely used as gelling agents in the food and pharmaceutical industries. The information on the SPs from freshwater and land plants are limited. In this review, we reviewed the taxonomic distribution and composition of SPs in different photosynthetic lineages, and explored the association of SP production in these diversified photosynthetic organisms with evolution history and environmental stresses. We also reviewed the genes/proteins involved in SP biosynthesis. Insights into SP biosynthetic machinery may shed light on the evolution that accompanied adaptation to life on earth