Kalaivani Nadarajah

Identification of functionally important microRNAs from rice inflorescence at heading stage of a qDTY4.1-QTL bearing Near Isogenic Line under drought conditions

A cross between IR64 (high-yielding but drought-susceptible) and Aday Sel (drought-tolerant) rice cultivars yielded a stable line with enhanced grain yield under drought screening field trials at International Rice Research Institute. The major effect qDTY4.1 drought tolerance and yield QTL was detected in the IR77298-14-1-2-10 Backcrossed Inbred Line (BIL) and its IR87705-7-15-B Near Isogenic Line (NIL) with 93.9% genetic similarity to IR64. Although rice yield is extremely susceptible to water stress at reproductive stage, currently, there is only one report on the detection of drought-responsive microRNAs in inflorescence tissue of a Japonica rice line. In this study, more drought-responsive microRNAs were identified in the inflorescence tissues of IR64, IR77298-14-1-2-10 and IR87705-7-15-B via next-generation sequencing. Among the 32 families of inflorescence-specific non-conserved microRNAs that were identified, 22 families were up-regulated in IR87705-7-15-B. Overall 9 conserved and 34 non-conserved microRNA families were found as drought-responsive in rice inflorescence with 5 conserved and 30 non-conserved families induced in the IR87705-7-15-B. The observation of more drought-responsive non-conserved microRNAs may imply their prominence over conserved microRNAs in drought response mechanisms of rice inflorescence. Gene Ontology annotation analysis on the target genes of drought-responsive microRNAs identified in IR87705-7-15-B revealed over-representation of biological processes including development, signalling and response to stimulus. Particularly, four inflorescence-specific microRNAs viz. osa-miR5485, osa-miR5487, osa-miR5492 and osa-miR5517, and two non-inflorescence specific microRNAs viz. osa-miR169d and osa-miR169f.2 target genes that are involved in flower or embryonic development. Among them, osa-miR169d, osa-miR5492 and osa-miR5517 are related to flowering time control. It is also worth mentioning that osa-miR2118 and osa-miR2275, which are implicated in the biosynthesis of rice inflorescence-specific small interfering RNAs, were induced in IR87705-7-15-B but repressed in IR77298-14-1-2-10. Further, gene search within qDTY4.1 QTL region had identified multiple copies of NBS-LRR resistance genes (potential target of osa-miR2118), subtilisins and genes implicated in stomatal movement, ABA metabolism and cuticular wax biosynthesis.

Identification and validation of sheath blight resistance in rice (Oryza sativa L.) cultivars against Rhizoctonia solani

Abstract Rice sheath blight, caused by Rhizoctonia solani, is a devastating disease of rice which causes major yield loss in most rice growing regions of the world. Hence, identification and subsequent development of disease resistance in rice cultivars is crucial. Six moderately resistant cultivars, namely ‘Teqing’, ‘Jasmine85’, ‘Tetep’, ‘Pecos’, ‘Azucena’ and ‘Taducan’, one susceptible local cultivar, ‘MR 219’, and two new advanced breeding lines, ‘UKMRC 2’ and ‘UKMRC 9’, were screened using micro-chamber and mist-chamber methods. The fungal isolate was confirmed as R. solani using ITS-rDNA sequencing. Severe sheath blight was recorded following inoculation with R. solani under micro-chamber conditions. The most resistant cultivar was ‘Tetep’, followed by ‘Teqing’. In mist-chamber screening, ‘UKMRC 2’ showed the highest level of susceptibility with a disease severity index (DSI) of 6.67, while ‘MR 219’ produced the highest DSI of 7.22 in the micro-chamber. Significant correlation of plant height and disease was obtained with relative lesion height (RLH) indices. Significant correlations were also observed among diseased plant affected area (DPAA), VRT (visual rating) and RLH, with VRT being the most accurate. On the basis of the disease reactions, ‘Tetep’ and ‘Teqing’ were identified as suitable donors to improve resistance in ‘UKMRC 2’ and ‘MR 219’. Mist-chamber screening method was more reliable to evaluate sheath blight under greenhouse conditions than the micro-chamber method.

Induced Systemic Resistance in Rice

Plants possess a plethora of defense mechanisms that respond to both biotic and abiotic stresses. The response of a plant to various pathogens and pests can vary dependent on factors such as host variety, strain, as well as environmental factors. How quickly a plant responds to these stresses will determine the level of resistance of a plant species. The SAR and ISR mechanisms in plants work together to provide the host with protection against pathogen and pest attacks. Unlike SAR, ISR is induced by nonpathogenic allies from belowground in the form of plant growth-promoting bacteria. ISR is induced in the root and in foliar tissue and is able to provide the host plant with systemically induced resistance against a broad spectrum of microorganisms. Selected strains of plant growth-promoting rhizobacteria suppress diseases and pest infestation by inhibition of pathogens/pests as well as resulting in the induction of systemic resistance in planta. In rice these organisms have been known to activate the JA/ETH and auxin pathways. Due to the higher levels of endogenous SA in rice, the SA-independent pathways are a preferred way of inducing resistance within the rice host. There are various types of determinants that have been implicated to play a role in ISR. These determinants can either work individually or in combination to induce ISR in plants. From in vitro, greenhouse and field studies on rice, several strains of bacteria such as Pseudomonas spp., Bacillus spp., Serratia spp., and Azospirillum spp. have been listed as organisms with potential to function as biofertilizers and biopesticides in rice.

Molecular Characterization and Screening for Sheath Blight Resistance Using Malaysian Isolates of Rhizoctonia solani

Two field isolates of Rhizoctonia solani were isolated from infected paddy plants in Malaysia. These isolates were verified via ITS-rDNA analysis that yielded ~720 bp products of the ITS1-5.8S-ITS4 region, respectively. The sequenced products showed insertion and substitution incidences which may result in strain diversity and possible variation in disease severity. These strains showed some regional and host-specific relatedness via Maximum Likelihood and further phylogenetic analysis via Maximum Parsimony showed that these strains were closely related to R. solani AG1-1A (with 99-100% identity). Subsequent to strain verification and analysis, these isolates were used in the screening of twenty rice varieties for tolerance or resistance to sheath blight via mycelial plug method where both isolates (1801 and 1802) showed resistance or moderate resistance to Teqing, TETEP, and Jasmine 85. Isolate 1802 was more virulent based on the disease severity index values. This study also showed that the mycelial plug techniques were efficient in providing uniform inoculum and humidity for screening. In addition this study shows that the disease severity index is a better mode of scoring for resistance compared to lesion length. These findings will provide a solid basis for our future breeding and screening activities at the institution.

The 172-kb genomic DNA region of the O. rufipogon yld1.1 locus: comparative sequence analysis with O. sativa ssp. japonica and O. sativa ssp. indica

Common wild rice (Oryza rufipogon) plays an important role by contributing to modern rice breeding. In this paper, we report the sequence and analysis of a 172-kb genomic DNA region of wild rice around the RM5 locus, which is associated with the yield QTL yld1.1. Comparative sequence analysis between orthologous RM5 regions from Oryza sativa ssp. japonica, O. sativa ssp. indica and O. rufipogon revealed a high level of conserved synteny in the content, homology, structure, orientation, and physical distance of all 14 predicted genes. Twelve of the putative genes were supported by matches to proteins with known function, whereas two were predicted by homology to rice and other plant expressed sequence tags or complementary DNAs. The remarkably high level of conservation found in coding, intronic and intergenic regions may indicate high evolutionary selection on the RM5 region. Although our analysis has not defined which gene(s) determine the yld1.1 phenotype, allelic variation and the insertion of transposable elements, among other nucleotide changes, represent potential variation responsible for the yield QTL. However, as suggested previously, two putative receptor-like protein kinase genes remain the key suspects for yld1.1.

Morphological and molecular characterization of Magnaporthe oryzae (fungus) from infected rice leaf samples

Magnaporthe oryzae is a plant-pathogenic fungus that causes a serious disease affecting rice called rice blast. Outbreaks of rice blast have been a threat to the global production of rice. This fungal disease is estimated to cause production losses of US

Biofuel Sector in Malaysia: Challenges and Future Prospects

55 million each year in South and Southeast Asia. It has been used as a primary model for elucidating various aspects of the host-pathogen interaction with its host. We have isolated five isolates of Magnaporthe oryzae from diseased leaf samples obtained from the field at Kompleks Latihan MADA, Kedah, Malaysia. We have identified the isolates using morphological and microscopic studies on the fungal spores and the lesions on the diseased leaves. Amplification of the internal transcribed spacer (ITS) was carried out with universal primers ITS1 and ITS4. The sequence of each isolates showed at least 99% nucleotide identity with the corresponding sequence in GenBank for Magnaporthe oryzae.

In Silico Identification of Plant-Derived Secondary Metabolites in Defense

The energy demands of the world and the eventual depletion of fossil fuel have urged the search for alternative fuel sources. The R&D on biofuels in Malaysia first commenced in 1980s, and since then it’s commercialization has progressed at a very slow pace. with many uncertainties. In the last two decades, researchers and scientists have looked into identifying resources with immense potential for production of biofuel as a renewable, sustainable energy resource of the future, and palm oil and palm oil waste have remained the main sources for production of renewable energy for the last decades. Various policies and acts were put in place to assist Malaysia with the agenda of developing renewable energy sources as an environmentally friendly and sustainable alternative to fossil fuels. This chapter attempts to compile the state of the renewable energy scenario in Malaysia, its potential, governmental involvement, challenges, and future prospects of the biofuel industry in Malaysia.

Rhizobium in Rice Yield and Growth Enhancement

Plant secondary metabolites contribute significantly to the field of agriculture, medicine, and biofuels. These compounds have been a focal point in plant breeding and metabolic engineering. However information on these compounds is lacking severely especially in non-model plants. Through integrated omics approach, we can now study secondary metabolites in model and non-model plants to determine genes, predict gene function, and provide information on pathways that may regulate its biosynthesis and function. Online resources have provided a means to fast-track our understanding on the mechanism involved in the biosynthesis of secondary metabolites and how these products are regulated by their environment, developmental stages, and species. The information derived may be utilized in metabolic engineering or in elicitation of the mechanisms involved in its production. As secondary metabolites have been implicated in plant defense mechanism, the understanding of the genes, their function, and their pathways will definitely assist in improving plant defenses against biotic and abiotic stresses. Here we provide a brief overview on the databases and resources available to conduct in silico analysis of plant secondary metabolites and future prospects in utilizing the derived information to improve metabolite function and production in crops.

Induction of Systemic Resistance for Disease Suppression

The agricultural industry faces issues that affect its productivity such as fertility, pests, pathogens, and climate change. In line with moving towards sustainable agriculture, eco-friendly approaches such as biofertilizers, biopesticides, and bioremediation have been implemented through the utilization of various types of microbial inoculums such as PGPRs. PGPRs exert their influence on plants through the production of various determinants such as siderophores, enzymes, lipopolysaccharide, exopolysaccharide, lipopeptides, and signal molecules such as salysilic acid. These compounds are capable of promoting growth and yield directly through processes such as nitrogen fixation, siderophore production, phosphate solubilization, phytohormone production, and ACC deaminase. Indirectly, these organisms address biotic and abiotic stresses through the induction of systemic resistance, biocontrol, and stress management. While the role of Rhizobium has been extensively researched in legumes, the information derived in non-legume systems has not been as extensive. Here, we provide a brief overview of the role of Rhizobium species in increasing the yield and growth of rice.