Marco Papageorgiou

Marco Papageorgiou Proposal The oil palm crop was brought to South East Asia via the British in the 1870s, from its original location in West Africa (Hushiarian et al., 2013). Oil palm (Elaeis guineensis) production from Malaysia and Indonesia, the two largest producers (Durand-Gasselin et al., 2005), contribute between 84-85% of the worlds production (Hushiarian et al., 2013; Ho et al., 2014). Further, oil palm is agriculturally vital to Malaysia, producing a range of products from vegetable oil, cosmetics and biofuels (Paterson et al., 2008), and, consisting a nationwide total of 5 million hectares, which concurrently contributes 31.4% of the world’s oil palm (Rakib et al., 2014). Oil palm is subsequently affected by several pests and diseases; basal stem rot (BSR) and upper stem rot (USR) are such oil palm diseases (Rakib et al., 2014; Sahebi et al., 2014; Lim et al., 2005), caused from the basidiomycete, Ganoderma boninense (Pilotti et al., 2003). The source of BSR has been linked to basidiospores, in which high numbers are capable of long distance travelling from their initial release from basidiocarps; ultimately entering oil palm wounds hitherto created from planting, harvesting and crop management practices (Ho et al., 2015; Rees et al., 2009). It has also ben suggested that another source of Ganoderma spp. infections occur through previous palm plantation debris, in which Ganoderma utilise in order to initiate oil palm root infection (Ho et al., 2015). Although there are indeed several different species of Ganoderma, Ganoderma boninense has been labelled as a major oil palm virulent, which continues on to be the causative agent of BSR; with several other species attributes to diseases in grapevines, pal, rubber, and tea (Ho et al., 2015; Sahebi et al., 2014). Collectively, a total of 15 Ganoderma species have been detected in oil palm (Ho et al., 2015). The severity of these stem rot diseases is further exacerbated from the lack of understanding and clarity of this pathogen. From an economical perspective, G. boninense has caused financial losses from between RM225 million to RM1.5 billion each year (Husharian et al., 2013). With these facts taken into consideration, the oil palm pathogenic infection has lowered the overall productivity of the crop. To date, there is still no economically feasible approach at controlling disease caused by G. boninense (Durand-Gasselin et al., 2005). The fungus, caused by Ganoderma boninense, consequently causes white rot of the wood from the breakdown of lignin, thus exposing spongy and fibrous cellulose (Tan et al., 2013; Paterson 2007). Ganoderma spp. produce and secrete several key compounds that work to degrade this host cell lignin (syringyl uniting oil palm trunks), lowering the shielding effect from microbial attack. A plant will recognise and respond to pathogenic attack through means pertaining to the expression of molecular effectors and other molecules. The mode of Ganoderma invasion begins with a oil palm root invasion of fungal mycelia which penetrate and spread to the shoots (Sahebi et al., 2014). This is followed by the collapse of the trunk. Ganoderma can be spread via airborne basidiospores, insects, spore transfer, and mycelial root contact (Kwan et al., 2014); and, it is considered that infection of oil palm by Ganoderma occurs via contact of palm roots with colonised debris living within soil (Pilotti et al., 2003). Additionally, and secondary to this mode of infectivity by Ganoderma, is the spreading of Ganoderma pathogens through the contact of living palm roots with each-other (Pilotti et al., 2003). Page !1 of 5! Marco Papageorgiou Next Generation Sequencing (NGS) technologies, such as Genome-wide associations studies (GWAS) can be readily employed in order to map and identify a magnitude of allelic variations (Yano et al., 2016). Current methods to control basal stem rot (BSR) involve the use of fungicides, along with conventional cultural practices which include elimination and burning of those infected oil palm crops (Tan et al., 2013). Oil palm genes relating to the tolerance and resistance of G. boninense are yet to be fully characterised; and this places a clear emphasis and need to profile those differentially expressed genes, and their transcripts, which are associated with molecular events that occur between the host and G. boninense virulent. This profiling can be undertaken by the incorporation of next-generation sequencing methodologies. As a result, from generating and charactering molecular interactions, several biomarkers may help the process of detecting BSR. These studies could also facilitate, and incorporate, the use of conventional PCR and qPCR to quantify molecular biomarker candidates based on G. boninense - oil palm interactions. A molecular screening approach, also referred to as an oil palm genetic improvement programs (Kwan et al., 2014), can be classified as a more targeted and effective option when compared to current disease management practices, in place to eradicate the BSR disease. Gene-to-function using functional genomics (Robinson et al., 2009); the incorporation of mutagenised oil palm lines could provide by utilised to show those genes which have a multipurpose role during inception with G. boninense. By creating mutant phenotypes of oil palm genes, before treatment with G. boninense, a more targeted approach, based on gene mutants, could facilitate a map of genetic pathways that are enabled through infection from G. boninense providing a narrative built upon a gene or gene sets which have been inactivated. Oil palm resistance could be a strategy (Ho et al., 2015) whereby an alteration of lignin biosynthesis is facilitated (Paterson et al., 2008); these genetic manipulations would require changes in key enzymes that lead to strengthened lignin, however would presume an additional layer of public discourse from the marketing of GM palm oil products. Nonetheless, approaches to creating mutagenesis within oil palm genes could include: • • • • RNAi T-DNA inserts Transposon inserts EMS At this stage, it would be advantageous to uncover the molecules representing defence mechanisms/pathways of Ganoderma and oil palm interactions which can provide data pertaining to transcript abundance levels. This can be assisted, and sped up, with appropriate screening and marker-assisted breeding programs which will subsequently expose DNA makers, inherently associated with these defence-related transcripts (Ho et al., 2015). Molecular markers, identified through application of marker technologies, can be utilised against a criterion which considers high value traits (Appleby et al., 2009) associated with Ganoderma and oil palm interactions. Page !2 of 5! Marco Papageorgiou A new approach is currently underway; a genetic/molecular approach to identify those genes involved in defence against Ganoderma spp; specifically G. boninense. By utilising large-scale genetic screening on oil palm - Ganoderma interactions, the downstream expression of genes associated with this plant-pathogen will provide insights as to which oil palm species are more tolerable and/or resistant to G. boninense infections. The next steps of oil palm research will require a closer focus and analysis of oil palm defence pathways, in G. boninense infections, in alignment with those already established and outlined. This disease-resistance of oil palm research should also consider hormonal responses to other Ganodema species at different infection phases (Ho et al., 2015). In addition to pinning the exact expressed genes, and their mRNA transcript abundances, involved in oil palm - Ganoderma spp, it could also be beneficial to apply structural biology studies to determine the biological processes that unfold at the protein interaction level. This not only adds value by more precisely illustrating gene function from comparative studies on non-inoculated and inoculated oil palm with Ganoderma; but also contributes to oil palm gene databases (Hrmova et al., 2009). Digging deeper, 3D structural studies on oil palm defence molecules can help define the possibility of any complex interactions between gene/protein and pathogenic protein from assemblies transcription complexes, and/or plant membrane-bound transporters, and signalling transduction (Hrmova et al., 2009). The merging of functional genomics, withs structural biology and plant cell biology will be better positioned to model oil palm defence pathways in reaction to Ganoderma infection; this can be practically applied within the purview of generating oil palm genomics programs that seek to label, compare, and clearly describe those oil palm products associated with mRNA transcript data, based on Ganoderma inoculation, with their respective function at the protein-protein interaction level. This combination of NGS, transcript abundance data, and subsequent 3D structural information, should be appropriately included and carried out within the context of comparative studies based on G. boninense stage infection on oil palm. Page !3 of 5! Marco Papageorgiou References: Nikki Appleby, David Edwards, and Jacqueline Batley, 2009. New Technologies for Ultra-High Throughput Genotyping in Plants. Methods in Molecular Biology, Plant Genomics, vol. 513. T. Durand-Gasselin, H. Asmady, A. Flori, J.C. Jacquemard, Z. Hayun, F. Breton and H. de Franqueville, 2005. Possible sources of genetic resistance in oil palm (Elaeis guineensis Jacq.) to basal stem rot caused by Ganoderma boninense - prospects for future breeding. Mycopathologia, vol. 159, pp. 93-100. Maria Hrmova and Geoffrey B. Fincher, 2009. Functional Genomics and Structural Biology in the Definition of Gene Function. Methods in Molecular Biology, Plant Genomics, vol. 513. Roozbeh Hushiarian, Nor Azah Yusof, and Sabo Wada Dutse, 2013. Detection and control of Ganoderma boninense: strategies and perspectives. SpringerPlus, 2:555. C.L. Ho, Y.C. Tan, 2015. Molecular defence response of oil palm to Ganoderma infection. Photochemistry, vol. 114, pp. 160-169. Yee-Min Kwan, Sariah Meon Chai-Ling Ho, Mui-Yun Wong, 2015. Cloning of nitric oxide associated 1 (NOA1) transcript from oil palm (Elaeis guineensis) and its expression during Ganoderma infection. Journal of Plant Physiology, vol. 174, pp. 131-136. H.P. Lim and Y.K. Fong, 2005. Research on basal stem rot (BSR) of ornamental palms caused by basidiospores from Ganoderma boninense. Mycopathologia, vol. 159, pp. 171-179. R.R.M Paterson, 2006. Ganoderma disease of oil palm - A white rot perspective necessary for integrated control. Crop Protection, vol. 26, pp- Robert R.M. Paterson, Sariah Meon, and Nelson Lima, 2009. The Feasibility of Producing Oil Palm with Altered Lignin Content to Control Ganoderma Disease. Journal of Phytopathology, vol. 157, pp. 649-656. C.A. Pilotti, F.R. Sanderson and E.A.B. Aitken, 2003. Genetic structure of a population of Ganoderma Boninense on oil palm. Plant Pathology, vol. 52, pp. 455-463. Mohd Rashid Mohd Rakib, Choon-Fah Joseph Bong, Ahmad Khairulmazmi and Abu Seman Idris, 2014. Genetic and Morphological Diversity of Ganoderma Species Isolated from Infected Oil Palms (Elaeis guineensis). International Journal of Agriculture and Biology, 16: 691-699. R. W. Rees, J. Flood, Y. Hasan, U. Potter, and R. M. Cooper, 2009. Basal stem rot of oil palm; mode of root infection and lower stem invasion by Ganoderma boninense. Plant Pathology, vol. 58, pp. 982-989. Page !4 of 5! Marco Papageorgiou Mahbod Sahebi, Mohammad M. Hanafi, Mui-Yun Wong, A.S. Idris, Parisa Azizi, Mohammad Faseleh Jahromi, Parisa Shokryazdan, Rambod Abiri, Hasmah Mohidin, 2015. Towards immunity of oil palm against Ganoderma fungus infection. Acta Physiology Plant, vol. 37, no. 195. Yung-Chie Tan, Mui-Yun Wong, Chai-Ling Ho, 2015. Expression profiles of defence related cDNAs in oil palm (Elaeis guineensis Jacq.) inoculated with mycorrhizae and Trichoderma harzianum Rifai T32. Plant Physiology and Biochemistry, Vol. 96, pp. 296-300. Yung-Chie Tan, Keat-Ai Yeoh, Mui-Yun Wong, Chai-Ling Ho, 2013. Expression profiles of putative defencerelated proteins in oil palm (Elaeis guineensis) colonised by Ganoderma boninense. Journal of Plant Physiology, vol. 170, pp-. Page !5 of 5!