Category Archives: 2011 Vol 23 Aug

Genomics and plant breeding

The recent announcements of the breakthroughs in obtaining the oil palm genome sequence map herald a new chapter in oil palm genetic improvement. These breakthroughs will spur the further development of oil palm genomics. This article examines how genomics would impact plant and oil palm breeding.

The knowledge derived from genomics research in terms of the DNA structure of a gene, how it functions and interacts with other genes to produce a trait, its homology and synteny of genes across species, and its derived tools, as well as linkage maps, gene discovery (candidate genes), and efficient markers, would allow new genes or alleles to be discovered and transformed into breeding populations to broaden their genetic base for further breeding. Marker-assisted selection (MAS) saves effort, time and space, and can be more efficient than field phenotyping. Cultivars from MAS for monogenic traits are available for a number of crops. MAS for quantitative traits has still to contend with quantitative trait loci (QTL) x environment interaction, QTL x host interaction, linkage, epistasis, inaccurate phenotyping and false positive linkage issues. Genetically modified (GM) cultivars are becoming more available with decreasing biosafety concerns and public misperceptions.

The application of genomic knowledge and tools in oil palm breeding is hampered by the crop’s long generation cycle, large space requirement for field testing, and consequently small population sizes and paucity of diverse uniform experimental lines to develop and validate the tools. Hope lies in the use of model species to expedite this. MPOB has developed a number of putative transgenics, trait-linked markers and QTL, but what is needed is for the private industry to validate them with their own genetic materials and their forte to translate them into cultivars. With the rapid pace of development in genomic science and technology and the increasing number of plantation companies having genomics capability, good collaborative efforts and strategic partnerships to develop these genomic tools for the plant breeder to derive superior cultivars costeffectively and readily cannot be over-emphasised.

Utilisation of oil palm by-products as ruminant feed in Malaysia

The main by-products from the oil palm industry are palm kernel expeller (PKE), palm oil sludge (POS), palm pressed fibre (PPF), oil palm fronds (OPF) and oil palm trunks (OPT). The use of these by-products in ruminant feeding systems has been widely reported in Malaysia, and it is estimated that 2.2 million tones PKE, 2.2 million tonnes POS, 13 million tonnes of PPF, 35 million tonnes OPF and 9 million tonnes of OPT were available as feeds for ruminants in 2008. This article discusses the utilisation of oil palm by-products as ruminant feed in Malaysia. Studies on the characterisation and digestibility of PKE, PPF, POS, OPT and OPF and their use in practical rations for beef and dairy production have been reported. Factors which can affect nutrient utilisation include the chemical and physical structure of the feeds, feed intake, rate of passage and digestibility of the nutrients. Nutritive value data show that PKE with total digestible nutrients (TDN) of 75.8% and metabolisable energy (ME) of 11.13 MJ kg-1 is a high quality feed while POS (TDN 62.5%, ME 8.37 MJ kg-1) is a feed of moderate quality for ruminants. OPF (ME 5.65 MJ kg-1) and OPT (ME 5.95 MJ kg-1) are lower quality feeds and can be sources of roughage for ruminant livestock. The highly fibrous nature of PPF is reflected by its low degradability in the rumen and its low TDN (27.8%) and low ME (4.21 MJ kg-1) values. Due to its huge quantity and availability throughout the year, OPF has been widely used as a roughage source and as a component in complete rations for ruminant livestock. The optimum level of OPF inclusion in rations for ruminant feeding is 30%. Cattle fed OPF-based diets can achieve weight gains of 600-850 g per day.

Ecotoxicity of Bacillus thuringiensis, Terakil-1® and Teracon-1® against freshwater fish, Tilapia nilotica

Ecotoxicity test was conducted to study the effect of Terakil-1® and Teracon-1® against freshwater fish Tilapia nilotica by exposing it to various concentrations of the sample. Terakil-1® and Teracon-1®, each led to 30% and 12.5% corrected mortality of freshwater fish, Tilapia nilotica at 128 mg litre-1 at 4 days after treatment (96 hr). The LC50 of two MPOB Bt1 products was 100-1000 mg litre-1 implying that Terakil-1® and Teracon-1® are practically non-toxic. Terakil-1® and Teracon-1® are target specific to palm insect pests such as bagworms and nettle caterpillars.

Infestations by the bagworms Metisa plana and Pteroma pendula for the period 1986-2000 in major oil palm estates managed by Golden Hope Plantation Berhad in Peninsular Malaysia

Metisa plana Walker and Pteroma pendula Joannis are important pests of the oil palm, Elaeis guineensis Jacquin, which is the primary agricultural crop in Malaysia. Although there is a history of integrated management of the bagworms, information gaps exist with regard to their incidence, biology, dispersion and population dynamics. Such new information is needed to improve the current integrated management of these pests. Analysis of historical records of bagworm infestations over 63 955 ha of oil palm in 69 estates in Peninsular Malaysia showed M. plana and P. pendula to be the primary pests. Infestations were of single or mixed species, and ranged from nil to 7811 ha yr-1. Cumulative infestations were 18 297 ha, 4904 ha and 14 607 ha for single species of P. pendula and M. plana, and for mixed species of P. pendula and M. plana, respectively. This shows P. pendula to be the predominant species, and is attributed to its ability to survive very wet weather (>200 mm rain per month) and its propensity to balloon compared to M. plana, which is predisposed to wash-off by rain.

Palm oil-based methyl ester sulphonate premixes for use in dish-washing liquids

We describe palm-based methyl ester sulphonate premixes, which are mixtures of methyl ester sulphonates (MES) and fatty alcohol ethoxylate sulphonates (FAES), and their application in liquid detergent formulations. The best ratios of these compounds were obtained from ternary phase diagrams of MES, FAES and deionised water at 70ºC. The phase changes – from isotropic to liquid crystalline regions – were observed visually using polarised film, and the liquid crystalline birefringent optical patterns were subsequently confirmed using a polarising microscope. Based on the phase diagrams obtained, the optimal liquid crystalline region was selected for the preparation of a palm oil-based premix. Stable premixes can be used to produce liquid detergent products such as dish-washing liquids, laundry detergents, hand washes, kitchen cleaners and floor cleaners. The active levels of the palm-based MES premixes were measured using an autotitrator for dishwashing liquid formulation. The physical stability of the model dish-washing liquids (DWL) was assessed by conducting stability tests at room temperature (24°C) and also at 45°C, over a three-month period. Other properties such as detergency, foaming power, pH and viscosity were measured, and comparisons were made with current typical commercial products. A dermal irritation assay confirmed that the product is non-irritant to the skin.

Determination of palm oil residue in palm kernel and palm oil methyl esters using near infrared spectroscopy

An analytical method by near infrared spectroscopy using a partial least square regression was developed for the determination of palm oil residue in palm kernel methyl esters (Model 1) and palm oil methyl esters (Model 2). The wavelength region selected for modeling was between 4500 and 10 000 cm-1. For Model 1, the calibration plot had a coefficient correlation (R2) of 0.9996 and a standard error of calibration (SEC) of 0.06. Validation of the Model 1 calibration produced a plot with R2 of 0.9962 and a standard error of prediction (SEP) of 0.176. The Model 2 calibration plot had R2 of 0.9986 and SEC of 0.108. Validation of Model 2 produced a plot with R2 of 0.9978 and SEP of 0.128. Both models exhibited good linearity with low standard errors. The differences between the predicted and actual percentages of oil residue were minor. This method was able to predict oil residue contamination ranging from 1% to 10% in the two types of palm-based methyl esters.

Air gasification of palm biomass for producing tar-free higher heating value producer gas

The use of palm biomass for energy generation has been gaining momentum in recent times on a global level. A tar-free producer gas can be obtained in a properly designed biomass gasification process. In the current study, a tar-free palm biomass gasification system by high-temperature air is proposed. This concept was demonstrated on a pilot scale fixed bed using empty fruit bunches (EFB) under autothermic conditions. The pre-treated EFB were initially pyrolysed, and the resulting char was partially gasified in the gasification zone (oxidation zone) followed by combustion of the char residue at the reduction zone (bottom of gasifier) in an oxidation atmosphere. As the quality of the producer gas was found to be dependent on the smooth flow of the fuel and the uniformity of the pyrolysis, the difficulties encountered during the experiments are also discussed. The optimum operation of the gasifier ranged between 1.71 and 2.34 Nm3 kg-1 of air-fuel ratios at values of 28.2 and 37.0 kg hr-1 of 15% moisture feed rate, which gives a producer gas with a good heating value of about 5.18 MJ Nm-3 at a volumetric flow of 92.47-101.78 Nm3 hr-1 producer gas. It was concluded that the pre-treated empty fruit bunches are easy to gasify in a downdraft gasifier to produce good quality gas for process heating and power generation with minimum polluting by-products.

Detection of phytosterols in Ganoderma boninse-infected oil palm seedlings through GC-MS analysis

Ganoderma boninense is a fungus known to be pathogenic to oil palm. It causes the basal stem rot (BSR) and upper stem rot (USR) diseases. This study shows that the interaction between Ganoderma and oil palm produced many secondary metabolites including sterol compounds revealed by gas chromatography-mass spectrometry (GC-MS) analysis. The roots of progenies were artificially infected with G. boninense and subjected to metabolite extraction. A total of 13 sterol compounds and two tocopherols were identified from the root extracts of both tolerant and susceptible oil palm seedlings. The main sterol compounds identified were sitosterol, stigmasterol, campesterol and ergostenol. The GC-MS library, namely NIST 08, Wiley 229 and comparison of fragmentation patterns of the mass spectra reported in literature made it possible to identify the sterol components present in the root extracts. The results indicate that the number and level of sterol compounds induced in infected palms were significantly higher than in uninfected seedlings. Variations in the type and level of compounds detected were also observed between infected tolerant and susceptible progenies. This study provides information that relates sterols and tocopherol (antioxidant) compounds to the oil palm defence mechanism against G. boninense.

Best management practices for oil palm cultivation on peat: ground water-table maintenance in relation to peat subsidence and estimation of CO2 emissions at Sessang, Sarawak

The study on peat subsidence was carried out in an area of shallow and deep peat in MPOB Research Station in Sessang, Sarawak. Upon completion of the latest phase of peat development for oil palm planting in 2001, water management was improved to maintain the ground water-table at 30 to 50 cm over the whole plantation. Data on peat subsidence and oil palm yields were collected from 10 blocks of oil palm of different ages planted on peat of different depths ranging from shallow to deep peat. A regression equation was established with subsidence data as a dependent variable, while ground water-table and time with quadratic effects were independent variables. Two separate equations were developed for the different depths of peat. The study shows that the subsidence rate was very much related to the age of peat development, i.e. the number of years after oil palm had been planted. The subsidence rate over the years declined and stabilised after 15 years of peat development. A relationship between bulk density of the peat and age of peat development was also established. The CO2 emission was estimated using the method based on depth of ground water-table. From the current study, it was found that maintaining high ground water-table was better for oil palm agronomics, while at the same time, it reduced the decomposition and mineralisation rates of peat, and hence prevented excessive CO2 emission.

Greenhouse gas exchange of tropical peatlands – a review

This article presents data on greenhouse gas (GHG) exchange of tropical peat soils with emphasis on changes in emissions of gases during and following the conversion of native tropical peatlands to plantations of oil palm and other crops. The relevant GHGs are carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O). Establishment of plantations on peat requires drainage, which, even if controlled, results in peat aeration and subsidence. Subsidence is mainly due to natural consolidation, often augmented by mechanical compaction, and is manifested as increased bulk density. Aeration causes carbon to be released as CO2. Methods for distinguishing and quantifying these processes are discussed. Exchanges of CH4 and N2O are also changed by plantation development and are influenced by management practices but the quantities involved are small and in some cases peat soils even act as a sink and not a source, of these gases. There are seasonal changes in the GHG fluxes related to both water table depth and rainfall, and emissions of CH4 and N2O can be promoted by nitrogen application. GHG exchange of reclaimed peat is dominated by CO2 despite the higher global warming potential of CH4 and N2O. Methods for estimating CO2 fluxes are reviewed and their shortcomings are examined. The importance of adequately distinguishing between emission sources, e.g. root and microbial respiration when evaluating carbon fluxes at the surface of peat soils is emphasised.

Molecular approaches in the assessment of Oryctes rhinoceros virus for the control of rhinoceros beetle in oil palm plantations

The successful introduction of the Oryctes rhinoceros virus to control an outbreak of the rhinoceros beetle, O. rhinoceros on coconut in the South Pacific islands has led MPOB to embark on a project to study the potential use of the virus in oil palm plantations in Malaysia. Two DNA-based technologies, the polymerase chain reaction (PCR) and the restriction virus genome by an endonuclease enzyme, have been developed and intensively used in the project. PCR is a sensitive yet simple procedure allowing a more accurate estimation of the infection level of the O. rhinocerosvirus on adult beetles and larvae. PCR diagnosis showed that the adult beetles were more commonly infected (30%-65%) as compared with larvae (0%-35%). Pre-pupae and pupae were free from the virus infection. Virus genomic analysis by an endonuclease enzyme HindIII identified four types of O. rhinoceros virus, named as type A, B, C and D. Bioassays showed that the virus type B was more pathogenic against the third instar larvae and neonates. A virus field introduction system was then established. The virus solution was produced by an in vivo method using the larvae and adult beetles. Introduction of the O. rhinoceros virus type B in an estate with palms less than one year old with existing virus of type A resulted in a successful reduction of the adult population as well as in palm damage. The released virus established as early as three months after release (MAR) and persisted up to 15 MAR. The virus type B was then introduced in an immature area with palms more than three years old. The virus infection gradually increased and was maintained at a higher level of between 60% and 90%. The adult population was reduced, and stayed at a low level for a certain period of time before slowly increasing again to reach a second peak. The virus infection had a weak negative correlation with the adult population. A slow reduction in the proportion of males was observed, possibly due to slow virus transmission, as the adult population had probably already adapted to the virus infection. Genomic analysis showed that the virus type B was detected only at four MAR. Factors ensuring the success of virus transmission in the population were elaborated upon. Further research to fully utilise the O. rhinoceros virus to ensure maximum control of the rhinoceros beetle was also discussed.

New epoxy resins from oil palm components

New types of epoxy resins, which are derived from plant components, such as saccharides and lignin, have been developed in our laboratory. Oil palm components such as lignin, saccharides, lignocellulose, glycerol and fatty acids can be included in the above epoxy resin system. Alcoholysis lignin (AL) was dissolved in glycerol (GLY) and ethylene glycol (EG), and the obtained mixture was allowed to react with succinic anhydride to form a mixture of ester-carboxylic acid derivatives (AL-GLY polyacid, ALGLYPA and AL-EG polyacid, ALEGPA). The mixture of ALEGPA and ALEGPA was allowed to react with glycerol diglycidyl ether (GLYGDE) in the presence of a catalytic amount of dimethylbenzylamine to form epoxy resins. The molar ratio of epoxy groups to carboxylic acid groups (EPOXY/ACID ratio, mol mol-1) was maintained at 1.0. The contents of ALGLYPA in the mixture of ALGLYPA and ALEGPA (ALGLYPA content) were varied from 0% to 100%. The thermal properties of the epoxy resins were studied by differential scanning calorimetry (DSC) and thermogravimetry (TG). Glass transition temperature (Tg) of the epoxy resins increased with increasing ALGLYPA content, suggesting that the lignin and glycerol structures act as hard segments in the epoxy resin networks. Thermal decomposition temperature (Td) of the epoxy resins was almost constant regardless of ALGLYPA content.

A partial-length cyclophilin-encoding (cyp) cDNA isolated from Ganoderma boninense

Oil palm is subjected to various pests and diseases, one of the most important being basal stem rot (BSR) disease which is caused by a few species of Ganoderma. Ganoderma is a white rot fungus that attacks oil palm around the world. During plant infection, a few genes are highly expressed in the fungus and have been linked to fungal pathogenicity. One of these genes is the cyclophilin-encoding gene (cyp). In this study, degenerate primers have been designed based on the conserved regions of the gene. PCR amplification successfully amplified a 212 bp DNA fragment from Ganoderma boninense cDNAs. The DNA sequence analysis showed that the fragment has about 80% similarity to other plant pathogenic fungal cyp genes. The translated amino acid sequence was also highly identical to other plant pathogenic fungal cyclophilin. Conserve domain search results show that the obtained sequence has similarity to the cyclophilin_ABH-like domain.