Petaling Jaya, Malaysia
Petaling Jaya, Malaysia
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Ithnin M.,Malaysian Palm Oil Board | Teh C.-K.,Malaysian Palm Oil Board | Teh C.-K.,Sime Darby Plantation | Ratnam W.,National University of Malaysia
BMC Genetics | Year: 2017

Background: The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E. oleifera palms representing 19 populations distributed across Honduras, Costa Rica, Panama and Colombia. Results: In general, the genetic diversity decreased from Costa Rica towards the north (Honduras) and south-east (Colombia). Principle coordinate analysis (PCoA) showed a single cluster indicating low divergence among palms. The phylogenetic tree and STRUCTURE analysis revealed clusters based on country of origin, indicating considerable gene flow among populations within countries. Based on the values of the genetic diversity parameters, some genetically diverse populations could be identified. Further, a total of 34 individual palms that collectively captured maximum allelic diversity with reduced redundancy were also identified. High pairwise genetic differentiation (Fst>0.250) among populations was evident, particularly between the Colombian populations and those from Honduras, Panama and Costa Rica. Crossing selected palms from highly differentiated populations could generate off-springs that retain more genetic diversity. Conclusion: The results attained are useful for selecting palms and populations for core collection. The selected materials can also be included into crossing scheme to generate offsprings that capture greater genetic diversity for selection gain in the future. © 2017 The Author(s).


Goon J.A.,National University of Malaysia | Nor Azman N.H.E.,National University of Malaysia | Abdul Ghani S.M.,National University of Malaysia | Hamid Z.,Sime Darby Plantation | Wan Ngah W.Z.,National University of Malaysia
Clinical Nutrition ESPEN | Year: 2017

Vitamin E is a fat-soluble compound and powerful antioxidant that have been shown to protect the cell membranes against damage caused by free radicals. Human vitamin E supplementation studies are usually limited to α-tocopherol but currently tocotrienols are also available. This study aims to compare the effects of tocotrienol rich fraction (TRF) with α-tocopherol (α-TF) supplementation on oxidative stress in healthy male and female older adults aged 50-55 years old. A total of 71 subjects both male and female aged between 50 and 55 years were divided into groups receiving placebo (n = 23), α-TF (n = 24) and TRF (n = 24) for six months. Blood was taken at baseline (month 0), 3 months and 6 months osf supplementation for determination of plasma malondialdehyde (MDA), protein carbonyl, total DNA damage, vitamin D concentration and vitamin E isomers. α-TF supplementation reduced plasma MDA and protein carbonyl in female subjects after 3 and 6 months. TRF supplementation reduced MDA levels in both males and females as early as 3 months while DNA damage was reduced in females only at 6 months. Supplementation with α-TF and TRF increased plasma vitamin D concentration in both males and females after 6 months, but vitamin D concentration in male subjects were significantly higher compared to female subjects in TRF group. Vitamin E isomer determination showed α-TF, α-tocotrienol and γ-tocotrienol were increased in both male and female subjects. In conclusion, TRF supplementation effects were different from α-TF in reducing oxidative stress markers and vitamin D levels with a more pronounced effect in female subjects. © 2017 European Society for Clinical Nutrition and Metabolism.


PubMed | Loughborough University, National University of Singapore and Sime Darby Plantation
Type: Journal Article | Journal: Molecular plant | Year: 2016

High-density single nucleotide polymorphism (SNP) genotyping arrays are powerful tools that can measure the level of genetic polymorphism within a population. To develop a whole-genome SNP array for oil palms, SNP discovery was performed using deep resequencing of eight libraries derived from 132 Elaeis guineensis and Elaeis oleifera palms belonging to 59 origins, resulting in the discovery of >3 million putative SNPs. After SNP filtering, the Illumina OP200K custom array was built with 170860 successful probes. Phenetic clustering analysis revealed that the array could distinguish between palms of different origins in a way consistent with pedigree records. Genome-wide linkage disequilibrium declined more slowly for the commercial populations (ranging from 120 kb at r(2)= 0.43 to 146 kb at r(2)= 0.50) when compared with the semi-wild populations (19.5 kb at r(2)= 0.22). Genetic fixation mapping comparing the semi-wild and commercial population identified 321 selective sweeps. A genome-wide association study (GWAS) detected a significant peak on chromosome 2 associated with the polygenic component of the shell thickness trait (based on the trait shell-to-fruit; S/F %) in tenera palms. Testing of a genomic selection model onthe same trait resulted in good prediction accuracy (r= 0.65) with 42% of the S/F % variation explained. The first high-density SNP genotyping array for oil palm has been developed and shown to be robust for use in genetic studies and with potential for developing early trait prediction to shorten the oil palm breeding cycle.


PubMed | National University of Singapore, University of Nottingham and Sime Darby Plantation
Type: | Journal: Scientific reports | Year: 2016

GWAS in out-crossing perennial crops is typically limited by insufficient marker density to account for population diversity and effects of population structure resulting in high false positive rates. The perennial crop oil palm is the most productive oil crop. We performed GWAS for oil-to-dry-mesocarp content (O/DM) on 2,045 genotyped tenera palms using 200K SNPs that were selected based on the short-range linkage disequilibrium distance, which is inherent with long breeding cycles and heterogeneous breeding populations. Eighty loci were significantly associated with O/DM (p 10(-4)) and three key signals were found. We then evaluated the progeny of a Deli x AVROS breeding trial and a 4% higher O/DM was observed amongst those having the beneficial genotypes at two of the three key loci (p < 0.05). We have initiated MAS and large-scale planting of elite dura and pisifera parents to generate the new commercial tenera palms with higher O/DM potential.


Yeap W.-C.,Sime Darby Plantation | Lee F.-C.,Sime Darby Plantation | Shabari Shan D.K.,Sime Darby Plantation | Musa H.,Sime Darby Plantation | And 2 more authors.
Plant Journal | Year: 2017

The oil biosynthesis pathway must be tightly controlled to maximize oil yield. Oil palm accumulates exceptionally high oil content in its mesocarp, suggesting the existence of a unique fruit-specific fatty acid metabolism transcriptional network. We report the complex fruit-specific network of transcription factors responsible for modulation of oil biosynthesis genes in oil palm mesocarp. Transcriptional activation of EgWRI1-1 encoding a key master regulator that activates expression of oil biosynthesis genes, is activated by three ABA-responsive transcription factors, EgNF-YA3, EgNF-YC2 and EgABI5. Overexpression of EgWRI1-1 and its activators in Arabidopsis accelerated flowering, increased seed size and oil content, and altered expression levels of oil biosynthesis genes. Protein-protein interaction experiments demonstrated that EgNF-YA3 interacts directly with EgWRI1-1, forming a transcription complex with EgNF-YC2 and EgABI5 to modulate transcription of oil biosynthesis pathway genes. Furthermore, EgABI5 acts downstream of EgWRKY40, a repressor that interacts with EgWRKY2 to inhibit the transcription of oil biosynthesis genes. We showed that expression of these activators and repressors in oil biosynthesis can be induced by phytohormones coordinating fruit development in oil palm. We propose a model highlighting a hormone signaling network coordinating fruit development and fatty acid biosynthesis. © 2017 John Wiley & Sons Ltd and the Society for Experimental Biology.


Liaghat S.,University Putra Malaysia | Ehsani R.,University of Florida | Mansor S.,University Putra Malaysia | Shafri H.Z.M.,University Putra Malaysia | And 3 more authors.
International Journal of Remote Sensing | Year: 2014

Basal stem rot (BSR) is a fatal fungal (Ganoderma) disease of oil palm plantations and has a significant impact on the production of palm oil in Malaysia. Because there is no effective treatment to control this disease, early detection of BSR is vital for sustainable disease management. The limitations of visual detection have led to an interest in the development of spectroscopically based detection techniques for rapid diagnosis of this disease. The aim of this work was to develop a procedure for early and accurate detection and differentiation of Ganoderma disease with different severities, based on spectral analysis and statistical models. Reflectance spectroscopy analysis ranging from the visible to near infrared region (325-1075 nm) was applied to analyse oil palm leaf samples of 47 healthy (G0), 55 slightly damaged (G1), 48 moderately damaged (G2), and 40 heavily damaged (G3) trees in order to detect and quantify Ganoderma disease at different levels of severity. Reflectance spectra were pre-processed, and principal component analysis (PCA) was performed on different pre-processed datasets including the raw dataset, first derivative, and second derivative datasets. The classification models: linear and quadratic discrimination analysis, k-nearest neighbour (kNN), and Naïve-Bayes were applied to PC scores for classifying four levels of stress in BSR-infected oil palm trees. The analysis showed that the kNN-based model predicted the disease with a high average overall classification accuracy of 97% with the second derivative dataset. Results confirmed the usefulness and efficiency of the spectrally based classification approach in rapid screening of BSR in oil palm. © 2014 Taylor & Francis.


Ismail I.,National University of Malaysia | Iskandar N.F.,National University of Malaysia | Chee G.M.,National University of Malaysia | Abdullah R.,Sime Darby Plantation
Plant OMICS | Year: 2010

Bioplastics are an alternative substitute for petrochemical synthetic plastics. Polyhydroxybutyrate (PHB) genes are involved in bioplastic synthesis. In this study, bioplastic synthesis genes were incorporated into the genome of oil palm because this plant has a high concentration of the PHB precursor acetyl-CoA. Immature embryos (IEs) of Elaeis guineensis var Tenera were infected with Agrobacterium tumefaciens LBA4404 that contained the binary vector pJLPHB3, which encoded the phb genes, β-ketothiolase (bktB), acetoacetyl-CoA reductase (phaB) and PHA synthase (phaC) flanked by a modified CaMV35S promoter, a plastid targeting sequence and the nos terminator. GUS assay revealed that about 78-100% transient transformation frequency was obtained for calluses and 55-65% for plantlets 1 month after transformation. However, GUS assays of leaf tissue from 12-month-old plantlets showed that only 10-33% transformation frequency was obtained. The presence of the phb genes in GUS positive plantlets was confirmed using PCR and multiplex PCR analyses. Southern blot analyses verified that the phb genes were integrated in transformed leaves and calluses using the phaB probe (0.805 kb) and phaC probe (1.730 kb). Quantitative transgene expression comparison in the transformed tissues measured using real-time PCR showed that the expression levels of the phaB and phaC transgenes were 6.06- and 6.02-fold higher compared to the non-transformed oil palm.


Wagiran A.,National University of Malaysia | Ismail I.,National University of Malaysia | Zain C.R.C.M.,National University of Malaysia | Abdullah R.,Sime Darby Plantation
Australian Journal of Crop Science | Year: 2010

The global population is expected to grow from 6 to 8 billion people and rice consumers are projected to increase by 1.8% annually until 2020. Hence, rice production must be increased between 25-45% to fulfill the growing need. Efforts to genetically improve rice for high quality grains are extensively being carried out. The cloning vectors containing the ipt gene driven by the glutenin high molecular weight promoter were successfully constructed in pCAMBIA1305.2 and transformed into A. tumefaciens LBA4404, which were then used in the genetic transformation of a japonica suspension cell culture. The highest percentage of transformation frequency based on GUS activity was 93% in the variety Hayahishiki and 77% in Nippon Bare when 200 μM AS was included in the inoculation media. The highest percentage of GUS activity was 30% in the variety Fujisaka 5 in the presence of 100 μM AS. There was no difference in terms of GUS expression when different inoculation times were tested. A twenty minute post-dehydration treatment led to the highest GUS activity in all varieties tested. The inclusion of AS is critical and very important to obtain successful transformation. The sensitivity and response of suspension cells to different hygromycin concentrations was varied among the varieties tested. Selection of transformed cells in N6 liquid media containing 25 mg/L hygromycin proved to be easy and facilitated the removal of non-transformed cells. PCR analysis has shown that 2.3% of the putatively transformed rice variety Nippon Bare contained the ipt gene, while only 2.0% for the Hayahishiki variety. The finding of this research shows the potential for rice suspension cells in regeneration and genetic transformation systems by providing continuous explants and could be used as tools to obtain large scale transformation of rice plants via Agrobacterium tumefaciens.


Makpol S.,National University of Malaysia | Jam F.A.,National University of Malaysia | Rahim N.A.,National University of Malaysia | Khor S.C.,National University of Malaysia | And 3 more authors.
Clinica Terapeutica | Year: 2014

Background and Objective: Antioxidant has been recognized to inhibit UV-induced melanogenesis. This study aimed to elucidate the molecular mechanism of tyrostat, tocopherol and tocotrienol-rich fraction in inhibiting melanogenesis in human skin melanocytes. Materials and Methods: Primary culture of melanocytes was exposed to repeated doses of 0.6 J/cm2 UVA for 6 days and treated with tyrostat, tocotrienol-rich fraction or tocopherol alone or in combination. Results: UVA irradiation increased melanin content and tyrosinase activity and up-regulated TYR, TYRP1 and TYRP2 genes. Treatment with tyrostat, tocotrienol-rich fraction or tocopherol decreased melanin content and down-regulated TYR, TYRP1 and TYRP2 genes with decreased tyrosinase activity. Combined treatment exerted better effects as compared to treatment with single compound in decreasing the melanin content and down-regulating TYR, TYRP1 and TYRP2 genes. These findings indicated that tyrostat, tocotrienol-rich fraction and tocopherol inhibit melanogenesis by modulating the expression of genes involved in the regulation of melanin synthesis and inhibiting tyrosinase activity. Conclusion:s Tyrostat, tocopherol and tocotrienol-rich fraction possessed anti-melanogenic properties and might be useful in improving skin pigmentation caused by UVA exposure. © Società Editrice Universo (SEU).


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