Petaling Jaya, Malaysia
Petaling Jaya, Malaysia

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Kwong Q.B.,Sime Darby Plantation | Teh C.K.,Sime Darby Plantation | Ong A.L.,Sime Darby Plantation | Heng H.Y.,Sime Darby Plantation | And 9 more authors.
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 170 860 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 r2 = 0.43 to 146 kb at r2 = 0.50) when compared with the semi-wild populations (19.5 kb at r2 = 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 on the 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. © 2016 The Author


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.


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.


Makpol S.,National University of Malaysia | Jam F.A.,National University of Malaysia | Khor S.C.,National University of Malaysia | Ismail Z.,Sime Darby Plantation | And 2 more authors.
Oxidative Medicine and Cellular Longevity | Year: 2013

Biodynes, tocotrienol-rich fraction (TRF), and tocopherol have shown antiaging properties. However, the combined effects of these compounds on skin aging are yet to be investigated. This study aimed to elucidate the skin aging effects of biodynes, TRF, and tocopherol on stress-induced premature senescence (SIPS) model of human diploid fibroblasts (HDFs) by determining the expression of collagen and MMPs at gene and protein levels. Primary HDFs were treated with biodynes, TRF, and tocopherol prior to hydrogen peroxide (H2O 2) exposure. The expression of COL1A1, COL3A1, MMP1, MMP2, MMP3, and MMP9 genes was determined by qRT-PCR. Type I and type III procollagen proteins were measured by Western blotting while the activities of MMPs were quantified by fluorometric Sensolyte MMP Kit. Our results showed that biodynes, TRF, and tocopherol upregulated collagen genes and downregulated MMP genes (P < 0.05). Type I procollagen and type III procollagen protein levels were significantly increased in response to biodynes, TRF, and tocopherol treatment (P < 0.05) with reduction in MMP-1, MMP-2, MMP-3, and MMP-9 activities (P < 0.05). These findings indicated that biodynes, TRF, and tocopherol effectively enhanced collagen synthesis and inhibited collagen degradation and therefore may protect the skin from aging. © 2013 Suzana Makpol et al.


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).


Abd Gani S.S.,University Putra Malaysia | Basri M.,University Putra Malaysia | Abdul Rahman M.B.,University Putra Malaysia | Abdul Rahman M.B.,Malaysia Genome Institute | And 4 more authors.
Bioscience, Biotechnology and Biochemistry | Year: 2010

Formulations containing engkabang fat and engkabang fat esters, F10 and E15 respectively were prepared using a high-shear homogenizer, followed by a high-pressure homogenizer. Both formulations were stable at room temperature, at 45°C, and after undergoing freeze-thaw cycles. The particle sizes of F10 and E15 after high pressure were 115.75 nm and 148.41 nm respectively. The zeta potentials of F10 and E15 were - 36.4 m V and - 48.8 m V respectively, while, the pH values of F10 and E15 were 5.59 and 5.81 respectively. The rheology of F10 and E15 showed thixotropy and pseudoplastic behavior respectively. There were no bacteria or fungal growths in the samples. The short- term moisturizing effect on 20 subjects analyzed by analysis of variance (ANOVA), gave P-values of 7.35 × 10-12 and 2.77 x 10-15 for F10 and E15 respectively. The hydration of the skins increased after application of F10 and E15 with p-value below 0.05.


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