Sustainable production of palm oil can be boosted by the use of appropriate technological tools t... more Sustainable production of palm oil can be boosted by the use of appropriate technological tools to improve productivity within existing acreage. The discovery of the SHELL gene and subsequent development of a diagnostic assay to differentiate oil palm’s three fruit forms set the stage for the application of such technological tools by commercial estates prior to planting. The use of DNA-testing can ensure that new planting and re-planting programmes exploit the hybrid vigour expected from selected maternal (dura) and paternal (pisifera) lines. An expanded nationwide survey of more than a million seeds and seedlings not only confirmed the robustness and scalability of SHELL DNA-testing, but more importantly revealed a 12.8 per cent level of undesired planting material across the Malaysian supply chain, which far exceeds that allowed by the national standard. If SHELL testing had been deployed in the past, the value of crude palm oil (CPO) and crude palm kernel oil (CPKO) production i...
Additional file 6. List of QTL associated with the compactness traits and FAC in the independent ... more Additional file 6. List of QTL associated with the compactness traits and FAC in the independent and the integrated maps determined via Genstat. For a particular trait (Ex. RL and C16:0), a number of markers are present in the QTL interval. Although almost the same genomic region (determined via position on LG) is linked to the QTL in independent populations, a different marker is at times located closest to the QTL peak, in the integrated map. The original marker identified in the independent populations remains significant.
Additional file 7. Significant major QTLs detected for respective traits using MapQTL. Horizontal... more Additional file 7. Significant major QTLs detected for respective traits using MapQTL. Horizontal line indicates the 95% genome wide significant threshold value for declaring a QTL.
Additional file 2. Differential Expression analyses of fragrance-related genes between adaxial an... more Additional file 2. Differential Expression analyses of fragrance-related genes between adaxial and abaxial layers of Vanda Mimi Palmerâ s petal-sepal based on transcriptomic sequencing data.
Step Wise Protocols for Somatic Embryogenesis of Important Woody Plants, 2018
The effectiveness of oil palm (Elaeis guineensis) breeding from seed remains the basis for long t... more The effectiveness of oil palm (Elaeis guineensis) breeding from seed remains the basis for long term genetic improvement. However, there is still considerable unexploited genetic variability within selected crosses, thus inducing interest in vegetative propagation via tissue culture. This method enables true-to-type reproduction of the best genotypes. Through this, further oil yield improvements can be expected, amongst other advantages. The success in producing oil palm clones has spurred oil palm organizations to set up their own tissue culture laboratories. The average estimated projection of 20% yield increase from clones compared to commercial seedlings makes planting with clones a potentially good investment. This chapter includes accounts of detailed in vitro propagation protocols using solid and liquid culture systems, nursery practices and quality control measures using physical and molecular screening tools.
The proper development of oil palm fruit is important as the source of oil is the fruit mesocarp ... more The proper development of oil palm fruit is important as the source of oil is the fruit mesocarp and kernel. Prior to fruit formation, the development of flowers is therefore also important. Determination of the flower development stages in oil palm generally involves tedious histological analyses of each sampled inflorescence, making it a costly and inefficient way of gauging the developmental state. In this study, a statistical model was established from the association of physical or macroscopic measurement data to flower development, which was determined via histological analyses. The final reduced ordinal logistic regression model is a partial proportional odds model that uses inflorescence length and palm age as predictors to predict the flower development stage. The likelihood-ratio χ2 test suggested the model adequately fits the data (p<0.01). The model, with a prediction accuracy of 78.5%, can be used for selecting inflorescences of specific development stages from palms...
Background Molecular breeding has opened new avenues for crop improvement with the potential for ... more Background Molecular breeding has opened new avenues for crop improvement with the potential for faster progress. As oil palm is the major producer of vegetable oil in the world, its improvement, such as developing compact planting materials and altering its oils’ fatty acid composition for wider application, is important. Results This study sought to identify the QTLs associated with fatty acid composition and vegetative traits for compactness in the crop. It integrated two interspecific backcross two (BC 2 ) mapping populations to improve the genetic resolution and evaluate the consistency of the QTLs identified. A total 1,963 markers (1,814 SNPs and 149 SSRs) spanning a total map length of 1793 cM were integrated into a consensus map. For the first time, some QTLs associated with vegetative parameters and carotene content were identified in interspecific hybrids, apart from those associated with fatty acid composition. The analysis identified 8, 3 and 8 genomic loci significantly...
Vanda Mimi Palmer (VMP) is commercially valuable for its strong fragrance but little is known reg... more Vanda Mimi Palmer (VMP) is commercially valuable for its strong fragrance but little is known regarding the fragrance production and emission sites on the flowers. Olfactory perception detected fragrance only from the petals and sepals. Light and Environmental Scanning Electron microscopy analyses on fresh tissues showed distributions of stomata and trichomes concentrated mostly around the edges. These results paralleled the rich starch deposits and intense neutral red stain, indicating strong fragrance and trichomes as potential main fragrance release sites. Next Generation Sequencing (NGS) transcriptomic data of adaxial and abaxial layers of the tissues showed monoterpene synthase transcripts specifically linalool and ocimene synthases distributed throughout the tissues. qPCR analyses taken at different time points revealed high levels of linalool and ocimene synthases transcripts in the early morning with maximal level at 4.00 am but remained low throughout daylight hours. Knowle...
Transcriptomes generated by laser capture microdissected abnormal staminodes revealed adoption of... more Transcriptomes generated by laser capture microdissected abnormal staminodes revealed adoption of carpel programming during organ initiation with decreased expression of numerous HSPs, EgDEF1, EgGLO1 but increased LEAFY expression. The abnormal mantled phenotype in oil palm involves a feminization of the male staminodes into pseudocarpels in pistillate inflorescences. Previous studies on oil palm flowering utilized entire inflorescences or spikelets, which comprised not only the male and female floral organs, but the surrounding tissues as well. Laser capture microdissection coupled with RNA sequencing was conducted to investigate the specific transcriptomes of male and female floral organs from normal and mantled female inflorescences. A higher number of differentially expressed genes (DEGs) were identified in abnormal versus normal male organs compared with abnormal versus normal female organs. In addition, the abnormal male organ transcriptome closely mimics the transcriptome of abnormal female organ. While the transcriptome of abnormal female organ was relatively similar to the normal female organ, a substantial amount of female DEGs encode HEAT SHOCK PROTEIN genes (HSPs). A similar high amount (20%) of male DEGs encode HSPs as well. As these genes exhibited decreased expression in abnormal floral organs, mantled floral organ development may be associated with lower stress indicators. Stamen identity genes EgDEF1 and EgGLO1 were the main floral regulatory genes with decreased expression in abnormal male organs or pseudocarpel initials. Expression of several floral transcription factors was elevated in pseudocarpel initials, notably LEAFY, FIL and DL orthologs, substantiating the carpel specification programming of abnormal staminodes. Specific transcriptomes thus obtained through this approach revealed a host of differentially regulated genes in pseudocarpel initials compared to normal male staminodes.
Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the ... more Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the low rate of embryogenesis is a major hindrance for the adoption of this technology in oil palm tissue culture laboratories. In this study, we use proteomic technologies to compare differential protein profiles in leaves from palms of high and low proliferation rates in tissue culture in order to understand the underlying biological mechanism for the low level of embryogenesis. Two protein extraction methods, namely trichloroacetic acid/acetone precipitation and polyethylene glycol fractionation were used to produce total proteins and fractionated protein extracts respectively, with the aim of improving the resolution of protein species using two-dimensional gel electrophoresis. A total of 40 distinct differential abundant protein spots were selected from leaf samples collected from palms with proven high and low proliferation rates. The variant proteins were subsequently identified using...
Oil palm is one of the most productive oil bearing crops grown in Southeast Asia. Due to the dwin... more Oil palm is one of the most productive oil bearing crops grown in Southeast Asia. Due to the dwindling availability of agricultural land and increasing demand for high yielding oil palm seedlings, clonal propagation is vital to the oil palm industry. Most commonly, leaf explants are used for in vitro micropropagation of oil palm and to optimize this process it is important to unravel the physiological and molecular mechanisms underlying somatic embryo production from leaves. In this study, a proteomic approach was used to determine protein abundance of mature oil palm leaves. To do this, leaf proteins were extracted using TCA/acetone precipitation protocol and separated by 2DE. A total of 191 protein spots were observed on the 2D gels and 67 of the most abundant protein spots that were consistently observed were selected for further analysis with 35 successfully identified using MALDI TOF/TOF MS. The majority of proteins were classified as being involved in photosynthesis, metabolism, cellular biogenesis, stress response, and transport. This study provides the first proteomic assessment of oil palm leaves in this important oil crop and demonstrates the successful identification of selected proteins spots using the Malaysian Palm Oil Board (MPOB) Elaeis guineensis EST and NCBI-protein databases. The MS data have been deposited in the ProteomeXchange Consortium database with the data set identifier PXD001307.
Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the ... more Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the low rate of embryogenesis is a major hindrance for the adoption of this technology in oil palm tissue culture laboratories. In this study, we use proteomic technologies to compare differential protein profiles in leaves from palms of high and low proliferation rates in tissue culture in order to understand the underlying biological mechanism for the low level of embryogenesis. Two protein extraction methods, namely trichloroacetic acid/acetone precipitation and polyethylene glycol fractionation were used to produce total proteins and fractionated protein extracts respectively, with the aim of improving the resolution of protein species using two-dimensional gel electrophoresis. A total of 40 distinct differential abundant protein spots were selected from leaf samples collected from palms with proven high and low proliferation rates. The variant proteins were subsequently identified using...
The molecular basis of somaclonal variation is not known. However, evidence points towards the ex... more The molecular basis of somaclonal variation is not known. However, evidence points towards the existence of labile portions of the genome that can be modulated when the cells undergo the stress of tissue culture. Based on these observations a reasonable conclusion is that a set of variable sequences associated with the occurrence of somaclonal variation can be identified and used
The Journal of Horticultural Science and Biotechnology, 2006
Résumé/Abstract Recovering plants from embryogenic cell suspensions is a complex process starting... more Résumé/Abstract Recovering plants from embryogenic cell suspensions is a complex process starting with somatic embryo development which is synchronised on medium lacking plant growth regulators, followed by differentiation and regeneration of plants. An improved method for high frequency recovery of banana plants was investigated by incorporating a liquid-based, embryo-development medium. The highest regeneration rate (approx. 32,000 plants ml-1 settled cell volume) was obtained using this liquid protocol. ...
Sustainable production of palm oil can be boosted by the use of appropriate technological tools t... more Sustainable production of palm oil can be boosted by the use of appropriate technological tools to improve productivity within existing acreage. The discovery of the SHELL gene and subsequent development of a diagnostic assay to differentiate oil palm’s three fruit forms set the stage for the application of such technological tools by commercial estates prior to planting. The use of DNA-testing can ensure that new planting and re-planting programmes exploit the hybrid vigour expected from selected maternal (dura) and paternal (pisifera) lines. An expanded nationwide survey of more than a million seeds and seedlings not only confirmed the robustness and scalability of SHELL DNA-testing, but more importantly revealed a 12.8 per cent level of undesired planting material across the Malaysian supply chain, which far exceeds that allowed by the national standard. If SHELL testing had been deployed in the past, the value of crude palm oil (CPO) and crude palm kernel oil (CPKO) production i...
Additional file 6. List of QTL associated with the compactness traits and FAC in the independent ... more Additional file 6. List of QTL associated with the compactness traits and FAC in the independent and the integrated maps determined via Genstat. For a particular trait (Ex. RL and C16:0), a number of markers are present in the QTL interval. Although almost the same genomic region (determined via position on LG) is linked to the QTL in independent populations, a different marker is at times located closest to the QTL peak, in the integrated map. The original marker identified in the independent populations remains significant.
Additional file 7. Significant major QTLs detected for respective traits using MapQTL. Horizontal... more Additional file 7. Significant major QTLs detected for respective traits using MapQTL. Horizontal line indicates the 95% genome wide significant threshold value for declaring a QTL.
Additional file 2. Differential Expression analyses of fragrance-related genes between adaxial an... more Additional file 2. Differential Expression analyses of fragrance-related genes between adaxial and abaxial layers of Vanda Mimi Palmerâ s petal-sepal based on transcriptomic sequencing data.
Step Wise Protocols for Somatic Embryogenesis of Important Woody Plants, 2018
The effectiveness of oil palm (Elaeis guineensis) breeding from seed remains the basis for long t... more The effectiveness of oil palm (Elaeis guineensis) breeding from seed remains the basis for long term genetic improvement. However, there is still considerable unexploited genetic variability within selected crosses, thus inducing interest in vegetative propagation via tissue culture. This method enables true-to-type reproduction of the best genotypes. Through this, further oil yield improvements can be expected, amongst other advantages. The success in producing oil palm clones has spurred oil palm organizations to set up their own tissue culture laboratories. The average estimated projection of 20% yield increase from clones compared to commercial seedlings makes planting with clones a potentially good investment. This chapter includes accounts of detailed in vitro propagation protocols using solid and liquid culture systems, nursery practices and quality control measures using physical and molecular screening tools.
The proper development of oil palm fruit is important as the source of oil is the fruit mesocarp ... more The proper development of oil palm fruit is important as the source of oil is the fruit mesocarp and kernel. Prior to fruit formation, the development of flowers is therefore also important. Determination of the flower development stages in oil palm generally involves tedious histological analyses of each sampled inflorescence, making it a costly and inefficient way of gauging the developmental state. In this study, a statistical model was established from the association of physical or macroscopic measurement data to flower development, which was determined via histological analyses. The final reduced ordinal logistic regression model is a partial proportional odds model that uses inflorescence length and palm age as predictors to predict the flower development stage. The likelihood-ratio χ2 test suggested the model adequately fits the data (p<0.01). The model, with a prediction accuracy of 78.5%, can be used for selecting inflorescences of specific development stages from palms...
Background Molecular breeding has opened new avenues for crop improvement with the potential for ... more Background Molecular breeding has opened new avenues for crop improvement with the potential for faster progress. As oil palm is the major producer of vegetable oil in the world, its improvement, such as developing compact planting materials and altering its oils’ fatty acid composition for wider application, is important. Results This study sought to identify the QTLs associated with fatty acid composition and vegetative traits for compactness in the crop. It integrated two interspecific backcross two (BC 2 ) mapping populations to improve the genetic resolution and evaluate the consistency of the QTLs identified. A total 1,963 markers (1,814 SNPs and 149 SSRs) spanning a total map length of 1793 cM were integrated into a consensus map. For the first time, some QTLs associated with vegetative parameters and carotene content were identified in interspecific hybrids, apart from those associated with fatty acid composition. The analysis identified 8, 3 and 8 genomic loci significantly...
Vanda Mimi Palmer (VMP) is commercially valuable for its strong fragrance but little is known reg... more Vanda Mimi Palmer (VMP) is commercially valuable for its strong fragrance but little is known regarding the fragrance production and emission sites on the flowers. Olfactory perception detected fragrance only from the petals and sepals. Light and Environmental Scanning Electron microscopy analyses on fresh tissues showed distributions of stomata and trichomes concentrated mostly around the edges. These results paralleled the rich starch deposits and intense neutral red stain, indicating strong fragrance and trichomes as potential main fragrance release sites. Next Generation Sequencing (NGS) transcriptomic data of adaxial and abaxial layers of the tissues showed monoterpene synthase transcripts specifically linalool and ocimene synthases distributed throughout the tissues. qPCR analyses taken at different time points revealed high levels of linalool and ocimene synthases transcripts in the early morning with maximal level at 4.00 am but remained low throughout daylight hours. Knowle...
Transcriptomes generated by laser capture microdissected abnormal staminodes revealed adoption of... more Transcriptomes generated by laser capture microdissected abnormal staminodes revealed adoption of carpel programming during organ initiation with decreased expression of numerous HSPs, EgDEF1, EgGLO1 but increased LEAFY expression. The abnormal mantled phenotype in oil palm involves a feminization of the male staminodes into pseudocarpels in pistillate inflorescences. Previous studies on oil palm flowering utilized entire inflorescences or spikelets, which comprised not only the male and female floral organs, but the surrounding tissues as well. Laser capture microdissection coupled with RNA sequencing was conducted to investigate the specific transcriptomes of male and female floral organs from normal and mantled female inflorescences. A higher number of differentially expressed genes (DEGs) were identified in abnormal versus normal male organs compared with abnormal versus normal female organs. In addition, the abnormal male organ transcriptome closely mimics the transcriptome of abnormal female organ. While the transcriptome of abnormal female organ was relatively similar to the normal female organ, a substantial amount of female DEGs encode HEAT SHOCK PROTEIN genes (HSPs). A similar high amount (20%) of male DEGs encode HSPs as well. As these genes exhibited decreased expression in abnormal floral organs, mantled floral organ development may be associated with lower stress indicators. Stamen identity genes EgDEF1 and EgGLO1 were the main floral regulatory genes with decreased expression in abnormal male organs or pseudocarpel initials. Expression of several floral transcription factors was elevated in pseudocarpel initials, notably LEAFY, FIL and DL orthologs, substantiating the carpel specification programming of abnormal staminodes. Specific transcriptomes thus obtained through this approach revealed a host of differentially regulated genes in pseudocarpel initials compared to normal male staminodes.
Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the ... more Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the low rate of embryogenesis is a major hindrance for the adoption of this technology in oil palm tissue culture laboratories. In this study, we use proteomic technologies to compare differential protein profiles in leaves from palms of high and low proliferation rates in tissue culture in order to understand the underlying biological mechanism for the low level of embryogenesis. Two protein extraction methods, namely trichloroacetic acid/acetone precipitation and polyethylene glycol fractionation were used to produce total proteins and fractionated protein extracts respectively, with the aim of improving the resolution of protein species using two-dimensional gel electrophoresis. A total of 40 distinct differential abundant protein spots were selected from leaf samples collected from palms with proven high and low proliferation rates. The variant proteins were subsequently identified using...
Oil palm is one of the most productive oil bearing crops grown in Southeast Asia. Due to the dwin... more Oil palm is one of the most productive oil bearing crops grown in Southeast Asia. Due to the dwindling availability of agricultural land and increasing demand for high yielding oil palm seedlings, clonal propagation is vital to the oil palm industry. Most commonly, leaf explants are used for in vitro micropropagation of oil palm and to optimize this process it is important to unravel the physiological and molecular mechanisms underlying somatic embryo production from leaves. In this study, a proteomic approach was used to determine protein abundance of mature oil palm leaves. To do this, leaf proteins were extracted using TCA/acetone precipitation protocol and separated by 2DE. A total of 191 protein spots were observed on the 2D gels and 67 of the most abundant protein spots that were consistently observed were selected for further analysis with 35 successfully identified using MALDI TOF/TOF MS. The majority of proteins were classified as being involved in photosynthesis, metabolism, cellular biogenesis, stress response, and transport. This study provides the first proteomic assessment of oil palm leaves in this important oil crop and demonstrates the successful identification of selected proteins spots using the Malaysian Palm Oil Board (MPOB) Elaeis guineensis EST and NCBI-protein databases. The MS data have been deposited in the ProteomeXchange Consortium database with the data set identifier PXD001307.
Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the ... more Oil palm tissue culture is one way to produce superior oil palm planting materials. However, the low rate of embryogenesis is a major hindrance for the adoption of this technology in oil palm tissue culture laboratories. In this study, we use proteomic technologies to compare differential protein profiles in leaves from palms of high and low proliferation rates in tissue culture in order to understand the underlying biological mechanism for the low level of embryogenesis. Two protein extraction methods, namely trichloroacetic acid/acetone precipitation and polyethylene glycol fractionation were used to produce total proteins and fractionated protein extracts respectively, with the aim of improving the resolution of protein species using two-dimensional gel electrophoresis. A total of 40 distinct differential abundant protein spots were selected from leaf samples collected from palms with proven high and low proliferation rates. The variant proteins were subsequently identified using...
The molecular basis of somaclonal variation is not known. However, evidence points towards the ex... more The molecular basis of somaclonal variation is not known. However, evidence points towards the existence of labile portions of the genome that can be modulated when the cells undergo the stress of tissue culture. Based on these observations a reasonable conclusion is that a set of variable sequences associated with the occurrence of somaclonal variation can be identified and used
The Journal of Horticultural Science and Biotechnology, 2006
Résumé/Abstract Recovering plants from embryogenic cell suspensions is a complex process starting... more Résumé/Abstract Recovering plants from embryogenic cell suspensions is a complex process starting with somatic embryo development which is synchronised on medium lacking plant growth regulators, followed by differentiation and regeneration of plants. An improved method for high frequency recovery of banana plants was investigated by incorporating a liquid-based, embryo-development medium. The highest regeneration rate (approx. 32,000 plants ml-1 settled cell volume) was obtained using this liquid protocol. ...
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Papers by Meilina Abdullah