Research Projects Archive

0

TRANSLATIONAL GENOMICS

By
Ho Wei Seng (wsho)
– November 8, 2010

Acacia Translational Genomics

The overall aim of this research project is to assess the quality of Acacia sp. wood available to the pulp, paper and board industries
through an understanding of wood properties and genetic analyses of wood quality traits/candidate genes. By associating
genotypes with phenotypes, we could determine what particular economic trait loci (ETL) or candidate genes are
involved and also how much of phenotypic variation could be explained by genetic variation on these genes via translational
genomics.


Projects: [Project Leader: Assoc. Prof. Dr. Ismail Jusoh; Co-researcher: Dr Ho Wei Seng]

  • Wood Density and Cleaved Amplified Polymorphic Sequence (CAPS) in Acacia sp.
  • Genetic Diversity of Acacia mangium Superbulk


Projects: [Project Leader: Dr Ho Wei Seng; Co-researcher: Assoc. Prof. Dr. Ismail Jusoh]

  • Evaluation of Genetic Relatedness Among Acacia mangium Superbulk and Acacia Hybrid (Acacia mangium x Acacia auriculiformis) Plus Trees Using DAMD Markers
  • Gene associated single nucleotide polymorphism (SNP) in cinnamate 4-hydroxylase (C4H) and cinnamy alcohol dehydrogenase (CAD) genes from Acacia mangium Superbulk trees.

Research collaborators:

0

SEX IDENTIFICATION

By
Ho Wei Seng (wsho)
– November 3, 2010

Sex Identification in Canarium odontophyllum Miq. (dabai) using DNA Markers

Dabai (Canarium odontophyllum Miq.) is locally known in Sarawak as Sibu olives. It is an important indigenous fruit species that has immediate potential for commercial exploitation. It has been domesticated in Sarawak and cultivated extensively in Sibu, Kapit, Sarikei and Limbang. Dabai is dieocious with male and female flowers borne on different trees. The male trees are usually chopped down for economic purposes in order to save space and labour cost. It is desirable that only female individuals are cultivated in the field to increase the fruit production and profitability. Unfortunately for dabai growers, there is no way to determine a dabai’s sex from the external morphology of embryogenic form. Seed is still the most practical and economical propagation method of raising the crop due to the difficulties in propagating the tree using vegetative methods such as cuttings and grafting. The sex of the seedlings is known only after the trees attain reproductive maturity, i.e. after 4 years. Thus, the objective of the project is to determine the sex of dabai trees using molecular DNA marker technologies by developing the sex-specific DNA makers specific to male and female dabai trees. With the development of these markers, it is anticipated that the early sex identification of dabai seedlings using molecular marker approach prior to the flowering stage would avoid the need for removing undesired sex type, i.e. the male trees from the field, thus saving labour, time and other resources.

0

ASSOCIATION MAPPING

By
Ho Wei Seng (wsho)
– November 3, 2010

Gene Associated Single Nucleotide Polymorphism (SNP) Discovery Involved in Wood Formation of Kelampayan (Neolamarckia cadamba) and Acacia mangium superbulk

Quantitative trait loci (QTL) mapping has been used extensively as the key tool for identifying the genetic basis of quantitative traits, such as silvicultural traits, adaptability traits and wood quality traits. However, the long generation times and the difficulties in obtaining segregating or mapping populations of most forest tree species have led to slow progress in elucidating the genetic architecture of complex traits through traditional QTL-mapping approaches. Recently, suggestions have been made that association genetics or linkage disequilibrium (LD) mapping approaches might be more fruitful to dissect complex traits by using natural populations instead of standard mapping populations in forest tree species. Thus, this strategy would result very effective in Neolamarckia cadamba and Acacia mangium superbulk because no mapping population needs to be created. In this study, we use association genetics and single nucleotide polymorphisms (SNPs) in candidate genes to link genes or genotypes to phenotypes in Kelampayan. In principle, association genetic studies via SNP discovery by sequencing can identify variation down to the single-nucleotide substitutions that are responsible for variation in phenotypes (quantitative trait nucleotides, QTNs). Our recent preliminary studies of proof-of-concept on association genetic approaches showed that there were numerous genetic ‘hotspot’ detected in cellulose synthase (CesA) gene from Shorea parvifolia ssp. parvifolia. Another interesting finding from a group of researchers from the CRC Forestry (CSIRO, Australia) has also identified a link between variation in CAD2 (cinnamyl alcohol dehydrogenase) gene and growth of Eucalyptus globulus recently. Thus, by associating genotypes with phenotypes, early selection of improved planting materials for plantation establishment through biotechnological interventions can be achieved at the seedling stage, thus resulting in a better economic return due to the reduction of cost and time in the production of high quality planting materials for commercial plantation forests.

0

TRANSCRIPTOMICS

By
Ho Wei Seng (wsho)
– November 3, 2010

Transcriptomic Analysis of Wood Formation in Neolamarckia cadamba (Roxb.) Bosser (Kelampayan)

Forest trees represent the majority of terrestrial biomass production and a vital component of biodiversity. However, these slow growing trees are unable to meet current global demand for wood, resulting in the loss and degradation of forest. Neolamarkia cadamba (Roxb.) Bosser (kelampayan) has recently been identified as one of the potential fast growing species for forest plantation in Sarawak. This species is reported to grow vigorously, and is reported as one of the best materials for plywood industries. In forest trees, stem diameter growth results from the activity of the vascular cambium. Cambium derivatives develop into xylem cells through the process of cell division, cell expansion, secondary cell wall formation (involving cellulose, hemicellulose and lignin synthesis), and programmmed cell death. These processes are strongly interlinked and modulation of any one aspect of wood formation may affect many other aspects. Thus, the use of functional genomics approach can provide rapid information on the regulation of not just one gene, but an entire pathway or several pathways at the same time. This project is directed at understanding the wood formation of kelampayan based on sequencing analysis of cDNA clones (ESTs) derived from developing-xylem region tissues. The advances in the understanding of wood formation of Acacia hybrid, poplar and pine via ESTs could provide a powerful means for identifying novel genes and the mechanisms controlling xylem formation in N. cadamba. Moreover, the developing-xylem cDNA library and accompanying database will support research directed toward the mechanisms of wood formation, supply many new cloned genes for future endeavours to modify wood and fiber properties, and increase our knowledge of the environmental influence on wood properties. Comparison of N. cadamba ESTs with sequences from angiosperms will also generate value added information about the evolution of higher plants. Please feel free to visit us at CADAMOMICS for further information about the kelampayan EST project.

0

MOLECULAR MARKER DEVELOPMENT

By
Ho Wei Seng (wsho)
– November 3, 2010

Development and Characterization of Simple Sequence Repeat (SSR) Markers for Genotyping Neolamarckia cadamba (Roxb.) Bosser (Kelampayan) and Duabanga moluccana Blume (Sawih)

Efficient management of forest genetic resources whether for genetic improvement or conservation programme requires accurate and rapid assessment of genetic diversity. Simple sequence repeat (SSR) which is genetically co-dominant and multi-allelic has become a major concern recently to better characterise forest genetic diversity and address genetic resources questions. Because of these attributes, SSR markers are currently the excellent markers of choice for comparative genetic and genomic analyses in forest tree species. However, the availability of SSR markers especially for forest tree species is limited thus far due to the high development cost, labour-intensive and time-consuming. Neolamarckia cadamba and Duabanga moluccana are chosen in this study as there are the two out of eight selected fast growing species to be utilized for planted forest development in Sarawak. Despite its desirable wood properties and high economic importance, little genetic information is available of these species to date. Thus, this study will attempt to develop an array of SSR markers for use in genotyping N. cadamba and D. moluccana trees using a dual-suppression-PCR technique. This technique is relatively simple and rapid without enrichment and screening, and requires only basic skill in molecular biology and the time for procedures has been shortened. The characteristics and polymorphisms of each newly developed SSR marker of these species will also be determined. We expect the genetic information generated using these newly developed SSR markers will be a prerequisite/basis for effective selection of plus trees, provenance trials and establishment of forest seed production areas (SPAs) of N. cadambaD. moluccana in the selected forest areas dedicated for planted forest development and genetic improvement activities. and

0

GENETIC DIVERSITY

By
Ho Wei Seng (wsho)
– November 3, 2010

Genetic diversity of Neolamarckia cadamba (Roxb.) Bosser (Kelampayan)

Neolamarckia cadamba (Roxb.) Bosser (kelampayan) is a large, deciduous, and fast growing tree species that gives early economic returns within 8-10 years. It is one of the best raw materials for plywood industry. The wood can also be used as packing cases, panel boards, picture frames, pencils, toys, sports goods and various other products. Leaves and bark are used in medicine. Besides, it is also excellent as a shade tree for dipterocarps line planting. Due to its multipurpose function and utility, the species is favoured in plantation programmes. Since the supply of planting materials of forest species become a major contribution on the success of forest plantation programme, there is an urgent need to come up with strategy to cater the current demand of the improved planting materials and at the same time come up with more comprehensive tree improvement programme with a long-term strategy in continuously producing genetically improved planting materials. The establishment of SPA is the most effective way of producing improved seed in a large quantity to meet the immediate demand of planting materials. SPA is a stand where the poor phenotypes are roughed leaving good trees or called plus trees for production of improved seed. These improved seed can be used for establishing forest tree plantation and seed orchards. Currently, the selection of plus tree in any seed production areas (SPAs) is based on the phenotype characters without consideration of genetic quality of the selected plus trees for seed production. The seed produce is poor in terms of genetic quality with narrow gene pool. Thus, there are some prerequisites need to be addressed before embarking onto establishment of SPAs. The most important one is the knowledge on genetic quality of the selected plus trees for seed production as the genetic quality of the seed produce is more important than the quantity. As reported elsewhere, local collection for local planting will do nothing to improve local genetic diversity if a very limited genetic base is used for collection. If used widely, seed from poor collections or a poorly constructed seed production area may actually reduce genetic diversity and, over time, make the plantings less resilient to changes in the environment. Hence, research is directed at determining the genetic diversity of this commercially important plantation species using molecular DNA markers, i.e. RAPD and ISSR markers for more accurate means of plus tree selection, provenance trials, and establishment of seed production areas (SPAs) from natural populations in tropical forest reserve.

0

RESEARCH PROJECTS

By
Ho Wei Seng (wsho)
– November 3, 2010
0

fasTiP-X Kit

By
Ho Wei Seng (wsho)
– August 8, 2010

‘Touch-incubate-PCR’ Approach (aka fasTip-X Kit) for High Throughput Genotyping: System 1

The fasTiP-X approach is a rapid extraction method which allows direct amplification without going through conventional CTAB extraction. In the same time, it allows DNA extraction without contacting any harmful chemicals and liquid nitrogen. This method offers a great advantage whereby it requires only approximately 20 minutes for DNA preparation before PCR amplification thus increases the possibility for high-throughput genotyping. Apart from that, the requirement of small amount of plant material is greatly suitable for samples with limited quantity.

The initiative for developing this approach was due to the common hindrance faced by the researchers where sample collection and preparation was the most time consuming part of the project. Hence, this approach was developed to reduce the time, cost and consumable volume required for sample DNA extraction. This rapid DNA extraction approach only involves 3 simple steps before PCR amplification, which is: 1) transferring plant samples into the extraction buffer by touching the sample leaves by using pipette tips or Harris Uni-CoreTM puncher 0.5 mm; 2) incubate to lyse plant cells, and 3) the incubated solution can be directly used for PCR amplification. However, care must be taken if Harris Uni-CoreTM puncher is used for obtaining samples. A 2% solution of sodium hypochlorite (NaCIO) shall be used for cleaning the puncher to prevent cross-contamination.

The fasTiP-X approach was tested using 5S rRNA primers via PCR on 4 different species, namely Neolamarckia cadamba (Roxb.) Bosser (Kelampayan), Duabanga moluccana (Sawih), Durio zibelthinus (Durian) and Dimocarpus longan Lour. (Longan). The amplification of DNA template obtained from the fasTiP-X was comparable to the positive control which extracted using conventional CTAB method. The PCR analysis using DNA template isolated by the fasTiP-X approach for each species was repeated 3 times to prove the reliability and reproducibility of this method. This result showed that the fasTiP-X approach has higher potential for high-throughput genotyping compared to the conventional DNA extraction by considering its rapidity, simplicity and cost-effective features.


[Another completed project brought to you by fGiLab]

HOME → fasTip-X Kit