Researchers / Postgrads:
Project Title: Development of SSR Markers for Neolamarckia Cadamba (Roxb.) Bosser (Kelampayan)
Reliable information on the distribution of genetic variation is a crucial point for applicability and efficiency of any breeding, preservation and conservation programmes for forest trees. The emergence of DNA marker technologies have revolutionized the field of plant genetics by providing new tools for rapid genetic analysis, fingerprinting and studying relatedness among cultivars of many forest tree species. Recently, development of an ideal DNA marker system which is genetically co-dominant and multiallelic is becoming a major concern due to the genetic complexity of breeder’s populations and high levels of heterozygosity in individual genotypes. Simple sequence repeat (SSR) marker is a polymerase chain reaction (PCR)-based marker system of this kind, and becoming the excellent markers of choice for comparative genetic and genomic analysis, individual genotyping and studies of gene flow in forest trees. In this study, Neolamarckia cadamba was chosen due to its commercial value and fast growing ability. Although N. cadamba is important in ecosystems and tropical forestry and becoming one of the most frequently planted trees in the tropics, but genetic information about member species is limited. To date, none of the DNA markers has been developed from N. cadamba, compared with that from others economically important tropical tree. Therefore, in order to discover, investigate and determine the genetic diversity and structure of N. cadamba, the main goal of this study is to develop simple sequence repeat (SSR) markers specific for genotyping N. cadamba trees. The developed SSR markers later can be used to estimate the genetic diversity of natural and planted populations of Kelampayan.
Project Title: Development and Polymorphism of Simple Sequence Repeat (SSR) DNA Markers for Duabanga moluccana Blume
Efficient management of forest genetic resources whether for genetic improvement or conservation programmes requires accurate and rapid assessment of genetic diversity. With the advent of DNA sequencing, data analysis and polymerase chain reaction (PCR) technology, there has been a remarkable progress in the development of an array of potential DNA molecular markers in order to better characterize forest genetic diversity and address genetic resources questions. In recent year, simple sequence repeats (SSRs) are considered markers of choice in genetic studies because they are PCR-based, high discriminatory power, high information content arising from their multiallelic nature, co-dominant, small amount of DNA template necessary, randomly distributed throughout the genome, robust and reproducible assay, and transferability across closely related taxa. However, the isolation and characterization of SSR marker for a forest trees is limited until now because involves highly time-consuming and development cost. In this study, SSR markers will be developed for Duabanga moluccana Blume based on a simple method as reported by Lian et al. (2001). D. moluccana was chosen for study due to its economically and ecologically important. To date, baseline genetic information for this species is limited and none of the DNA-based markers has been developed. In order to determine the genetic diversity and structure of D. moluccana, thus, the main objective of this study is to develop a set of SSR markers specific for genotyping D. moluccana trees.
Project Title: Development of SCAR Markers for Sex Typing in Canarium odontophyllum Miq. (Dabai)
Dabai, being a Sarawak’s specialty fruit is well-known with its unique sexual characteristic. The female Dabai trees bear fruits while male Dabai trees do not and are normally removed 4 years later when the plants are reproductively mature. This lengthy life cycle along with inability to determine gender at early stage can result in undesirable waste of time, space, resources and nursery cost. Therefore, an ideal solution to overcome this constraint is to develop a Sequence Characterized Amplified Region (SCAR) marker to determine the Dabai sex-type at seedling stage. Through RAPD, sex-related diagnostic band can be identified and subsequently transformed into a co-dominant SCAR marker by means of cloning and sequencing. Once developed, SCAR marker has the massive potential to assist in Dabai crop management program and thereby in advance, proposing and economic and yet profitable planting approach for Dabai plantation.
Project Title: Seeds Cryopreservation, Viability and Mating System of Neolamarckia cadamba (Roxb.) Bosser
The supply of timber from natural forests has been rapidly declining over recent years as a result of previous over logging in some areas of tropical rain forests which has led the country to adopt sustainable forest management policies to maintain the existing natural resources. The cryopreservation of Neolamarckia cadamba (kelampayan) seeds can be an important complementary approach to the safeguarding of woody plant biodiversity, assuming that the development of a low-input and widely-applicable technology is pursued. The mating system is an important determinant of the genetic structure and evolutionary inherent of natural populations because it establishes the pattern of uniting gametes to form the next generation. The objectives of this study are: 1) to assess the viability and germination of N. cadamba seed lots; 2) to determine the influence of storage environments on viability and germination of N. cadamba seeds; 3) to determine suitable conditions of environment for storage of N. cadamba seeds for long-term conservation, and 4) to determine the mating system of N. cadamba using simple sequence repeat (SSR) DNA markers.
Project Title: Gene-associated SNP Discovery and Molecular Cloning of Full-length cDNA of Cinnamate 4-hydroxylase (C4H) and Cinnamyl Alcohol Dehydrogenase (CAD) in Kelampayan (Neolamarckia cadamba)
Genetic association or the correlation between the phenotypes and genotypes (i.e. SNPs) in candidate gene; is a powerful method for identification of the genes or loci that contribute to variation in complex traits. Once the quantitative trait nucleotides (QTNs) are identified, such powerful approach provides significant advantages to the forest industry. As the early selection of planting materials encoded desired traits can be performed at early seedling stages, thus better economic return in shortest period of time and at reasonable cost is achievable. Therefore, the objectives of this study are to (i) isolate and in silico characterizing the full length cDNA of cinnamyl alcohol dehydrogenase (CAD) and cinnamate 4-hydroxylase (C4H) from kelampayan; and determine gene-associated SNP in CAD and C4H genes from kelampayan. Sequence variations within these two genes in 30 kelampayan trees will be examined and an array of wood properties namely, specific gravity, wood density, fiber-length, cell wall thickness and microfibril angle will be meausred. Statistical analysis will be carried out to test for the association. It is expected that the full-length cDNA sequence of C4H and CAD will be obtained and in silico characterized. Moreover, gene-associated SNP discovery in C4H and CAD genes from kelampayan will be conducted.
Project Title: Full-length cDNA cloning and SNP discovery of xyloglucan endotransglycosylase (XET) and cellulose synthase (CesA) genes in kelampayan (Neolamarckia cadamba)
Neolamarckia cadamba or commonly known as kelampayan is one of the important forest tree species in Malaysia. This fast growing tree species is used in reforestation. Kelampayan is also involved in forest plantation for commercial purposes due to its wood characteristics that are suitable to produce different products, such as plywood and paper. Therefore, the study of wood quality is needed to monitor the quality of the trees planted. Molecular study of wood formation and wood properties of this tropical tree species is needed to choose the desired trait of kelampayan to be planted in forest plantation. A DNA marker, SNP has been chosen to determine the genetic variation of xyloglucan endotransglycosylase (XET) and cellulose synthase (CesA) in N. cadamba because it is a direct marker that gives more accurate genetic variation information. Xyloglucan endotransglycosylase and cellulose synthase are proteins that play an important role in regulating wood formation. XET is the enyme that regulate cell wall expension while CesA acts as a central catalyst in the generation of plant cell wall biomass. In this study, full length cDNA of XET and CesA will be cloned and SNP will be discovered. In silico characterization of these two gene sequences and the gene-associated SNP study will also be carried out. The association genetic study can help in identification of associations between variation in phenotypic traits and allelic polymorphism in known genes. This is useful in plant improvement programme to choose the desired traits of N. cadamba. A more economical and efficient forest planting then can be carried out and hence increases the source of income in forest field.
Project Title: Development and Characterization of EST-SSR markers for kelampayan (Neolamarckia cadamba (Roxb.) Bosser)
Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) markers are markers which are embedded in functional gene sequences and lead to the identification of genes controlling these traits. Apart from distinguish cultivars from the same species, the transferability of these markers helps to distinguish the relationship between related species. These markers are valuable for the study of variations and polymorphisms of the plant species. The application of ‘Touch-n-Go’ approach and FTA® technology will be used to further reduce the time and cost requirement in this study. The objectives of this study are to develop the one-step ‘Touch-n-Go’ approach and FTA® technology in preparation of plant tissue for PCR analysis, in silico analysis on the frequency and distribution of the identified EST-SSR markers, and determine the characteristics and polymorphisms of each newly developed EST-SSR markers. Computer software will be used to identify the EST-SSRs from kelampayan expressed sequence tag (EST) database (dbEST) and the primer pairs which flank those regions will be designed. The primers will be used in the amplification of DNA obtained through ‘Touch-n-Go’ approach and FTA® technology. Then, each SSR locus will be characterized and the genetic diversity parameter will be determined. ‘Touch-n-Go’ approach and FTA® technology will be successfully developed for high throughput genotyping, frequency and distribution of the identified EST-SSR markers will be determined, and the characteristics and polymorphisms of each newly developed EST-SSR markers will be determined. These newly developed markers will facilitate the selection of interested genotype and enhance the breeding in plantation forestry with kelampayan. Besides, the breeding period and the field workload will be reduced correspondently.
Angela Tida Anak Henry (FRST-UNIMAS)
Hafizah Abdul Razak (FRST-UNIMAS)