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From Conservation to Innovation: Building Research Capacity for Planted Forest Development in Sarawak

THINKING GLOBALLY, ACTING LOCALLY, FROM HERE…

The increase in global demand for wood requires increase in forest productivity. The alternative is to farm trees in plantations composed of fast-growing species with short rotation cycle (6-8 years). The rationale is that natural forests at the most produce about 3m3/ha/yr of commercial timber, whereas plantations can produce annually from 10m3/ha of hardwoods to 30m3/ha of softwoods and thus, decrease the effects of human pressure on our ecosystems while increasing the competitiveness of Sarawak’s forest industry.


Rapid socio-economic changes in the world are having profound impacts on all sectors, including forestry. While wood products demand is increasing, so is the demand for environmental services of forests. The increasing demand is triggered by population growth and rise in income (gross domestic income). Global demand for wood products is projected to increase from 3.5 billion m3 in 1990 to 6.4 billion m3 in 2020. Apart from that, the demand for environmental services of forest is also increasing whereby more natural forests will be excluded from wood production, and recently the bioenergy policy, the use of biomass, including wood is increasingly encouraged (Figure 1). Natural forests are unable to meet current global demand for wood due to the long generation intervals and slow growth rate, resulting in the loss and degradation of natural forests by logging. About 12 million ha of forests are lost every year. Africa, South East Asia and South America provide the best environment for tree growth but account for more than 75% of total losses.

Figure 1: The current and future values of forests (Source: FAO, State of World Forests 2009)

Therefore, the increased demand for wood is likely to require increased forest productivity. The alternative is to farm trees in plantations composed of fast-growing species with short rotation cycle (6-8 years). With more research, particularly in the production of improved planting materials, tree selection and improvement, the plantations could produce more of the industrial timber by the end of the next 2 decades. The rationale is that natural forests at the most produce about 3 m3/ha/yr of commercial timber, whereas plantations can produce annually from 10 m3/ha of hardwoods to 30 m3/ha of softwoods. Furthermore, plantations are easier to manage due to the mono or double species mix compared to very diverse natural forest stands. Hence, plantations development will serve as a strategy for maintaining a sustainable supply of timber and at the same time, reducing the logging pressure on natural forests for wood production to an acceptable level.

In Sarawak, the state government has introduced the Forest (Planted Forest) Rules (1997) to encourage the development of commercial forest plantations and has set a target of 1.0 million hectares for forest plantations to be established by 2020. It is estimated that 30 million of high quality seedlings are required for the annual planting programme. Realizing the needs, a joint research programme (URL: http://fgilab.com) focusing on two selected fast growing indigenous tree species, namely Neolamarckia cadamba (Kelampayan) and Duabanga moluccana (Sawih) has been carried out to provide solutions, in addressing the shortage of quality planting materials for licensed planted forest areas in the state. The programme covers R&D activities on forest genomics, biotechnology and tree improvement geared towards enhancing commercial plantation forests as well as sustainable management of forest resources in Sarawak (Ho, 2008). Furthermore, the programme via the use of state-of-the-art technologies and approaches will help respond to the need to develop adequate tools for producing trees that are better adapted to local conditions, so that we may achieve economic benefits of great significance. Over the years, we have conducted projects with special focused on molecular genetic studies. Among others are the development of highly informative and polymorphic DNA markers specific for identifying the genetic makeup of two fast growing indigenous tree species, i.e. Kelampayan and Sawih; 2) the one step ‘Touch-incubate-PCR’ approach (aka fasTip-X Kit) for preparing plant tissues for high throughput genotyping, and 3) a genomic resource database, aka CADAMOMICS (10,368 ESTs) for wood formation in Kelampayan via high-throughput DNA sequencing.

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Why Neolamarkia cadamba and Duabanga moluccana?

Neolamarkia cadamba (Roxb.) Bosser, locally known as Kelampayan belongs to the family of Rubiaceae, has been identified as a promising fast growing species for planted forest development in Sarawak. Kelampayan is a large, deciduous and fast growing tree species, thus with characteristics which guarantee early economic returns within 8 to 10 years. Under normal conditions, it reaches a height of 17 m and diameter of 25 cm at breast height (dbh) within 9 years. It is a lightweight hardwood with a density of 290-560 kg/m3 at 15% moisture content. Thus, kelampayan is one of the best sources of raw material for the plywood industry, besides pulp and paper production. It can also be used as a shade tree for dipterocarp line planting, whilst its leaves and bark have medical application. The dried bark can be used to relieve fever and as a tonic, whereas a leaf extract can serve as a mouth wash. Another plantation tree species, Duabanga moluccana Blume or Sawih from the family of Sonneratiaceae can grow up to 45 meters tall and 100 cm in diameter. This tree is of great economic importance for the production of various wood works and products such as plywood, veneer and pulping. Additionally, it is also suitable for interior paneling, matches, moulding and pulping (CIRAD Forestry Department).



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International Symposium on Forestry and Forest Products (ISFFP) 2010

BEST POSTER AWARD – FIRST PRIZE

in conjunction with the organization of

International Symposium on Forestry and Forest Products (ISFFP) 2010

5-7 October 2010, The Legend Hotel, Kuala Lumpur

Genetic Diversity of Kelampayan using Dominant DNA markers Based on Inter-Simple Sequence Repeats (ISSR) in Sarawak

by Ho Wei Seng, Liew Kit Siong, Elias Abu Bakar, Fedrick Brinau Julin, Mohamad Khairil Mohd Asyawandie and Phui Seng Loi

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CADAMOMICS

CADAMOMICS (aka Neolamarkia cadamba EST database, NCdbEST)

The first large scale genomic resource for wood formation in Kelampayan (Neolamarkia cadamba) or CADAMOMICS, also known as the Neolamarkia cadamba expressed sequence tags database (NCdbEST) was successfully generated by a group of researchers from the Forest Genomics and Informatics Laboratory (formerly known as Forest Genomics Laboratory, UNIMAS-SFC). Most genes involved in lignin biosynthesis and several other cell wall biosynthesis genes were identified in the CADAMOMICS.


The first large scale genomic resource for wood formation in Kelampayan (Neolamarkia cadamba) was successfully generated by a group of researchers from the Forest Genomics and Informatics Laboratory (formerly known as Forest Genomics Laboratory, UNIMAS-SFC). CADAMOMICS, also known as the Neolamarkia cadamba expressed sequence tags database (NCdbEST) contained 10,368 ESTs was generated through high-throughput 5’ EST sequencing of cDNA clones derived from developing xylem tissues.

Assembly of 6,622 high quality ESTs from 5’ end sequences generated 4,728 xylogenesis unigenes with an average length of 672 bp. The analysis formed 2,100 consensus contigs sequences (representing 3,994 or 60.3 % of the total high quality ESTs), with a length ranging from 132 bp to 2706 bp and an average length of 621 bp. The remaining 2,628 (representing 39.7 % of the total high quality ESTs) were singletons which ranged from 104 to 839 bp, with an average length of 723 bp. About 59.3 % of the ESTs were assigned with putative identifications whereas 40.7 % of the sequences showed no significant similarity to any sequences in the GenBank. Assembly analysis revealed a redundancy level of 28.5% in the kelampayan EST database. By comparison, the EST redundancy in the kelampayan EST database is comparable to the estimated redundancy of 28 % in Populus and the 28.8 % in Pinus radiata.

The most abundant protein in the ESTs whose putative function was inferred from sequence comparison was 60s ribosomal protein with 92 ESTs, followed by 40s ribosomal protein with 42 ESTs. Interestingly, most genes involved in lignin biosynthesis were present in the kelampayan EST database with 1 to 21 ESTs. These include phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), coumarate 3-hydroxylase (ρ-coumaryl shikimate/quinate 3-hydroxylase) (C3H), caffeic acid O-methyltransferase (COMT), caffeoyl-CoA-3-O-methyltransferase (CCoAOMT), 4-coumarate:CoA reductase (4CL), ferulate 5-hydroxylase (F5H), cinnamyl alcohol dehydrogenase (CAD), hydroxycinnamoyl-CoA: shikimate/quinate hydroxycinnamoyl transferase (HCT) and cinnamoyl-CoA reductase (CCR). COMT, CCoAOMT and C3H are in the 30 highly abundant genes with 18 to 21 ESTs. Also, several ESTs exhibiting homologies to cell wall biosynthesis genes were also identified in the kelampayan EST database. The most highly abundant cell wall genes are tubulin (42 ESTs), arabinogalactan protein (30 ESTs) and cellulose synthase (13 ESTs). Other cell wall related genes including sucrose synthase, expansin, UDP-glucose dehydrogenase, xyloglucan endotransglycosylase and pectate lyase are moderately abundant with 2 to 11 ESTs in the kelampayan EST database.

This study has generated an important genomic resource for wood formation in kelampayan. The identified genes in this study will provide a useful resource for identifying molecular mechanisms controlling wood formation and will also be candidates for association genetic studies in kelampayan aiming at the production of high value forests. Furthermore, comparison of kelampayan ESTs with sequences from angiosperms will also generate valuable information about the evolution of higher plants.

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[Another completed project brought to you by fGiLab]

What do we have in CADAMOMICS?
CADAMOMICS contained  the ESTs for all the lignin biosynthesis genes and some of the important wood formation genes. Apart from that, genes involved in biotic and abiotic stresses are also identified in this EST database.

What can CADAMOMICS offer?
CADAMOMICS provides a platform for gene discovery, especially for genes involved in wood formation and related pathways. This database can be used for association genetic studies aiming at the production of high value forests.

Who can use CADAMOMICS?
CADAMOMICS is available to all biotechnologists involved in the study of kelampayan and other forest tree species*. This database is very much relevant to researchers who are working on any tropical tree improvement programme , especially on our indigenous timber tree species.
* Terms and conditions applied

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What do we have in CADAMOMICS?

CADAMOMICS contained  the ESTs for all the lignin biosynthesis genes and some of the important wood formation genes. Apart from that, genes involved in biotic and abiotic stresses are also identified in this EST database.

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fasTiP-X Kit

‘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]

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The 21st International Invention Innovation & Technology Exhibition (ITEX’10)

The 21st International Invention Innovation & Technology Exhibition (ITEX’10)  Creativity: Pathway to innovative economy

14-16 May 2010 – Kuala Lumpur Convention Centre – Malaysia

Project: Building research capacity for planted forest development in Sarawak

1Ho Wei Seng, 2Pang Shek Ling, 1Lai Pei Sing, 1Liew Kit Siong, 2Phui Seng Loi, 1Nurfaizah Matra, 1Tiong Shing Yiing, 1Tchin Boon Ling, 1Ismail Jusoh, 1Cheksum Tawan, 1Petrus Bulan and 2Julaihi Abdullah

A joint-venture project between 1Faculty of Resource Science and Technology-Universiti Malaysia Sarawak and 2Sarawak Forestry Corporation

Result: Silver Medal. Congratulations!


HOMEThe 21st International Invention Innovation & Technology Exhibition (ITEX’10)

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GetintoGenes: Biotechnology Workshop

GetintoGenes: Biotechnology Workshop

18 MAY 2010

Jointly organized by the fGil, Faculty of Resource Science and Technology, MABIC and the Molecular Plant Breeding CRC, Victorian AgriBiosciences Centre, Melbourne (UNIMAS-MABIC-MPBCRC-MOE)


Malaysian Biotechnology Information Centre (MABIC) has been organizing biotechnology workshops for teachers in collaboration with the Ministry of Education for the past three years. Last year, MABIC created a milestone by organizing these workshops outside Kuala Lumpur and Selangor. This tradition is to be continued this year with a value-added feature.

MABIC has been fortunate this time to collaborate with Dr. Belinda Griffiths from Molecular Plant Breeding CRC, Victorian AgriBiosciences Centre, Melbourne. MPBCRC has a proven track record in science education and collaborative partnerships, running successful post-graduate biotechnology education workshops as well as Get into Genes, the award-winning biotechnology workshop for schools, in partnership with the Australian Centre for Plant Functional Genomics.

For the first time, this workshop will be conducted in East Malaysia, hosted by the Faculty of Resource Science and Technology, Universiti Malaysia Sarawak (UNIMAS). The objective of the workshop is to broaden the understanding among the science teachers in the secondary schools of biotechnology. It is hoped that this workshop will enhance their pedagogy and the teachers will be able to provoke the interest of the students in the field of biotechnology. This is crucial to create a pool of knowledge workers to fuel the growing biotechnology industry in Malaysia.

The decision to conduct this workshop in Sarawak was to enable resource-poor teachers to have access to research facilities and experts in the area of biotechnology, and expose them to the applications of modern biotechnology. The teachers will have hands-on experience in DNA extraction, fingerprinting and simple bioinformatics tools. Twenty teachers from around Kuching will attend this workshop.

(Extracted from http://www.bic.org.my/?action=events&do=body94)

Get into Genes poster

[Another completed project/workshop successfully organized by fGiL]

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Together We Succeed!

UNIMAS R&D Expo, 25-26 March 2010, CAIS-UNIMAS

From Conservation to Innovation: Building Research Capacity for Planted Forest Development in Sarawak

1Ho Wei Seng, 2Pang Shek Ling, 2Phui Seng Loi, 1Liew Kit Siong, 1Nurfaizah Matra, 1Tiong Shing Yiing, 1Tchin Boon Ling, 1Lai Pei Sing, 1Ismail Jusoh, 1Cheksum Tawan, 1Petrus Bulan and 2Julaihi Abdullah

A joint-venture project between 1Faculty of Resource Science and Technology-Universiti Malaysia Sarawak and 2Sarawak Forestry Corporation

Abstract

The increase in global demand for wood requires increase in forest productivity. The alternative is to farm trees in plantations composed of fast-growing species with short rotation cycle (6-8 years). The rationale is that natural forests at the most produce about 3m3/ha/yr of commercial timber, whereas plantations can produce annually from 10m3/ha of hardwoods to 30m3/ha of softwoods and thus, decrease the effects of human pressure on our ecosystems while increasing the competitiveness of Sarawak’s forest industry. This is in line with State Government’s aspiration to establish one million hectares of planted forests by year 2020 to meet the increasing demand from both domestic and international markets for raw materials. It is estimated at least 30 million seedlings are required for annual planting or reforestation programmes. The forest biotechnology research will help respond to the need to develop adequate tools that enable us to produce quality planting materials that are of faster growth, high-yield and high wood quality, and also adapted to local conditions, so that we may achieve economic benefits of great significance. Realizing the needs, we have centered our research on the development of tools via biotechnological innovations for tree breeders. Over the past 2½ years, we have successfully developed 1) an array of highly informative and polymorphic DNA markers specific for identifying the genetic makeup of two fast growing indigenous tree species, i.e. Kelampayan and Sawih; 2) the ‘Touch-incubate-PCR’ approach (aka fasTip-X) for preparing plant tissues for high-throughput genotyping, and 3) a genomic resource database, aka Cadamomics (10,368 ESTs) for wood formation in Kelampayan via high-throughput DNA sequencing. These tools will greatly facilitate the selection of quality planting materials for planted forest development in Sarawak as well as long-term tree improvement activities by integrating genomics into our breeding programme via association mapping. The overall benefit of application of genomics to tree improvement programme will be in terms of greater certainty in the outcome of results, specifically the performance of the forest plantations, as well as the savings in time and cost in the production and supply of quality planting materials.

Result: Bronze Medal. Congratulations!

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Greetings from fGiL!

Welcome and greetings from the Forest Genomics and Informatics Laboratory (fGiL)!

TIME for CHANGE

The Forest Genomics Laboratory (aka FGL) has been in business over 2¼ years and for sure we start from a very humble beginning but with a great spirits of innovation and enterprise in R&D especially in forest genomics and bioinformatics researchers. We have achieved several important milestones over the years. However, we will never forget our humble roots because as we remember where we come from and utilize the best traditions of the past, this will help us to move forward progressively. Indeed, we have pride in our past and faith in our future.

As someone working in forest genomics and bioinformatics-related areas, I just can’t help but notice how rapidly the field is changing ahead with the next generation sequencing technologies (the 3rd generation sequencing technologies is coming this year!). In this respect, I notice that the name of ‘FGL’ is no longer reflecting what we are currently doing in this lab.

After a serious thought of the future of our lab/research group together with the fruitful discussions with researchers from the Cambridge University and Wellcome Trust Sanger Institute, UK (Dec 2009) during the Genome Informatics Workshop, I have decided to have another RE-BRANDING exercise for our research group as well as renaming the ‘FGL’ to Forest Genomics and Informatics Lab (aka fGiL), consolidating and strengthening the resources and facilities both hard-and soft-wares in year 2010 – it’s going to be another exciting year ahead for us. We will see more national and international collaborations this year ahead.

Let us all work together to help shape an environment that would provide exceptional research environment to attract the world’s best talents and make the best products for our users.

A Trust To Keep, A Dream To Fulfill!

Thank you.

Dr Ho Wei Seng

Coordinator,  fGiLab

HOMEgreetings from the Forest Genomics and Informatics Laboratory (fGiL)!

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thestar online

Wednesday November 22, 2006

Corp signs MoU with Unimas

KUCHING: The Sarawak Forestry Corporation and Universiti Malaysia Sarawak (Unimas) will collaborate on research and development (R&D) towards the development of planted forests and the sustainable management of forest resources in the state.

Both parties recently signed a memorandum of understanding (MoU) on the collaboration, which will last for a period of five years.

The MoU covers R&D activities on forest genomics, biotechnology and tree improvement geared towards enhancing planted forests as well as conservation.

Cheong (second left) and Prof Dr Khairuddin exchanging the MoU documents as Lim (left) and Unimas deputy vice chancellor (research and innovation) Prof Dr Murtedza Mohamed look on.

Sarawak Forestry managing director Datuk Cheong Ek Choon, who signed on behalf of the corporation, said the research would benefit the forest industry.

“We hope to strengthen our scientific resources and contribute towards sustainable forest management,” he added.

Deputy general manager of applied forest science and industry development Nigel Lim said the R&D would focus on two fast-growing indigenous tree species, kelampayansawih, for the state’s planted forests. and

In addition, researchers will also study the commercial species of kapur bukit and meranti sarang punai to ensure their sustainability.

Unimas acting vice-chancellor Dr Khairuddin Abdul Hamid said researchers from the resource science and technology faculty would be directly involved in the joint R&D programme.

“It brings us closer to the industry and gives opportunities for our researchers to conduct applied R&D that is relevant to the needs of the industry,” he said.

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