Molecular Characterization and Similarity Relationships Among Selected Kelampayan (Neolamarchia cadamba) Genotypes from Kelampayan Provenance Trial Plot I Using ISSR Markers

Neolamarckia cadamba or Kelampayan is a fast growing timber species that has economical and medicinal value. Kelampayan is one of the species widely used for reforestation programme, so as high commercial value in plywood manufacturing and wound cleansing. Therefore, molecular characterization of this species is important to enable further species improvement. In this project, determination of genetic relatedness and diversity of kelampayan was accomplish using ISSR primers namely (GTG)6, (AC)10 and (AG)10. Selected primers had successful amplified 64 loci with 73.44% of polymorphic in block I population. Shannon’s diversity index of all three combined primes was reported to be 0.350. Molecular diversity based on Jaccard’s similarity coefficient of 79 trees was in the ranged of 0.14 to 0.94. UPGMA dendrograms and neighbor joining tree were also constructed to show the genetic relationship of N. cadamba trees. In the outcome of the dendrograms reveals that, a total of four clusters were grouped for block 1 kelampayan trees indicating that N. cadamba trees are genetically diverse

Applications of Genomics to Plantation Forestry with Kelampayan in Sarawak

Wood-based industries in Sarawak are increasingly encouraged to adapt to " new wood " from planted forests composed of fast-growing species such as Kelampayan with short rotation cycle (6-8 years). The rationale is that natural forests at the most produce about 3m 3 /ha/yr of commercial timber, whereas plantations can produce annually from 10m 3 /ha to 30m 3 /ha of commercial timber. It is estimated at least 30 million seedlings are required for annual planting or reforestation programmes to meet the increasing global demand for raw materials. To date, several molecular genetics studies have been completed for Kelampayan. These include genetic diversity of Kelampayan, genetic marker (SSRs) development, 'Touch-incubate-PCR' approach for preparing plant tissues for high throughput genotyping, and transcriptomics and bioinformatics on wood formation of Kelampayan. This information provides a useful resource for genomic selection of Kelampayan aiming at the production of high value forests for maximum returns

In Silico Analysis of Cellulose Synthase Gene (NcCesA1) in Developing Xylem Tissues of Neolamarckia Cadamba

This study reported the isolation and in silico characterization of full-length cellulose synthase (CesA) cDNA from Neolamarckia cadamba, an important tropical plantation tree species. CesA is a member of processive glycosyltransferases that involved in cellulose biosynthesis of plants. CesA acts as a central catalyst in the generation of plant cell wall biomass or cellulose. It also plays an important role in regulating wood formation. The hypothetical full-length CesA cDNA (NcCesA1; JX134621) was assembled by contig mapping approach using the CesA cDNA sequences from NcdbEST and the amplified 5�-and 3�-RACE PCR sequences. The NcCesA1 cDNA has a length of 3,472 bp with 3,126 bp open reading frame encoding a 1,042 amino acid sequence. The predicted NcCesA1 protein contained N-terminal cysteine rich zinc binding domain, 7 putative Transmembrane Helices (TMH), 4 U-motifs that contain a signature D, D, D, QxxRW motif, an alternating Conserved Region (CR-P) and 2 Hypervariable Regions (HVR). These entire shared domain structures suggest the functional role of NcCesA1 is involved in glycosyltransferation of the secondary cell wall cellulose biosynthesis of N. cadamba. Sequence comparison also revealed the high similarity (90%) among NcCesA1 and PtrCesA2 of Populus tremuloides. This further implies the involvement of NcCesA1 that catalyzes the cellulose biosynthesis of secondary cell wall rather than primary cell wall. This full-length NcCesA1 cDNA can serve as good candidate gene in association genetics study which leads to Gene-Assisted Selection (GAS) in the N. cadamba tree breeding programme. Furthermore, the isolation of new CesA genes from tropical tree genomes is essential for enhancing knowledge of cellulose biosynthesis in trees that has many fundamental and commercial implications

Bioinformatics Analysis of Xyloglucan Endotransglycosylase/Hydrolase (XTH) Gene from Developing Xylem of a Tropical Timber Tree Neolamarckia Cadamba

This study reported the isolation and in silico characterization of a full-length Xyloglucan endotransglycosylase/Hydrolase (XTH) cDNA from Neolamarckia cadamba, an important tropical light hardwood plantation tree species. XTH is considered as a key agent to regulate cell wall expansion and is believed to be responsible for the incorporation of newly synthesised xyloglucan into the wall matrix. The full-length of NcXTH was firstly predicted using the XTH singletons from the NcdbEST through contig mapping approach. Further validation and confirmation were conducted by amplifying the full-length XTH cDNA using RT-PCR approach. Two fulllength XTH cDNAs, namely NcXTH1 (JX134619) and NcXTH2 (JX134620) were discovered and the nucleotide sequences were 893 and 1,024 bp in length, respectively. The open reading frames for NcXTH1 and NcXTH2 were 858 and 915 bp, respectively. Results predicted that NcXTH1 and NcXTH2 proteins carry out XET activity but they are from different XTH family members. This full-length NcXTH cDNA can serve as good candidate genes in association genetics study which leads to Gene-Assisted Selection (GAS) in the N. cadamba tree breeding programme

Applications Of Genomics To Plantation Forestry With Kelampayan In Sarawak

Wood-based industries in Sarawak are increasingly encouraged to adapt to “new wood” from planted forests composed of fast-growing species such as Kelampayan 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 to 30m3 /ha of commercial timber. It is estimated at least 30 million seedlings are required for annual planting or reforestation programmes to meet the increasing global demand for raw materials. To date, several molecular genetics studies have been completed for Kelampayan. These include genetic diversity of Kelampayan, genetic marker (SSRs) development, ‘Touch-incubate-PCR’ approach for preparing plant tissues for high throughput genotyping, and transcriptomics and bioinformatics on wood formation of Kelampayan. This information provides a useful resource for genomic selection of Kelampayan aiming at the production of high value forests for maximum returns

Genomics studies on plantation tree species in Sarawak

Rapid socio-economic changes in the world are having profound impacts on all sectors, including forestry. 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 cycles (6–8 y). The rationale is that natural forests at the most produce about 3 m3 ha y-1 of commercial timber, whereas plantations can produce annually from 10 m3 ha y-1 of hardwoods to 30 m3 ha-1 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 the 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. In this regard, forest genomics 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 need, we have centred our research on the development of tools via biotechnological innovations for tree breeders. Over the years, we have successfully developed: 1) simple sequence repeat (SSR) 173 DNA markers specific for identifying the genetic make-up of two fastgrowing indigenous tree species, i.e. kelampayan and sawih; 2) the ‘Touch-incubate-PCR’ approach for preparing plant tissues for high throughput genotyping, and 3) a kelampayan tree transcriptome database (NcdbEST aka CADAMOMICS) for wood formation. 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 genomics application 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

From Conservation To Innovation Building Research Capacity For Planted Forest Development In Sarawak

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. In this regard, the forest genomics 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. 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 one step ‗Touchincubate- PCR‘ approach 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 longterm tree improvement activities by integrating genomics into our breeding programme via association mapping. The overall benefit of genomics application 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

Full-length cDNA cloning and SNP discovery of xyloglucan endotransglycosylase/hydrolase (xth) and cellulose synthase (cesa) genes in a tropical timber tree (neolamarckia cadamba)

Neolamarckia cadamba or commonly known as Kelampayan is one of the fast growing forest tree species in Sarawak with high commercial value. The wood is used for producing different products such as plywood, pulp, paper, and furniture. This study was carried out as a part of a tree breeding and improvement programme for forest plantation. Since wood is composed of cell walls, studies on cell wall formation and regulation are important. Single nucleotide polymorphisms (SNPs) were chosen to determine the genetic variations of the xyloglucan endotransglycosylase/hydrolase (XTH) and the cellulose synthase (CesA) genes in N. cadamba. XTH and CesA are proteins that play an important role in regulating wood formation. XTH enzymes regulate cell wall expansion while CesA acts as a central catalyst in the generation of plant cell wall biomass (cellulose). Two full-length XTH cDNAs, namely NcXTH1 (JX134619) and NcXTH2 (JX134620) were discovered. The nucleotide sequences were 893 bp and 1,024 bp in length, respectively. The open reading frames for NcXTH1 and NcXTH2 were 858 bp and 915 bp, respectively. Results predicted that NcXTH1 and NcXTH2 proteins carry out XET activity but they were from different XTH family members. The hypothetical full-length CesA cDNA (NcCesA1; JX134621) was assembled by in silico analysis using the selected CesA cDNA sequences from NcdbEST and the amplified 5’- and 3’-RACE sequences. The NcCesA1 cDNA has a length of 3,472 bp with 3,126 bp open reading frame encoding 1,042 amino acids. Sequence analyses showed that NcCesA1 protein is involved in glycosyltransferation of the secondary cell wall cellulose biosynthesis. Wood properties (basic density) associated single nucleotide polymorphisms (SNPs) were discovered in the NcXTH1 and NcCesA1 genes. A total of 34 SNPs with 2.65% occurrence was found in 15 partial genomic DNA sequences of NcXTH1 with two SNPs significantly associated with wood basic density (p<0.05). For the NcCesA1 gene, only three SNPs were iv found in 15 partial targeted regions of the NcCesA1 DNA sequences (~779 bp). The low occurrence of SNPs (0.39%) in NcCesA1 showed no quantitatively significant association with wood basic density. In the linkage disequilibrium (LD) study, a total of 496 pairwise comparisons were estimated from the polymorphic sites (SNPs) detected in the NcXTH1 and NcCesA1 genes of N. cadamba with a mean R 2 value of 0.000687. The LD graph plotted decayed very slowly with distance of polymorphic sites in a consistent and linear pattern. In conclusion, this study showed an association between NcXTH1 genes with wood basic density