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.