Interests in the changes of gene expression patterns of palms infected by Ganoderma boninense have increased especially since basal stem rot (BSR) caused by the species of Ganoderma is the most serious disease of oil palm in Malaysia. In addition, an indication that there are differences in susceptibility to BSR between germplasm materials from different genetic origins have provide hope in generating oil palm varieties with reduced level of susceptibility using existing genetic materials. There is also an interest in developing diagnostic tools such as using PCR primers for the detection of the pathogen in oil palms. A novel method combining elements of suppression subtractive hybridization (SSH) with high throughput differential screening permits the efficient and rapid cloning of rarely transcribed differentially expressed genes. The experimental strategy virtually excludes the possibility of isolating false positive clones. The potential of the method is demonstrated by the isolation of 615 differentially expressed cDNAs from the Ganoderma-inoculated oil palm seedlings T1 from various numbers of weeks after inoculation when subtracted from its uninoculated counterpart, T2. Sequence data indicated that of the 615 clones obtained, 251 scored perfect or near perfect matches with already known genes. Analysis of sequencing data also revealed an increased expression of defense-related genes which function in the defense against fungal and insect pathogens in plants.
301 clones scored between 60 and 95% homology to known plant genes, whereas 314 clones did not match sequences in the GenBank/EMBL database, indicating that they may be novel genes. Northern and reverse northern analysis of 8 selected clones demonstrated that 7 were differentially expressed with respect to T1, indicating a true positive rate of 87.5%. All 7 selected clones are PR-proteins. Additionally, a large proportion of these clones represented rare transcripts as determined by the exposure time required to detect a signal. The method we describe is ideally suited whenever subtle changes in gene expression profiles need to be determined and has been proven to be successful in identifying differentially expressed genes related to infection of Ganoderma boninense in oil palm. These findings will definitely enhance the understanding of molecular mechanism in response to infection and in the manifestation of disease symptoms in oil palms. Development of diagnostic tools to detect infections of Ganoderma boninense at an early stage could be initiated and hopefully we will be able to identify resistant or less susceptible oil palm varieties based on this findings.