Research Focus

Banana Somatic Variants Resistant to Fusarium Wilt: Molecular Markers and Resistance Mechanisms 

Fusarium wilt of banana is a soil-borne fungal disease that blocks the vascular bundles of infected banana plants, causing yellowing of the leaves and eventual wilting. The disease has devastated the global banana export industry based on Gros Michel, forcing banana farmers to switch to Cavendish, a resistant cultivar that now dominates the current market. However, a new fungal race TR4 (tropical race 4) can infect Cavendish, posing a growing threat to the global banana industry. The spores of the fungus can survive in the soil for decades and there is no effective fungicide to control this disease. Cavendish bananas are triploid and do not produce seeds, making it impossible to introduce resistance genes by crossing. The Taiwan Banana Research Institute has obtained dozens of TR4-resistant somatic variants by screening a large number of tissue culture derived plantlets in TR4 heavily infested fields. Several of these lines, such as Tai-Chiao No. 5, No. 7 and Formosana, have been well accepted by banana farmers in Taiwan and abroad for their stable resistance and good yield. Through the analysis of high-throughput sequencing data, we have developed unique molecular markers for these commercial lines to protect their breeders’ rights and ensure the purity of banana plantlet production. In addition, by genomic analysis, we have identified mutated regions common to TR4-resistant lines. Using virus-induced gene silencing and physiological and biochemical assays, we are now elucidating the molecular mechanisms that enhance the Cavendish resistance to Fusarium wilt TR4.

Mechanisms and Functions of Post-transcriptional Gene Regulations in Plant Defense Pathways

Plants have evolved a wide variety of defense pathways against the attack from pathogens and pests. When plants sense pathogens or pests, defense responses are activated. However, the activation of defense responses is often associated with growth repression. The attempt to enhance resistance through overexpression of resistance genes (R genes) might cause growth retardation or cell death. To reduce the cost of defense, plants have evolved various mechanisms to tightly regulate defense pathways at the transcriptional and post-transcriptional levels. In recent years, the rapid development of next generation sequencing technologies has enabled a rapid and global profiling of RNA degradation intermediates, ribosome footprints, RNA structures or RNA modifications on a genome-wide scale. Making good use of these big data of RNA can facilitate the identification of the genes regulated at the post-transcriptional level and the underlying mechanisms. Previously, we applied a new method on the analyses of the big data of RNA and discovered that a length of 22 nt is the key determinant for plant miRNAs to trigger the production of secondary siRNAs. The 22-nt miRNA mediated regulation is used by many plant species to repress the expression of R gene family. Currently, we are studying how pathogen infection alters post-transcriptional regulation of plant defense-related genes and identifying key sequence factors that control post-transcriptional regulation.

Application of Next-generation Sequencing (NGS) Data to Basic and Translational Research

With the rapid development of next-generation sequencing technologies, it has become very easy to obtain huge amounts of sequence data. When properly applied, these data can be extremely valuable for basic or translational research. Our laboratory has developed new methods to analyze next-generation sequencing data to uncover clues to the molecular mechanisms involved or to help solve agriculture-related problems (e.g., molecular markers and breeding).