Genome-Wide Association Study (GWAS) Reveals the Genetic Architecture of Resistance to Yellow Leaf Disease in Phalaenopsis Orchids

Phalaenopsis orchids are a key export horticultural crop in Taiwan; however, yellow leaf disease caused by Fusarium phalaenopsidis severely threatens production stability. This study, conducted collaboratively by National Cheng Kung University, National Chung Hsing University, and the Taiwan Agricultural Research Institute, performed whole-genome resequencing on 177 Phalaenopsis accessions, identifying 19.68 million high-quality single nucleotide polymorphism (SNP) loci.

Through a genome-wide association study (GWAS), the research team successfully identified multiple genetic loci significantly associated with resistance to yellow leaf disease and further pinpointed two key candidate genes, Peq001041 and Peq022991. The gene Peq001041, located on chromosome 2, is annotated as a ubiquitin carboxyl-terminal hydrolase involved in protein degradation regulation, while Peq022991, located on chromosome 16, encodes a beta-glucosidase associated with cell wall lignification-based defense responses. For both genes, Hap1 corresponded to significantly higher AUDPC values (indicating higher susceptibility), whereas Hap4 exhibited the strongest resistance.

These results demonstrate that combinations of key genetic loci can be used to accurately predict disease resistance at the seedling stage. Furthermore, population genetic analysis revealed that although ornamental traits such as flower diameter and plant height varied significantly among genetic groups, resistance alleles were widely distributed across existing Taiwanese orchid germplasm, indicating strong potential for resistance breeding.

In summary, this study provides the first chromosome-level genetic resource for disease resistance in Phalaenopsis, enabling the development of precise molecular markers. These markers will assist breeders in early-stage selection of high-quality, disease-resistant orchid varieties, thereby enhancing the international competitiveness of Taiwan’s orchid industry.

Publication:

Chen L.Y., Huang Y.H., Kao C.F., Wu Y.J., Hsieh T.F., Su J.F., Lai Y.H., Lai P.C., Lin Y.Y., Lin T.C., Chen W.H., Chen H.H.*, and Chen S.Y.* 2026. Whole-genome resequencing-based GWAS reveals loci associated with yellow leaf disease resistance in Phalaenopsis. Scientia Horticulturae 359, 114767.

https://www.sciencedirect.com/science/article/pii/S0304423826001603