Whole-genome resequencing-based GWAS reveals loci associated with yellow leaf disease resistance in Phalaenopsis

• Whole-genome resequencing of 177 Phalaenopsis accessions generated 19.7 million high-quality SNPs. • Two independent inoculation tests quantified YLD resistance by AUDPC with high heritability (H² = 0.85). • DAPC resolved four genetic clusters differing in YLD susceptibility and key ornamental traits. • GWAS integrating single- and multi-locus models identified resistance-associated loci on chromosomes 2, 5, 8, and 16. The orchid industry in Taiwan is dominated by Phalaenopsis spp., which consistently maintain the highest export value among floral crops. However, yellow leaf disease (YLD), caused by the fungal pathogen Fusarium solani , is a major threat to greenhouse-cultivated Phalaenopsis . To investigate the genetic basis of YLD resistance, 174 commercial cultivars and three native species were collected from ten nurseries and subjected to whole-genome resequencing, yielding 19.7 million high-quality single-nucleotide polymorphisms (SNPs). Disease resistance was evaluated in two independent inoculation tests using the area under the disease progress curve (AUDPC). Discriminant analysis of principal components (DAPC) divided the samples into four genetic clusters, which differed significantly in YLD resistance and key ornamental traits such as flower size and plant height. Nevertheless, resistant individuals were distributed across all clusters, suggesting that resistance alleles are broadly present in Taiwanese Phalaenopsis germplasm. Genome-wide association studies (GWAS) based on single-locus models using the complete genotype dataset identified four lead SNPs associated with YLD resistance in both tests. In contrast, multi-locus models applied to the LD-pruned dataset detected five lead SNPs in Test 1, whereas no significant associations were observed in Test 2, likely reflecting differences in phenotypic distribution and statistical power between experiments. These findings provide new insights into the genetic architecture of YLD resistance and establish a foundation for developing molecular markers and precision breeding strategies in Phalaenopsis orchids.