Genetic loci and functional genes underlying black spot disease resistance across multiple environments in chrysanthemum

Abstract

Black spot disease (BSD), caused by Alternaria alternata, is a devastating threat to the chrysanthemum industry, yet its genetic basis remains largely elusive. The present study aimed to decipher the genetic architecture of chrysanthemum BSD resistance and to discover genetic loci and candidate genes using genome-wide association studies (GWAS) in a biparental F1 population (n = 164). Phenotypic evaluations of BSD resistance were conducted using both multi-stage detached-leaf assays and seedling-stage in vivo inoculations. The disease severity index (DSI) exhibited wide coefficient of variation (CV: 26.21%–54.84%) and high broad-sense heritability (0.71–0.95), with significant transgressive segregation observed in the F1 progeny. 375 865 high-quality SNPs-based GWAS identified 220 quantitative trait nucleotides (QTNs) and 36 QTN-by-environment interactions (QEIs), explaining up to 7.39% and 3.46% of the phenotypic variance, respectively. Among 26 stable QTNs, 17 favorable alleles displayed significant additive effects and a clear dosage-pyramiding effect (P < 0.001). By integrating functional annotation with transcriptome profiling, 34 candidate genes involved in immune defense were identified within the candidate intervals. Notably, three key candidate genes, CmABF1, CmSINAT3, and CmLTPG1, were validated as positive regulators of BSD resistance through transient overexpression and silencing assays. The research findings provide crucial genetic resources for the molecular improvement of resistance to BSD in chrysanthemums.