Exploring favorable QTNs and candidate genes for chrysanthemum resistance against black spot disease

Black spot disease (BSD), induced by Alternaria alternata, constitutes a significant menace to chrysanthemum. Identifying resistant germplasm resources underscores its critical importance in chrysanthemum breeding. To elucidate the genetic basis and candidate genes underpinning chrysanthemum BSD resistance, we conducted a multi-locus genome-wide association study (GWAS) using a panel of 152 accessions and 351555 single nucleotide polymorphisms (SNPs) via the 3VmrMLM method. We observed extensive phenotypic variation for the disease severity index (DSI) of BSD, with coefficients of variation ranging from 70.79% to 85.00%, and the broad-sense heritability was calculated at 74.36%. GWAS result detected seventy-one quantitative trait nucleotides (QTNs) and seven QTN-by-environment interactions (QEIs), accounting for 1.53%—7.06% and 0.68%—3.16% of the phenotypic variation, respectively. Eighteen stable QTNs were identified in more than two methods, from which eight highly favorable SNP alleles were extracted for BSD resistance. Furthermore, we observed a significant dosage-pyramiding effect (P < 0.001) among the favorable alleles. Among the genes surrounding the QTNs and QEIs, 12 were homologous to known disease-resistance genes in Arabidopsis, and 14 candidate genes were mined by combining the functional annotation and transcriptomics data, respectively. Our results help better understand the genetic architecture of BSD resistance, and the identified significant SNPs and candidate genes pave the way for future molecular breeding of chrysanthemums with enhanced BSD resistance.