Multi-locus GWAS uncovers favorable alleles and candidate genes underlying water stress response in chrysanthemum

Drought is one of the most serious abiotic stresses limiting plant productivity and becomes increasingly extreme worldwide due to the ongoing deterioration of the global climate. Chrysanthemum (Chrysanthemum morifolium Ramat.), one of the four most popular cut flowers in the world, is sensitive to water-limited environment. However, the genetic basis and causal genes underlying drought tolerance (DT) remain largely unknown. In this research, multi-locus GWAS was employed to detect the genetic loci and candidate genes for DT in a diverse panel of 200 cut chrysanthemum accessions that were genotyped with 330,710 high-quality SNPs. As a result, 43 stable QTNs in single-environment analysis, 18 stable QTNs and 115 QEIs in multiple-environments analysis were identified via the 3VmrMLM method. Among the genes around stable QTNs and QEIs, eleven were homologous to known DT regulatory genes in other plants such as WRKY57, MYB121, GH3.6. In addition, seven candidate genes were predicted to be associated with DT related traits by combing the functional annotation, transcriptomics data and quantitative real-time PCR. More importantly, four drought-tolerant cultivars harboring favorable alleles were identified as pre-bred material to improve tolerance of cultivated chrysanthemum. These findings provide robust insights into the genetic architecture of DT and offer valuable prospects for the molecular breeding of chrysanthemum.