Genome-wide association study uncovers the genetic architecture and genomic selection of salt tolerance in chrysanthemum

Abstract

Soil salinization has emerged as a critical abiotic constraint in chrysanthemum cultivation; however, the genetic basis and candidate genes of salt tolerance remain largely unexplored. In this work, we performed a comprehensive assessment of genetic variation of 119 chrysanthemum accessions in response to salt stress by integrating mathematical methods, genome-wide association study (GWAS), and gene expression analysis. Substantial variation was observed for 13 salt tolerance traits relevant to injury symptoms, plant height, biomass, and root traits across two environments. Based on 320,407 high-quality SNPs, 171 quantitative trait nucleotides (QTNs) were identified in single-environment, while 174 QTNs and 110 QTN-by-environment interactions (QEIs) were detected in multi-environment to be significantly associated with these salt tolerance traits. A significant dosage-pyramiding effect was observed for favorable alleles (R  2 = 0.551, P = 4.2e-22) linked to the salt tolerance index, D value. Candidate genes around the GWAS loci were predicted, and nine key candidate genes in response to salt stress were discovered via expression analysis. Functional validation via transient overexpression assays revealed two novel salt tolerance regulators, CmMYB9 and CmABCG21. Furthermore, we developed a preliminary genomic selection model with moderate prediction accuracy for salt tolerance and found that genomic selection using all SNPs outperformed models based on GWAS-selected SNP subsets. This work presents the first GWAS-based investigation of the genetic architecture and key candidate genes underlying salt tolerance in chrysanthemum, thereby providing valuable insights for future molecular improvement and mechanistic research.