Abstract
Chrysanthemum, a globally renowned economic crop, primarily relies on vegetative propagation methods such as cutting for commercial cultivation. However, certain varieties with exceptional ornamental qualities often encounter difficulties in widespread adoption due to poor rooting ability and suboptimal root quality. The genetic underpinnings of rooting ability in chrysanthemum cuttings have remained largely unexplored. This study marks a significant advancement in this field. By evaluating 11 rooting traits across a diverse panel of 188 chrysanthemum genotypes, we found that spray cut chrysanthemums exhibit superior rooting ability compared to other cultivated types and wild species. Selective sweep analysis identified 534 selected genomic regions potentially linked to rooting traits during the domestication and improvement of chrysanthemums. Genome-wide association studies (GWAS) conducted on four key rooting traits - total root length, root surface area, average root diameter, and number of roots, using multiple models discovered 71 significant SNPs and 98 candidate genes, including 21 differentially expressed genes identified via transcriptomic sequencing. A weighted gene co-expression network analysis further revealed two key modules (yellow and lightyellow) related to rooting traits. By integrating GWAS, transcriptomic data, and functional verification, we pinpointed the candidate gene CmNRAMP3 as a negative regulator of rooting ability. These findings substantially enrich our understanding of the genetic mechanisms underlying rooting ability in chrysanthemum cuttings and provide a promising gene pool for improving rooting traits in future breeding programs.