Construction of an interspecific genetic map and multiyear phenotype QTL mapping of the pentaploid Chrysanthemum

Chrysanthemum morifolium is highly regarded as one of the most esteemed traditional floral specimens globally and is valued for both its aesthetic beauty and cultural significance. The ground-cover chrysanthemum represents a crucial subgroup of C. morifolium , contributing significantly to landscaping, ecological restoration, and rural tourism. However, owing to its complex genetic background and diverse ploidy levels, coupled with the lack of high-quality polyploid reference genomes, the precise mapping of key candidate genes that control important traits presents considerable challenges. Here, we established a novel pentaploid interspecific hybrid population of chrysanthemum comprising 764 F 1 progeny individuals. We subsequently conducted a thorough investigation and analysis of 37 critical phenotypic traits over a three-year period. Additionally, we employed genotyping-by-sequencing (GBS) to genotype the parental lines, ‘FH’ ( C. morifolium , female) and ‘CY’ ( C. yantaiense , male), as well as 201 individuals from the F 1 mapping population. This enabled the construction of HA (maternal), AH (paternal), and HH linkage genetic maps, resulting in average marker distances of 1.54, 1.61, and 4.45 cM, respectively. Moreover, we successfully identified 66 main-effect quantitative trait loci (QTLs) with a high degree of confidence, which collectively accounted for 10.08%–73.86% of the phenotypic variation. Finally, we developed and validated 15 kompetitive allele-specific PCR (KASP) markers that are tightly linked to these QTLs and are significantly associated with nine important horticultural traits. Overall, the findings of this study significantly enhance the understanding of the genetic basis underlying key ornamental traits in chrysanthemum and have the potential to facilitate marker-assisted breeding and the exploration of candidate genes in this species.