Genetic analysis of anemone-type and single-type inflorescences in chrysanthemum using genotyping-by-sequencing

Flower shape is a key trait of ornamental and commercial importance in breeding programs for chrysanthemum (Chrysanthemum morifolium Ramat.). Understanding the genetic basis of the phenotypic variation seen in inflorescence-related traits will contribute to genetic improvement and to the development of new varieties. In this study, we investigated the genetic determinants of inflorescence traits using an F-1 segregating population derived from a cross between two cultivars with different inflorescence types, 'Puma White' (anemone-shaped inflorescence) and 'Dancer' (single-type inflorescence). Genotyping-by-sequencing identified 26,847 single-nucleotide polymorphisms (SNPs) between 182 F-1 progenies and their parents. A genome-wide association study highlighted 17 SNPs mapping to 15 GBS-tags as being significantly associated with three inflorescence traits: flower type, number of ray florets, and disk flower diameter. No single SNP was associated with flower diameter. These SNP-harboring sequences defined ten candidate genes associated with inflorescence traits. We explored the transcript levels for nine of these in flower buds, disk florets and ray florets using publicly available genome and transcriptome data. These results will provide the genetic and genomic foundation to harness important horticultural traits and explore new avenues in chrysanthemum breeding.