Genetic and QTL analysis of flower color and pigments in small-flowered chrysanthemum based on high-density genetic map

Abstract

Flower color is an important trait for ornamental plants and is determined by the pigments. Variations in the flower color of chrysanthemum are abundant, which is an important feature related to its ornamental and commercial value. However, few reports have elucidated the inheritance of the flower color and pigmentation of chrysanthemum. In this study, an F1 hybrid population, including 319 hybrids of small-flowered chrysanthemum cultivars with different flower color, was constructed. The genetic variation rules for some color and pigment-related traits were discussed based on major gene and polygene mixed inheritance analyses. Both the total anthocyanin and carotenoid contents were controlled by 2 pairs of additive dominant major genes and the heritability of the major genes was 70.44% and 86.03%, respectively. Based on the high-density genetic map constructed for the hybrid population, QTL analysis for the above traits was carried out by using the interval mapping method. A total of 25 related QTLs and 517 closely linked markers were detected, including 3 QTLs controlling the total anthocyanin content and 2 QTLs controlling the total carotenoid content, all of which were major QTLs. Furthermore, 17 unigenes related to pigments were identified via BLAST searches with Chrysanthemum nankingense genome. For such genes, the collinearity was observed in four chromosome level genomes, including three genomes of the genus Chrysanthemum and the first genome of cultivated chrysanthemum. The results lay a foundation for in-depth exploration of flower color and pigmentation in chrysanthemum and provide a reference for future research in other ornamental plants.