Insights into the genetic architecture of the reciprocal interspecific hybrids derived from Chrysanthemum dichrum and C. nankingense

Chrysanthemums are versatile ornamental plants, and improving leaf and flower traits is an important breeding objective. Distant hybridization is a powerful method for plant breeding and genetic improvement, whereas the genetic basis in interspecific F₁ progeny of chrysanthemums needs to be better understood for breeding purposes. In this study, the leaf and floral traits of the 273 reciprocal interspecific F₁ hybrids of diploid C. dichrum (YSJ) and C. nankingense (JHN) were analyzed along with their SNP-derived genetic structure to elucidate the influence of differences in genetic background between the parents on the hybrid performance. We then performed a genome-wide association analysis (GWAS) to reveal the investigated traits' genomic loci and candidate genes. Considerable phenotypic variation (8.81% ~ 55.78%) and heterosis with transgressive segregation in both directions were observed in the reciprocal progenies. We observed a higher level of phenotypic variation in JHN × YSJ rather than in YSJ × JHN. Also, a significant reciprocal effect was observed for most examined traits. Based on the SNP data, we separated the hybrid progenies into three groups (I, II, and III), albeit imperfectly dependent on the cross directions, except for some reciprocal hybrids clustering into group II. Group I from YSJ × JHN and Group III from YSJ × JHN differed with contrasting F_ST and π ratios, indicating the genetic changes in the reciprocal populations. The outcome of GWAS via the IIIVmrMLM method detected 339 significant quantitative trait nucleotides (QTNs) and 40 suggestive QTNs, and the phenotypic variation explained by a single QTN ranged from 0.26% to 7.42%. Within 100 kb upstream and downstream of the important QTNs, we discovered 49 known genes and 39 new candidate genes for the investigated leaf and floral traits. Our study provides profound insights into the genetic architecture of reciprocal hybrid progenies of chrysanthemum species, facilitating future breeding activities.