The Maternal Donor of Chrysanthemum Cultivars Revealed by Comparative Analysis of the Chloroplast Genome

Abstract

Chrysanthemum (Chrysanthemum morifolium Ramat) is an important floricultural crop and medicinal herb. Modern chrysanthemum cultivars have complex genetic backgrounds because of multiple cycles of hybridization, polyploidization, and prolonged cultivation. Understanding the genetic background and hybrid origin of modern chrysanthemum cultivars can provide pivotal information for chrysanthemum genetic improvement and breeding. By now, the origin of cultivated chrysanthemums remains unclear. In this study, 36 common chrysanthemum cultivars from across the world and multiple wild relatives were studied to identify the maternal donor of modern chrysanthemum. Chloroplast (cp) genomes of chrysanthemum cultivars were assembled and compared with those of the wild relatives. The structure of cp genomes was highly conserved among cultivars and wild relatives. Phylogenetic analyses based on the assembled cp genomes showed that all chrysanthemum cultivars grouped together and shared 64 substitutions that were distinct from those of their wild relatives. These results indicated that a diverged lineage of the genus Chrysanthemum, which was most likely an extinct or un-sampled species/population, provided a maternal source for modern cultivars. These findings provide important insights into the origin of chrysanthemum cultivars, and a source of valuable genetic markers for chrysanthemum breeding programs.

Maternal Donor and Genetic Variation of Lagerstroemia indica Cultivars

“…The nrDNA sequence included 25 variable sites and divided the 20 cultivars into 3 clades ( Figure 5 ). The plastome and nrDNA sequences exhibited high variability in crape myrtle cultivars, compared to Chrysanthemum [ 27 ], sweet potato ( Ipomoea batatas ) [ 38 ], and Panax ginseng [ 39 ] cultivars. Compared to the SSR and AFLP markers, the plastome sequence markers show lower genetic variability; however, as maternal markers, it is essential to identify the maternal parentage.…”

“…Plastome and nuclear ribosomal DNA (nrDNA) sequences are popular molecular markers used for plant phylogeny [ 13 , 14 , 15 , 16 , 17 ] and species identification [ 18 , 19 ] because these sequences are conserved across plant species and show variability among interspecies levels. Past studies show that the plastome and nrDNA sequences contain numerous SSRs, indels, and SNPs at the intraspecies levels, which have been used to research the genetic divergence of endangered species [ 20 , 21 ], biogeographical structure [ 22 , 23 , 24 ], gene flow among subpopulations [ 25 , 26 ], and origins and domestication of cultivars [ 27 , 28 , 29 ]. For the Lagerstroemia species, more than 17 species have sequenced the whole chloroplast genome, using these data to infer the phylogeny and divergence time of Lagerstroemia [ 30 ].…”

Characterization of the Chloroplast Genome of Argyranthemum frutescens and a Comparison with Other Species in Anthemideae

“…The coding genes including ndhF , ycf1 , ccsA, and ycf2 genes were found to be relatively divergent as previous studies [ 67 ]. The relatively high variation of ycf1 have been reported in the genus of chrysanthemums [ 5 , 15 ]. Seven highly polymorphic regions in intergenic regions were also detected.…”

“…The complete chloroplast genomes have been demonstrated to be efficient, robust, and authentic in species discrimination and phylogenetic relationship resolution among species [ 5 , 10 , 13 ]. With the decreasing costs of next-generation sequencing, chloroplast genomes have been widely used to resolve the phylogenetic relationships of various plant species, e.g., in Amaranthus L. [ 14 ], chrysanthemums [ 5 , 15 ], and Vitis L. [ 16 ]. Comparative analyses of complete chloroplast genome could help us deepen penetrating insight into the evolution of chloroplast genomes and detect valuable polymorphic loci for phylogenetic analysis in plant [ 17 , 18 ].…”

“…Anthemideae belongs to Asteraceae, which contains 109 genera, including 1740 species [ 15 ]. There are abundant germplasm resources with excellent stress resistance, which is important for plant breeding, e.g., the improvement of cultivated chrysanthemums [ 19 ].…”