title: A SNP-Enabled Assessment of Genetic Diversity, Evolutionary Relationships and the Identification of Candidate Genes in Chrysanthemum.
abstract: Varieties of the economically important ornamental species chrysanthemum have been bred to fit a number of market niches, but the genetic basis and evolutionary relationships among various cultivated types are poorly understood. Here, a DNA marker-based analysis of 199 chrysanthemum entries representing each of the five cultivated types is presented. A set of >90,000 single nucleotide polymorphisms (SNPs) associated with a minor allele frequency of at least 5% was defined, and used to perform a phylogenetic analysis which corresponded well with the phenotypic classification. The analysis revealed that the small-flowered types, spray cut chrysanthemum (SCC) and potted and ground chrysanthemum (PGC), are more closely related to the wild progenitor species (WC) than are the large-flowered ones, disbud cut chrysanthemum (DCC) and traditional chrysanthemum (TC); and the PGC type was closest. Some 550 genetic regions appeared to have experienced selection in the separation of potted and ground-cover types from disbud cut types, and that between potted and ground-cover types from traditional types. A genome-wide association analysis revealed that seven SNPs lying within six genes were predictive of three important traits (ray floret type, cultivated type and flower shape), but no association with flower color was detected. The study has provided a number of novel insights into evolutionary relationships, the population structure and the genetic basis of some key ornamental traits.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Xinran
authors.initials: X
authors.lastname: Chong
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Yangyang
authors.initials: Y
authors.lastname: Wu
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Xiaodong
authors.initials: X
authors.lastname: Yang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Nan
authors.initials: N
authors.lastname: Zhao
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Haibin
authors.initials: H
authors.lastname: Wang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Guan
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Weimin
authors.initials: W
authors.lastname: Fang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing, China.
authors.forename: Fadi
authors.initials: F
authors.lastname: Chen
mesh_terms: D001947:Breeding; D031202:Chrysanthemum / Q000235:genetics*; D019143:Evolution, Molecular; D035264:Flowers / Q000235:genetics*; D005787:Gene Frequency; D014644:Genetic Variation; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D005838:Genotype; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
keywords: association analysis; chrysanthemum; evolutionary relationship; genetic differentiation; single nucleotide polymorphisms