title: Genetic diversity, population structure and association analysis in cut chrysanthemum (Chrysanthemum morifolium Ramat.).
abstract: Characterizing the genetic diversity present in a working set of plant germplasm can contribute to its effective management and genetic improvement. The cut flower chrysanthemum (Chrysanthemum morifolium Ramat.) is an economically important ornamental species. With the repeated germplasm exchange and intensive breeding activities, it remains a major task in genetic research. The purpose of the present study was to characterize the genetic diversity and the population structure of a worldwide collection of 159 varieties, and to apply an association mapping approach to identify DNA-based markers linked to five plant architecture traits and six inflorescence traits. The genotyping demonstrated that there was no lack of genetic diversity in the collection and that pair-wise kinship values were relatively low. The clustering based on a Bayesian model of population structure did not reflect known variation in either provenance or inflorescence type. A principal coordinate analysis was, however, able to discriminate most of the varieties according to both of these criteria. About 1 in 100 marker pairs exhibited a degree of linkage disequilibrium. The association analysis identified a number of markers putatively linked to one or more of the traits. Some of these associations were robust over two seasons. The findings provide an in-depth understanding of genetic diversity and population structure present in cut flower chrysanthemum varieties, and an insight into the genetic control of plant architecture and inflorescence-related traits.
authors.affiliation: College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
authors.forename: Pirui
authors.initials: P
authors.lastname: Li
authors.affiliation: College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
authors.forename: Fei
authors.initials: F
authors.lastname: Zhang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
authors.forename: Sumei
authors.initials: S
authors.lastname: Chen
authors.affiliation: College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
authors.forename: Jiafu
authors.initials: J
authors.lastname: Jiang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
authors.forename: Haibin
authors.initials: H
authors.lastname: Wang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
authors.forename: Jiangshuo
authors.initials: J
authors.lastname: Su
authors.affiliation: College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
authors.forename: Weimin
authors.initials: W
authors.lastname: Fang
authors.affiliation: College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China.
authors.forename: Zhiyong
authors.initials: Z
authors.lastname: Guan
authors.affiliation: College of Horticulture, Nanjing Agricultural University, No. 1, Weigang, Nanjing, 210095, Jiangsu, People's Republic of China. chenfd@njau.edu.cn.
authors.forename: Fadi
authors.initials: F
authors.lastname: Chen
mesh_terms: D031202:Chrysanthemum / Q000145:classification / Q000235:genetics*; D014644:Genetic Variation; D055106:Genome-Wide Association Study; D005838:Genotype; D015810:Linkage Disequilibrium; D010641:Phenotype; D040641:Quantitative Trait Loci
keywords: Association analysis; Chrysanthemum; Linkage disequilibrium; Molecular marker; Population structure