Identification of favorable SNP alleles and candidate genes responsible for inflorescence-related traits via GWAS in chrysanthemum

  • Xinran Chong
  • Jiangshuo Su
  • Fan Wang
  • Haibin Wang
  • Aiping Song
  • Zhiyong Guan
  • Weimin Fang
  • Jiafu Jiang
  • Sumei Chen
  • Fadi Chen
  • Fei ZhangEmail author


Key message

81 SNPs were identified for three inflorescence-related traits, in which 15 were highly favorable. Two dCAPS markers were developed for future MAS breeding, and six candidate genes were predicted.


Chrysanthemum is a leading ornamental species worldwide and demonstrates a wealth of morphological variation. Knowledge about the genetic basis of its phenotypic variation for key horticultural traits can contribute to its effective management and genetic improvement. In this study, we conducted a genome-wide association study (GWAS) based on two years of phenotype data and a set of 92,617 single nucleotide polymorphisms (SNPs) using a panel of 107 diverse cut chrysanthemums to dissect the genetic control of three inflorescence-related traits. A total of 81 SNPs were significantly associated with the three inflorescence-related traits (capitulum diameter, number of ray florets and flowering time) in at least one environment, with an individual allele explaining 22.72–38.67% of the phenotypic variation. Fifteen highly favorable alleles were identified for the three target traits by computing the phenotypic effect values for the stable associations detected in 2 year-long trials at each locus. Dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between highly favorable allele numbers and corresponding phenotypic performance were observed. Two highly favorable SNP alleles correlating to flowering time and capitulum diameter were converted to derived cleaved amplified polymorphic sequence (dCAPS) markers to facilitate future breeding. Finally, six putative candidate genes were identified that contribute to flowering time and capitulum diameter. These results serve as a foundation for analyzing the genetic mechanisms underlying important horticultural traits and provide valuable insights into molecular marker-assisted selection (MAS) in chrysanthemum breeding programs.


Chrysanthemum Genome-wide association study Favorable allele Derived cleaved amplified polymorphic sequence (dCAPS) Candidate gene Marker-assisted selection 



Capitulum diameter


Derived cleaved amplified polymorphic sequence


Flowering time


Genome-wide association study


Minor allele frequency


Marker-assisted selection


Mixed linear model


Number of ray florets


Principal component analysis


Specific locus amplified fragment


Single nucleotide polymorphism



This work was financially supported by the National Natural Science Foundation of China (31572152, 31425022).

Author contributions

XC, FC and FZ conceived and designed the project. FC, WF and ZG provided the materials. XC, JS, FW and AS conducted experiments. XC, FZ, JJ and SC analyzed the data and discussed the results. XC and FZ wrote the manuscript. FZ and HW revised the manuscript. All authors read and approved the final manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11103_2019_826_MOESM1_ESM.jpg (1.5 mb)
Fig. S1 The population structure of the 107-entry germplasm panel. (a) The coefficient of variation (CV) value for each K-value, ranging from 1 to 10, and used to determine the true K values of the two groups (K = 2). (b) Population structure analysis. Each entry is represented by a thin vertical bar, and the length of each colored segment in a given vertical bar represents inferred membership in the given number of sub-populations. (c) PCA plots of the three components based on the SNP dataset. (JPG 1568 KB)
11103_2019_826_MOESM2_ESM.jpg (1022 kb)
Fig. S2 Phylogenetic tree of the 107-entry germplasm panel based on 92,617 SNPs. The code by two lower letters represents the entry (JPG 1022 KB)
11103_2019_826_MOESM3_ESM.jpg (137 kb)
Fig. S3 Phenotypic diversity of three quantitative traits for the GWAS of chrysanthemum varieties in two years. The axes of ordinate: Frequency distributions of three inflorescence-related traits of 107-entry germplasm panel. The axes of abscissas: The phenotypic values of the three inflorescence-related traits (CD, NRF and FT). I: 2011 trial; II: 2012 trial (JPG 137 KB)
11103_2019_826_MOESM4_ESM.jpg (69 kb)
Fig. S4 Distribution of pair-wise relative kinship coefficients in the 107-entry germplasm panel (JPG 68 KB)
11103_2019_826_MOESM5_ESM.jpg (438 kb)
Fig. S5 Targeted polymorphisms, restriction sites and sequence information for the 7840-50 dCAPS marker and 7810-165 dCAPS marker. The red letters in brackets are SNP loci. The underlined sequence is the designed primer sequence (JPG 437 KB)
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Supplementary material Table S1 (XLSX 18 KB)
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Supplementary material Table S2 (XLSX 38069 KB)
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Supplementary material Table S3 (XLSX 15 KB)
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Supplementary material Table S4 (DOCX 21 KB)
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Supplementary material Table S5 (DOCX 23 KB)
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Supplementary material Table S6 (XLSX 15 KB)
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Supplementary material Table S7 (DOCX 17 KB)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Xinran Chong
    • 1
  • Jiangshuo Su
    • 1
  • Fan Wang
    • 1
  • Haibin Wang
    • 1
  • Aiping Song
    • 1
  • Zhiyong Guan
    • 1
  • Weimin Fang
    • 1
  • Jiafu Jiang
    • 1
  • Sumei Chen
    • 1
  • Fadi Chen
    • 1
  • Fei Zhang
    • 1
    Email author
  1. 1.College of HorticultureNanjing Agricultural UniversityNanjingChina

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