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Identification and development of a core set of informative genic SNP markers for assaying genetic diversity in Chinese cabbage

  • Peirong Li
  • Tongbing Su
  • Shuancang Yu
  • Huiping Wang
  • Weihong Wang
  • Yangjun Yu
  • Deshuang Zhang
  • Xiuyun Zhao
  • Changlong Wen
  • Fenglan ZhangEmail author
Research Report
  • 13 Downloads

Abstract

Rapid, economical, and reliable genotyping is an important requirement for germplasm analysis and cultivar identification in crop species. Chinese cabbage (Brassica rapa L. subsp. pekinensis (Lour.) Hanelt) originated in China and is now an economically important vegetable crop worldwide, especially in East Asia. In this study, we evaluated 1167 single nucleotide polymorphisms (SNPs) among 166 representative Chinese cabbage inbred lines using a KASP genotyping assay. On the basis of polymorphisms and principal component analysis, we selected 60 core SNPs distributed on all Brassica rapa chromosomes with allele frequencies sufficiently balanced so as to provide adequate information for genetic identification. The core set of SNPs was used for construction of a neighbor-joining dendrogram, in which the 166 inbred lines were clustered into spring, summer, and autumn ecotype groups. Clustering of the ecotype groups was better resolved than that achieved with 1167 and 360 polymorphic SNP datasets. Stability and resolution of the core SNP markers were tested using 178 commercial hybrid Chinese cabbage cultivars to confirm their utility in genetic identification. The set of 60 informative and stable SNP markers showed high discriminatory power and relatively uniform genomic distribution (4–9 markers per chromosome). The SNPs represent a cost-efficient and accurate marker set for germplasm analysis and cultivar identification and are suitable for molecular marker-assisted breeding in Chinese cabbage.

Keywords

Chinese cabbage Genetic diversity Molecular markers Single nucleotide polymorphism (SNP) KASP assays 

Notes

Acknowledgements

This work was supported by grants from the Technology Innovation Program, BAAFS (KJCX20161503), the Key Program of the Beijing Municipal Science and Technology Committee (D171100002517001), the National Key Research and Development Program of China (2017YFD0102004), and the Earmarked Fund for China Agriculture Research System (CARS-23-A-05). We thank Robert McKenzie, PhD, from Liwen Bianji, Edanz Group China (www.liwenbianji.cn/ac), for editing the English text of a draft of this manuscript.

Compliance with ethical standards

Conflict of interest

All authors confirm that they have no conflict of interest.

Supplementary material

13580_2019_138_MOESM1_ESM.jpg (5.9 mb)
Supplementary Fig. 1 Cluster analysis of the 1167 SNP dataset for 166 Chinese cabbage inbred lines. The inbred lines of spring, summer, and autumn ecotype are shown using green, red, and yellow lines, respectively. (JPEG 6084 kb)
13580_2019_138_MOESM2_ESM.jpg (5.9 mb)
Supplementary Fig. 2 Cluster analysis of the 360 SNP dataset for 166 Chinese cabbage inbred lines. The inbred lines of spring, summer, and autumn ecotype are shown using green, red, and yellow lines, respectively. (JPEG 6072 kb)
13580_2019_138_MOESM3_ESM.jpg (7.8 mb)
Supplementary Fig. 3 DNA fingerprinting of 178 Chinese cabbage hybrid cultivars using the core SNP markers. The order of the SNP markers is the same as the order in Table 1. The order of the cultivars is the same as the order in Supplementary Table 2. (JPEG 7984 kb)
13580_2019_138_MOESM4_ESM.docx (19 kb)
Supplementary material 4 (DOCX 18 kb)
13580_2019_138_MOESM5_ESM.docx (36 kb)
Supplementary material 5 (DOCX 36 kb)
13580_2019_138_MOESM6_ESM.docx (28 kb)
Supplementary material 6 (DOCX 28 kb)
13580_2019_138_MOESM7_ESM.docx (26 kb)
Supplementary material 7 (DOCX 26 kb)

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Copyright information

© Korean Society for Horticultural Science 2019

Authors and Affiliations

  • Peirong Li
    • 1
    • 2
    • 3
  • Tongbing Su
    • 1
    • 2
    • 3
  • Shuancang Yu
    • 1
    • 2
    • 3
  • Huiping Wang
    • 1
    • 2
    • 3
  • Weihong Wang
    • 1
    • 2
    • 3
  • Yangjun Yu
    • 1
    • 2
    • 3
  • Deshuang Zhang
    • 1
    • 2
    • 3
  • Xiuyun Zhao
    • 1
    • 2
    • 3
  • Changlong Wen
    • 1
    • 2
    • 3
  • Fenglan Zhang
    • 1
    • 2
    • 3
    Email author
  1. 1.Beijing Vegetable Research Center (BVRC)Beijing Academy of Agricultural and Forestry Sciences (BAAFS)BeijingChina
  2. 2.Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China)Ministry of AgricultureBeijingChina
  3. 3.Beijing Key Laboratory of Vegetable Germplasm ImprovementBeijingChina

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