Plant Molecular Biology Reporter

, Volume 37, Issue 1–2, pp 63–73 | Cite as

Application of High-Throughput Sequencing to Evaluate the Genetic Diversity Among Wild Apple Species Indigenous to Shandong, China, and Introduced Cultivars

  • Yuansheng Chang
  • Ping He
  • Haibo Wang
  • Huifeng Li
  • Sen Wang
  • Linguang LiEmail author
Original Paper


The Taiyi mountainous region of Shandong province in eastern China has an abundance of wild Malus species. We evaluated the genetic diversity of 88 Malus accessions (45 Asian apple cultivars, 10 American apple cultivars, 12 European apple cultivars, 19 Chinese wild apples, and two apple cultivars with unknown origins) based on single-nucleotide polymorphism (SNP) markers. A total of 38,364 SNPs were obtained with an average of 2256 SNPs per chromosome. The average of the polymorphism information content (PIC), gene diversity, and allele frequency for SNPs was 0.268, 0.306, and 0.364, respectively. A circular phylogenetic tree constructed based on SNP data revealed that the 88 Malus accessions could be divided into three groups. However, a population structure analysis suggested the 88 Malus accessions could be divided into four groups. A principal component analysis (PCA) revealed some population stratification. The first three PCs accounted for 41.62% of the population-wide SNP variation, with PC1 accounting for 33.9%. Moreover, the kinship values of the 88 Malus accessions ranged from 0 to 2.36, with 96.42% of the kinship values between 0 and 0.2. A phylogenetic tree and a PCA indicated the Chinese wild apples widely distributed among the cultivated apples had a diverse genetic background. Characterizing the genetic relationships between cultivated apples and Chinese wild apples is essential for increasing the genetic diversity of the germplasms used by apple breeders.


Malus Genetic diversity SLAF-seq Cluster analysis 



We would like to thank China agriculture scientific research institutions and agriculture university supplying the experimental materials. We also would like to thank Liwen Bianji, Edanz Editing China (, for editing the English text of a draft of this manuscript.

Funding Information

This project was supported by the Youth Fund for Shandong Academy of Agriculture Sciences (2016YQN30), the Agricultural Innovation Project for Shandong Academy of Agriculture Sciences (CXGC2016B07), and the Earmarked Fund for China Agriculture Research System (CARS-28).

Supplementary material

11105_2019_1138_MOESM1_ESM.xlsx (62 kb)
ESM 1 (XLSX 62 kb)


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  • Yuansheng Chang
    • 1
  • Ping He
    • 1
  • Haibo Wang
    • 1
  • Huifeng Li
    • 1
  • Sen Wang
    • 1
  • Linguang Li
    • 1
    Email author
  1. 1.Shandong Institute of PomologyTai’anPeople’s Republic of China

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