Development and characterization of microsatellite markers based on whole-genome sequences and pathogenicity differentiation of Pyrenophora graminea, the causative agent of barley leaf stripe

  • Erjing Si
  • Yaxiong Meng
  • Xiaole Ma
  • Baochun Li
  • Juncheng Wang
  • Panrong Ren
  • Lirong Yao
  • Ke Yang
  • Yu Zhang
  • Xunwu Shang
  • Huajun WangEmail author


Barley leaf stripe, caused by the fungal pathogen Pyrenophora graminea, is becoming a destructive disease in the Hexi corridor of the Gansu province (China). Knowledge of the genetic diversity, population structure, and specific pathogenicity of P. graminea is essential for barley resistance breeding and efficient control of leaf stripe. In this study, whole-genome sequences of P. graminea were applied to identify microsatellites and develop simple sequence repeat (SSR) markers. These SSR markers were used to examine the genetic diversity and population structure of barley leaf stripe fungus in China. A total of 403 SSR primers were designed and synthesized, and target fragments were amplified by 390 microsatellite markers. These fragments corresponded to 789 alleles (1–5 alleles per locus) in eight strains (average, 2.02 alleles per marker locus). The cluster analysis and population structure were analyzed by means of 100 markers, and a total of 696 alleles were detected from 44 accessions (mean, 6.96 alleles per marker; range, 3–17). The average gene diversity was 0.63, and ranged from 0.11 to 0.92. The polymorphism information content (PIC) ranged from 0.11 to 0.91 with an average of 0.59. The Shannon’s Information Index ranged from 0.29 (for Pgm254 and Pgm337) to 2.64 (for Pgm371), with an average of 1.36. Results of cluster analysis showed that 44 accessions were divided into four clusters. Overall, 44 strains were divided into three subpopulations, comprising 19, 17, and eight strains each. Six isolates were tested for pathogenicity differentiation on 10 barley cultivars. Cultivar Ganpi2 was found to be resistant to all six isolates; nine of 10 cultivars had varied reactions to six isolates. Genome sequencing of P. graminea enabled SSR marker development, and SSR markers are applicable to studies of population genetic structure in P. graminea. We conclude that pathogenicity differentiation exists among the six isolates in the study.


Barley leaf stripe Pyrenophora graminea Microsatellite Genetic diversity Population structure Pathogenicity differentiation 



Simple sequence repeat


Short tandem repeats


Intersimple sequence repeats


Potato dextrose agar

P. graminea

Pyrenophora graminea



This study was supported by Science and Technology Innovation Funds of Gansu Agricutural University-Special funds for discipline construction(GAU-XKJS-2018-082), Science and Technology Innovation Funds of Gansu Agricutural University-Special funds for discipline construction(GAU-XKJS-2018-083). Science and Technology Innovation Funds of Gansu Agricutural University-Scientific research start-up funds for openly-recuited doctors(GSAU-RCZX201706), Science and Technology Innovation Funds of Gansu Agricutural University-Sheng Tongsheng innovation funds (GSAU-STS-1735); (the National Natural Science Foundation of China (CN)(31171558; 31460347), China Agriculture Research System(CARS-05).

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of authors.

Informed consent

Informed consent was obtained from all individual participants included in the study.

Supplementary material

10658_2018_1651_MOESM1_ESM.docx (37 kb)
Table S1 Details of primer sequence, Motif, Tm and amplification length in P. graminea strain QWC. (DOCX 36 kb)
10658_2018_1651_MOESM2_ESM.xlsx (17 kb)
Table S2 Genetic similarity coefficient analysis of 44 strains (XLSX 16 kb)


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Copyright information

© Koninklijke Nederlandse Planteziektenkundige Vereniging 2019

Authors and Affiliations

  • Erjing Si
    • 1
    • 2
  • Yaxiong Meng
    • 1
    • 2
  • Xiaole Ma
    • 1
    • 2
  • Baochun Li
    • 1
    • 3
  • Juncheng Wang
    • 1
    • 2
  • Panrong Ren
    • 1
    • 2
  • Lirong Yao
    • 1
    • 2
  • Ke Yang
    • 1
    • 2
  • Yu Zhang
    • 4
  • Xunwu Shang
    • 1
  • Huajun Wang
    • 1
    • 2
    Email author
  1. 1.Gansu Provincial Key Laboratory of Aridland and Crop Science /Gansu Key Laboratory of Crop Improvement & Germplasm EnhancementLanzhouChina
  2. 2.College of AgronomyGansu Agricultural UniversityLanzhouChina
  3. 3.College of Life Science and TechnologyGansu Agricultural UniversityLanzhouChina
  4. 4.Gansu Plant Seed Administrative StationLanzhouChina

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