Genetic diversity and population structure analysis of synthetic and bread wheat accessions in Western Siberia

  • Madhav Bhatta
  • Vladimir Shamanin
  • Sergey Shepelev
  • P. Stephen Baenziger
  • Violetta Pozherukova
  • Inna Pototskaya
  • Alexey MorgounovEmail author
Plant Genetics • Original Paper


Recurrent selection and intercrossing between best of the best parents in each generation of breeding cycle resulted in a narrower genetic diversity in elite wheat (Triticum aestivum L.) germplasm. Therefore, we investigated diverse source of 143 synthetic and bread wheat accessions for identifying potentially rich genetic resources for improving the genetic diversity in wheat. This study identified 47,526 genotyping-by-sequencing-derived SNP markers that were nearly evenly distributed across three genomes of wheat. The population structure analysis identified three distinct clusters (Japan synthetics, CIMMYT synthetics, and bread wheat) of wheat genotypes on the basis of type and geographical origin of wheat accessions. Population differentiation using analysis of molecular variance indicated 21% of the total genetic variance among subgroups and the remainder within subgroups. This study also identified that the Japan synthetic group was the most divergent group compared with other subgroups. The genetic diversity comparisons between synthetic and bread wheat lines showed that the gene diversity of synthetic wheat was 33% higher than bread wheat accessions, indicating the potential use of these lines for broadening the genetic diversity of modern wheat cultivars. The results from this study will be helpful in further understanding genomic features of wheat and facilitate their use in wheat breeding programs.


Genotyping-by-sequencing SNP markers Genomic diversity Population differentiation Analysis of molecular variance Triticum aestivum 



The authors would like to acknowledge Jesse Poland lab at Kansas State University for providing the GBS data, and Vikas Belamkar and Sarah Blecha at the University of Nebraska-Lincoln for their help and valuable suggestions.

Author contributions

Conceptualization, A.M. and V.S.; methodology, M.B. and A.M.; validation, M.B. and A.M.; formal analysis, M.B.; investigation, M.B. and A.M.; resources, A.M., V.S., S.S.,V.P., I.P., and P.S.B.; data curation, M.B. and A.M..; writing-original draft preparation, M.B.; writing-review and editing, M.B., A.M., V.S., S.S., V.P., I.P., and P.S.B.; supervision, A.M., V.S., and P.S.B.; project administration, A.M., V.S., and P.S.B. All authors read and approved the final version of the manuscript.

Funding information

The study at Omsk State Agrarian University is supported by the Russian Science Foundation Project No. 16-16-10005. International Maize and Wheat Improvement Center (CIMMYT) at Turkey is supported by CRP WHEAT; Ministry of Food, Agriculture and Livestock of Turkey; Bill and Melinda Gates Foundation; and UK Department for International Development, grant OPP1133199.

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 the authors.

Supplementary material

13353_2019_514_MOESM1_ESM.xlsx (26 kb)
Table S1 (XLSX 25 kb)


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Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2019

Authors and Affiliations

  • Madhav Bhatta
    • 1
  • Vladimir Shamanin
    • 2
  • Sergey Shepelev
    • 2
  • P. Stephen Baenziger
    • 3
  • Violetta Pozherukova
    • 2
  • Inna Pototskaya
    • 2
  • Alexey Morgounov
    • 4
    Email author
  1. 1.Department of AgronomyUniversity of Wisconsin-MadisonMadisonUSA
  2. 2.Omsk State Agrarian UniversityOmskRussia
  3. 3.Department of Agronomy and HorticultureUniversity of NebraskaLincolnUSA
  4. 4.International Maize and Wheat Improvement Center (CIMMYT)AnkaraTurkey

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