, 214:200 | Cite as

Genome-wide association study reveals favorable alleles associated with common bunt resistance in synthetic hexaploid wheat

  • Madhav Bhatta
  • Alexey Morgounov
  • Vikas Belamkar
  • Aysel Yorgancılar
  • P. Stephen BaenzigerEmail author


Genetic resistance to common bunt is a cost-effective, environmentally friendly, and sustainable approach to controlling the disease. To date, 16 race specific common bunt resistance genes (Bt1-Bt15 and Btp) have been reported in wheat. However, a limited number have been mapped and few markers have been identified, which limits the usage of molecular markers in a marker-assisted breeding program. A total of 125 synthetic hexaploid wheats (SHWs) were evaluated for reactions to a mixture of common bunt races under field conditions in Turkey in 2016 and 2017. The objectives of this study were to identify common bunt resistant genotypes, identify genomic regions conferring resistance to common bunt using 35,798 genotyping-by-sequencing derived single nucleotide polymorphisms (SNPs), and investigate the significant SNPs present within genes using the functional annotations of the underlying genes. We found 29 resistant SHWs that can be used in wheat breeding. The genome-wide association study identified 15 SNPs associated with common bunt resistance and a haplotype block comprising three SNPs in perfect linkage disequilibrium. Five of them were novel and were located on chromosomes 2A, 3D, and 4A. Furthermore, seven of the 15 SNPs were found within genes and had annotations suggesting potential role in disease resistance. This study identified several favorable alleles that decreased common bunt incidence up to 26% in SHWs. These resistant SHWs and candidate genomic regions controlling common bunt resistance will be useful for wheat genetic improvement and could assist in further understanding of the genetic architecture of common bunt resistance.


Genetic resistance Genomic regions Genotyping-by-sequencing Molecular markers Resistance genes Wheat genetic improvement 



Synthetic hexaploid wheat




Marker-trait association


Best linear unbiased predictor


Genome-wide association study


Minor allele frequency

Q–Q plot

Quantile–quantile plot


Single nucleotide polymorphism


International Wheat and Genome Sequencing Consortium



This work was funded by the Monsanto Beachell-Borlaug International Scholarship Program. This project is a collaborative effort between the University of Nebraska-Lincoln, Lincoln, USA, the International Maize and Wheat Improvement Center (CIMMYT) in Turkey (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), and Omsk State Agrarian University (supported by the Russian Science Foundation project No. 16-16-10005). We would like to thank CIMMYT-Turkey for providing seeds of synthetic hexaploid wheat and Dr. Jesse Poland for providing the GBS data. We would like to acknowledge CIMMYT-Turkey staffs including Dr. Amer Dabadat, Dr. Gul Erginbas-Orakci, Adem Urglu, Ibrahim Ozturk, and the Transitional Zone Agricultural Research Institute, Eskisehir, Turkey for providing experimental station and assisted on managing common bunt experiments. Partial funding for P.S. Baenziger is from Hatch project NEB-22-328, AFRI/2011-68002-30029, the USDA National Institute of Food and Agriculture as part of the International Wheat Yield Partnership award number 2017-67007-25939, the CERES Trust Organic Research Initiative, and USDA under Agreement No. 59-0790-4-092 which is a cooperative project with the U.S. Wheat and Barley Scab Initiative. Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the authors and do not necessarily reflect the view of the USDA. Cooperative investigations of the Nebraska Agric. Res. Div., Univ. of Nebraska, and USDA-ARS.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interests.

Supplementary material

10681_2018_2282_MOESM1_ESM.xlsx (5.3 mb)
Supplementary material 1 (XLSX 5435 kb)
10681_2018_2282_MOESM2_ESM.docx (297 kb)
Supplementary material 2 (DOCX 296 kb)


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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.Department of Agronomy and HorticultureUniversity of Nebraska-LincolnLincolnUSA
  2. 2.International Maize and Wheat Improvement Center (CIMMYT)AnkaraTurkey
  3. 3.Transitional Zone Agricultural Research InstituteEskisehirTurkey

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