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Original Research ARTICLE Provisionally accepted The full-text will be published soon. Notify me

Front. Genet. | doi: 10.3389/fgene.2019.01224

GWAS assisted genomic prediction to predict resistance to Septoria tritici blotch in Nordic winter wheat at seedling stage

  • 1Department of Plant Breeding, Faculty of Landscape Architecture, Horticulture and Crop Production Science, Swedish University of Agricultural Sciences, Sweden
  • 2Lithuanian Research Centre for Agriculture and Forestry, Lithuania
  • 3NordGen, Sweden

Septoria tritici blotch (STB) disease caused by Zymoseptoria tritici is one of the most damaging diseases of wheat causing significant yield losses worldwide. Identification and employment of resistant germplasm is the most cost-effective method to control STB. In this study, we characterized seedling stage resistance to STB in 175 winter wheat landraces and old cultivars of Nordic origin. The study revealed significant (p<0.05) phenotypic differences in STB severity in the germplasm. Genome-wide association analysis (GWAS) using five different algorithms identified ten significant markers on five chromosomes. Six markers were localized within a region of 2 cM that contained seven candidate genes on chromosome 1B. Genomic prediction (GP) analysis resulted in a model with an accuracy of 0.47. To further improve the prediction efficiency, significant markers identified by GWAS were included as fixed effects in the GP model. Depending on the number of fixed effect markers, the prediction accuracy improved from 0.47 (without fixed effects) to 0.62 (all non-redundant GWAS markers as fixed effects) respectively. The resistant genotypes and SNP markers identified in the present study will serve as a valuable resource for future breeding for STB resistance in wheat. The results also highlight the benefits of integrating GWAS with GP to further improve the accuracy of GP.

Keywords: GWAS, GWAS - genome-wide association study, genomic prediction (GP), genomic selection (GS), wheat, Septoria tritici blotch (STB), QTL

Received: 01 Jun 2019; Accepted: 05 Nov 2019.

Copyright: © 2019 Odilbekov, Armoniene, Koc, Svensson and Chawade. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Dr. Aakash Chawade, Department of Plant Breeding, Faculty of Landscape Architecture, Horticulture and Crop Production Science, Swedish University of Agricultural Sciences, Alnarp, 23053, Sweden, aakash.chawade@slu.se