GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage
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 seedli...
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Frontiers Media S.A.
2019-11-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2019.01224/full |
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| author | Firuz Odilbekov Rita Armoniené Rita Armoniené Alexander Koc Jan Svensson Aakash Chawade |
| author_facet | Firuz Odilbekov Rita Armoniené Rita Armoniené Alexander Koc Jan Svensson Aakash Chawade |
| author_sort | Firuz Odilbekov |
| collection | DOAJ |
| description | 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 single-nucleotide polymorphism (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. |
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| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-13T07:41:23Z |
| publishDate | 2019-11-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj.art-e707bd9460b24a7c98889cc5ade8b3fc2022-12-21T23:54:58ZengFrontiers Media S.A.Frontiers in Genetics1664-80212019-11-011010.3389/fgene.2019.01224476082GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling StageFiruz Odilbekov0Rita Armoniené1Rita Armoniené2Alexander Koc3Jan Svensson4Aakash Chawade5Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SwedenDepartment of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SwedenInstitute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Akademija, LithuaniaDepartment of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SwedenNordic Genetic Resource Centre, Alnarp, SwedenDepartment of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SwedenSeptoria 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 single-nucleotide polymorphism (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.https://www.frontiersin.org/article/10.3389/fgene.2019.01224/fullGWAS - genome-wide association studygenomic prediction (GP)genomic selection (GS)wheatSeptoria tritici blotch (STB)Quantitative trait loci (QTL) |
| spellingShingle | Firuz Odilbekov Rita Armoniené Rita Armoniené Alexander Koc Jan Svensson Aakash Chawade GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage Frontiers in Genetics GWAS - genome-wide association study genomic prediction (GP) genomic selection (GS) wheat Septoria tritici blotch (STB) Quantitative trait loci (QTL) |
| title | GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage |
| title_full | GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage |
| title_fullStr | GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage |
| title_full_unstemmed | GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage |
| title_short | GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage |
| title_sort | gwas assisted genomic prediction to predict resistance to septoria tritici blotch in nordic winter wheat at seedling stage |
| topic | GWAS - genome-wide association study genomic prediction (GP) genomic selection (GS) wheat Septoria tritici blotch (STB) Quantitative trait loci (QTL) |
| url | https://www.frontiersin.org/article/10.3389/fgene.2019.01224/full |
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