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GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage.
Front Genet. 2019; 10:1224.FG

Abstract

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.

Authors+Show Affiliations

Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden. Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry (LAMMC), Akademija, Lithuania.Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.Nordic Genetic Resource Centre, Alnarp, Sweden.Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31850073

Citation

Odilbekov, Firuz, et al. "GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage." Frontiers in Genetics, vol. 10, 2019, p. 1224.
Odilbekov F, Armoniené R, Koc A, et al. GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage. Front Genet. 2019;10:1224.
Odilbekov, F., Armoniené, R., Koc, A., Svensson, J., & Chawade, A. (2019). GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage. Frontiers in Genetics, 10, 1224. https://doi.org/10.3389/fgene.2019.01224
Odilbekov F, et al. GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage. Front Genet. 2019;10:1224. PubMed PMID: 31850073.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage. AU - Odilbekov,Firuz, AU - Armoniené,Rita, AU - Koc,Alexander, AU - Svensson,Jan, AU - Chawade,Aakash, Y1 - 2019/11/26/ PY - 2019/06/01/received PY - 2019/11/05/accepted PY - 2019/12/19/entrez PY - 2019/12/19/pubmed PY - 2019/12/19/medline KW - GWAS - genome-wide association study KW - Quantitative trait loci (QTL) KW - Septoria tritici blotch (STB) KW - genomic prediction (GP) KW - genomic selection (GS) KW - wheat SP - 1224 EP - 1224 JF - Frontiers in genetics JO - Front Genet VL - 10 N2 - 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. SN - 1664-8021 UR - https://www.unboundmedicine.com/medline/citation/31850073/GWAS_Assisted_Genomic_Prediction_to_Predict_Resistance_to_Septoria_Tritici_Blotch_in_Nordic_Winter_Wheat_at_Seedling_Stage_ L2 - https://doi.org/10.3389/fgene.2019.01224 DB - PRIME DP - Unbound Medicine ER -
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