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Genome-wide association study and genomic prediction of Fusarium ear rot resistance in tropical maize germplasm

Creator: Yubo Liu
Creator: Guanghui Hu
Creator: Ao Zhang
Creator: Loladze, A.
Creator: Yingxiong Hu
Creator: Hui Wang
Creator: Jingtao Qu
Creator: Zhang, X.
Creator: Olsen, M.
Creator: San Vicente, F.M.
Creator: Crossa, J.
Creator: Feng Lin
Creator: Prasanna, B.M.
Year: 2020
URI: https://hdl.handle.net/10883/21045
Language: English
Publisher: Elsevier
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose
Type: Article
Place of Publication: Netherlands
Volume: In press
DOI: 10.1016/j.cj.2020.08.008
Keywords: Fusarium Ear Rot
Keywords: Genome-Wide Association Study
Keywords: Genomic Prediction
Keywords: Genomic Selection
Description: Fusarium ear rot (FER) is a destructive maize fungal disease worldwide. In this study, three tropical maize populations consisting of 874 inbred lines were used to perform genome-wide association study (GWAS) and genomic prediction (GP) analyses of FER resistance. Broad phenotypic variation and high heritability for FER were observed, although it was highly influenced by large genotype-by-environment interactions. In the 874 inbred lines, GWAS with general linear model (GLM) identified 3034 single-nucleotide polymorphisms (SNPs) significantly associated with FER resistance at the P-value threshold of 1 × 10−5, the average phenotypic variation explained (PVE) by these associations was 3% with a range from 2.33% to 6.92%, and 49 of these associations had PVE values greater than 5%. The GWAS analysis with mixed linear model (MLM) identified 19 significantly associated SNPs at the P-value threshold of 1 × 10−4, the average PVE of these associations was 1.60% with a range from 1.39% to 2.04%. Within each of the three populations, the number of significantly associated SNPs identified by GLM and MLM ranged from 25 to 41, and from 5 to 22, respectively. Overlapping SNP associations across populations were rare. A few stable genomic regions conferring FER resistance were identified, which located in bins 3.04/05, 7.02/04, 9.00/01, 9.04, 9.06/07, and 10.03/04. The genomic regions in bins 9.00/01 and 9.04 are new. GP produced moderate accuracies with genome-wide markers, and relatively high accuracies with SNP associations detected from GWAS. Moderate prediction accuracies were observed when the training and validation sets were closely related. These results implied that FER resistance in maize is controlled by minor QTL with small effects, and highly influenced by the genetic background of the populations studied. Genomic selection (GS) by incorporating SNP associations detected from GWAS is a promising tool for improving FER resistance in maize.
Agrovoc: MAIZE
Agrovoc: FUSARIUM
Agrovoc: GENOMICS
Agrovoc: MARKER-ASSISTED SELECTION
ISSN: 2214-5141
Journal: The Crop Journal


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  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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