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Genetic dissection of quantitative resistance to common rust (Puccinia sorghi) in tropical maize (Zea mays L.) by combined genome-wide association study, linkage mapping, and genomic prediction

Creator: Jiaojiao Ren
Creator: Zhimin Li
Creator: Penghao Wu
Creator: Ao Zhang
Creator: Yubo Liu
Creator: Guanghui Hu
Creator: Shiliang Cao
Creator: Jingtao Qu
Creator: Dhliwayo, T.
Creator: Hongjian Zheng
Creator: Olsen, M.
Creator: Prasanna, B.M.
Creator: San Vicente, F.M.
Creator: Zhang, X.
Year: 2021
URI: https://hdl.handle.net/10883/21593
Language: English
Publisher: Frontiers
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: Switzerland
Volume: 12
DOI: 10.3389/fpls.2021.692205
Keywords: Common Rust
Keywords: Quantitative Resistance
Keywords: Genome-Wide Association Study
Keywords: Linkage Mapping
Keywords: Genomic Prediction
Description: Common rust is one of the major foliar diseases in maize, leading to significant grain yield losses and poor grain quality. To dissect the genetic architecture of common rust resistance, a genome-wide association study (GWAS) panel and a bi-parental doubled haploid (DH) population, DH1, were used to perform GWAS and linkage mapping analyses. The GWAS results revealed six single-nucleotide polymorphisms (SNPs) significantly associated with quantitative resistance of common rust at a very stringent threshold of P-value 3.70 × 10–6 at bins 1.05, 1.10, 3.04, 3.05, 4.08, and 10.04. Linkage mapping identified five quantitative trait loci (QTL) at bins 1.03, 2.06, 4.08, 7.03, and 9.00. The phenotypic variation explained (PVE) value of each QTL ranged from 5.40 to 12.45%, accounting for the total PVE value of 40.67%. Joint GWAS and linkage mapping analyses identified a stable genomic region located at bin 4.08. Five significant SNPs were only identified by GWAS, and four QTL were only detected by linkage mapping. The significantly associated SNP of S10_95231291 detected in the GWAS analysis was first reported. The linkage mapping analysis detected two new QTL on chromosomes 7 and 10. The major QTL on chromosome 7 in the region between 144,567,253 and 149,717,562 bp had the largest PVE value of 12.45%. Four candidate genes of GRMZM2G328500, GRMZM2G162250, GRMZM2G114893, and GRMZM2G138949 were identified, which played important roles in the response of stress resilience and the regulation of plant growth and development. Genomic prediction (GP) accuracies observed in the GWAS panel and DH1 population were 0.61 and 0.51, respectively. This study provided new insight into the genetic architecture of quantitative resistance of common rust. In tropical maize, common rust could be improved by pyramiding the new sources of quantitative resistance through marker-assisted selection (MAS) or genomic selection (GS), rather than the implementation of MAS for the single dominant race-specific resistance gene.
Agrovoc: MAIZE
Agrovoc: RUSTS
Agrovoc: GENOMES
Agrovoc: CHROMOSOME MAPPING
Related Datasets: https://hdl.handle.net/11529/10548575
Related Datasets: https://figshare.com/collections/Genetic_Dissection_of_Quantitative_Resistance_to_Common_Rust_Puccinia_sorghi_in_Tropical_Maize_Zea_mays_L_by_Combined_Genome-Wide_Association_Study_Linkage_Mapping_and_Genomic_Prediction/5495559
ISSN: 1664-462X
Journal: Frontiers in Plant Science
Article number: 692205


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

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