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Genetic architecture of maize chlorotic mottle virus and maize lethal necrosis through GWAS, linkage analysis and genomic prediction in tropical maize germplasm

Author: Sitonik, C.
Author: Mahabaleswara, S.L.
Author: Beyene, Y.
Author: Olsen, M.
Author: Makumbi, D.
Author: Kiplagat, O.
Author: Das, B.
Author: Jumbo, M.B.
Author: Mugo, S.
Author: Crossa, J.
Author: Amsal Tesfaye Tarekegne
Author: Prasanna, B.M.
Author: Gowda, M.
Year: 2019
ISSN: ISSN: 0040-5752
ISSN: ISSN: 1432-2242
URI: https://hdl.handle.net/10883/20133
Abstract: Maize lethal necrosis (MLN) is a serious threat to the food security of maize-growing smallholders in sub-Saharan Africa. The ability of the maize chlorotic mottle virus (MCMV) to interact with other members of the Potyviridae causes severe yield losses in the form of MLN. The objective of the present study was to gain insights and validate the genetic architecture of resistance to MCMV and MLN in maize. We applied linkage mapping to three doubled-haploid populations and a genome-wide association study (GWAS) on 380 diverse maize lines. For all the populations, phenotypic variation for MCMV and MLN was significant, and heritability was moderate to high. Linkage mapping revealed 13 quantitative trait loci (QTLs) for MCMV resistance and 12 QTLs conferring MLN resistance. One major-effect QTL, qMCMV3-108/qMLN3-108, was consistent across populations for both MCMV and MLN resistance. Joint linkage association mapping (JLAM) revealed 18 and 21 main-effect QTLs for MCMV and MLN resistance, respectively. Another major-effect QTL, qMCMV6-17/qMLN6-17, was detected for both MCMV and MLN resistance. The GWAS revealed a total of 54 SNPs (MCMV-13 and MLN-41) significantly associated (P ≤ 5.60 × 10−05) with MCMV and MLN resistance. Most of the GWAS-identified SNPs were within or adjacent to the QTLs detected through linkage mapping. The prediction accuracy for within populations as well as the combined populations is promising; however, the accuracy was low across populations. Overall, MCMV resistance is controlled by a few major and many minor-effect loci and seems more complex than the genetic architecture for MLN resistance.
Format: PDF
Language: English
Publisher: Springer
Type: Article
Place of Publication: Berlin (Germany)
Pages: 2381–2399
Issue: 8
Volume: 132
DOI: 10.1007/s00122-019-03360-x
Agrovoc: MAIZE CHLOROTIC MOTTLE VIRUS
Agrovoc: GENOMICS
Agrovoc: DISEASE RESISTANCE
Agrovoc: QUANTITATIVE TRAIT LOCI
Agrovoc: PUCCINIA SORGHI
Agrovoc: GENOMES
Agrovoc: MAIZE
Agrovoc: PATHOGENS
Agrovoc: POTYVIRIDAE
Agrovoc: SUGARCANE MOSAIC VIRUS
Journal: Theoretical and Applied Genetics
Related Software: http://hdl.handle.net/11529/10201


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  • Genetic Resources
    Genetic Resources including germplasm collections, wild relatives, genotyping, genomics, and IP
  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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