title: Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm.
abstract: Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1-4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize.
authors.affiliation: College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.|International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico.
authors.forename: Jiafa
authors.initials: J
authors.lastname: Chen
authors.affiliation: International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico.
authors.forename: Rosemary
authors.initials: R
authors.lastname: Shrestha
authors.affiliation: College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.
authors.forename: Junqiang
authors.initials: J
authors.lastname: Ding
authors.affiliation: International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico.|Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shangai 201403 China.
authors.forename: Hongjian
authors.initials: H
authors.lastname: Zheng
authors.affiliation: International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico.|Maize Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, China.
authors.forename: Chunhua
authors.initials: C
authors.lastname: Mu
authors.affiliation: College of Agronomy, Synergetic Innovation Center of Henan Grain Crops and National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450002, China.|College of Life Sciences, Henan Agricultural University, Zhengzhou 450002, China.
authors.forename: Jianyu
authors.initials: J
authors.lastname: Wu
authors.affiliation: International Maize and Wheat Improvement Center, 06600 Mexico Distrito Federal, Mexico g.mahuku@cgiar.org.|International Institute of Tropical Agriculture, 34441 Dar es Salaam, Tanzania.
authors.forename: George
authors.identifier: 0000-0001-8444-8651
authors.initials: G
authors.lastname: Mahuku
mesh_terms: D000483:Alleles; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D060467:Disease Resistance / Q000235:genetics*; D005670:Fusarium; D005787:Gene Frequency; D005828:Genetics, Population; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods; D005838:Genotype; D006239:Haplotypes; D054884:Host-Pathogen Interactions / Q000235:genetics*; D015810:Linkage Disequilibrium; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci; D003313:Zea mays / Q000235:genetics* / Q000382:microbiology
keywords: Fusarium verticillioides; GenPred; Genomic Selection; Shared Data Resources; association analysis; disease resistance; maize; quantitative trait