A genome-wide association study reveals genes associated with fusarium ear rot resistance in a maize core diversity panel

Fusarium ear rot is a common disease of maize that affects food and feed quality globally. Resistance to the disease is highly quantitative, and maize breeders have difficulty incorporating polygenic resistance alleles from unadapted donor sources into elite breeding populations without having a negative impact on agronomic performance. Identification of specific allele variants contributing to improved resistance may be useful to breeders by allowing selection of resistance alleles in coupling phase linkage with favorable agronomic characteristics. We report the results of a genome-wide association study to detect allele variants associated with increased resistance to Fusarium ear rot in a maize core diversity panel of 267 inbred lines evaluated in two sets of environments. We performed association tests with 47,445 singlenucleotide polymorphisms (SNPs) while controlling for background genomic relationships with a mixed model and identified three marker loci significantly associated with disease resistance in at least one subset of environments. Each associated SNP locus had relatively small additive effects on disease resistance (±1.1% on a 0-100% scale), but nevertheless were associated with 3 to 12% of the genotypic variation within or across environment subsets. Two of three identified SNPs colocalized with genes that have been implicated with programmed cell death. An analysis of associated allele frequencies within the major maize subpopulations revealed enrichment for resistance alleles in the tropical/subtropical and popcorn subpopulations compared with other temperate breeding pools. © 2013 Zila et al.This research was supported by the National Science Foundation (projects DBI-0321467, IOS- 0820619 and IOS-0604923), USDA-ARS, the National Plan for Research and Development of Spain (AGL2009-12770), and the Excma. Diputación Provincial de Pontevedra. USDA-ARS supported the graduate fellowship of C.T. Zila. R. Santiago acknowledges postdoctoral contract “Isidro Parga Pondal” supported by the Autonomous Government of Galicia and the European Social Fund.National Science FoundationUSDA-ARSMICINNExcma. Diputación Provincial de PontevedraAutonomous Government of GaliciaEuropean Social FundPeer Reviewe