Testing the Hypothesis: Validating Association Mapping Findings for Northern Leaf Blight in Maize

Genome-wide association studies (GWAS) detect many significant genotype-phenotype interactions, which can be used to identify candidate genes. These candidate genes must be validated. We utilized nested association mapping (NAM) in maize to identify genes putatively associated with disease resistance. The NAM population consists of 5,000 recombinant inbred lines derived from 25 founder lines (Yu et al. 2008). The Hapmap2 GWAS for Northern Leaf Blight (NLB; Chia et al. 2012) was used to develop a list of candidate genes. Mutants were identified from the UniformMu project that corresponded to the candidate genes. To determine the proportion of significant associations that could be confirmed through mutant phenotypes, we inoculated mutant maize lines corresponding to >100 genes identified by GWAS and measured their quantitative NLB phenotypes.  We phenotyped 114 UniformMu families to find lines with significant differences in disease phenotype. Among them, approximately 10% yielded significant differences. Approximately 75% of those significant lines were derived from associations that fell within joint linkage mapping NLB QTL (Poland et al., 2011). In some cases, multiple lines with mutations in the same gene showed opposite effects. We are confirming a role in disease resistance for those genes with significant mutant phenotypes.