Fine-Mapping and Candidate Gene Analysis for qNLB1.02, a Locus Conditioning Quantitative Resistance to Multiple Diseases in Maize

The mechanisms of disease resistance conditioned by quantitative trait loci remain largely elusive.  In this study, we chose to fine map a known QTL in maize, qNLB1.02, which confers resistance to three foliar diseases of maize: northern leaf blight (NLB), caused by Setosphaeria turcica; Stewart’s wilt, caused by Pantoea stewartii; and common rust, caused by Puccinia sorghi. qNLB1.02 provides broad-spectrum resistance to S. turcica, and qNLB1.02 has been previously shown to provide protection against vascular invasion by S. turcica. Using a population derived from introgression lines developed using the nested association mapping (NAM) founders B73 and Tx303, a 27-Mb interval was reduced to 3 Mb.  The NLB and Stewart’s wilt QTL co-localized to the same 3-Mb region, while rust resistance localized to an adjacent 5 Mb interval.  Using an independent analysis, roughsheath2-interacting KH domain protein (rik) was implicated as a putative candidate gene for qNLB1.02 by genome-wide association (GWA) of the maize 282-line diversity panel. rik was found to be up-regulated during infection by S. turcica.  Subsequently, additional recombinants were identified and evaluated, and the region was further reduced to 21.2 kb, corresponding to six genes, not including rik. GWA in the NAM and 282-line diversity panel did not provide additional resolution for candidates in the interval.