Noel Ndlovu ¹ Manje S. Gowda ^2* Yoseph Beyene ² Biswanath Das ² SURESH L. M. ² Dan Makumbi ² Veronica Ogugo ² Juan Burgueño ³ Jose Crossa ³ Charles Spillane ¹ PETER C. MCKEOWN ¹ Galina Brychkova ¹ Prasanna Boddupalli ²

• ¹ Plant & AgriBiosciences Research Centre, Ryan Institute, National University of Ireland, Galway, Ireland
• ² The International Maize and Wheat Improvement Center (CIMMYT), Nairobi, Kenya
• ³ International Maize and Wheat Improvement Center (Mexico), Texcoco, Tabasco, Mexico

Northern corn leaf blight (NCLB) caused by Setosphaeria turcica, is a major fungal disease affecting maize production in sub-Saharan Africa (SSA). Utilizing host plant resistance to mitigate yield losses associated with NCLB can serve as a cost-effective strategy. In this study, we conducted a high-resolution genome-wide association study (GWAS) in an association mapping panel and linkage mapping with three doubled haploid (DH) and three F3 populations of tropical maize. These populations were phenotyped for NCLB resistance across six hot spot environments in Kenya. Across environments and genotypes, NCLB scores ranged from 2.12 to 5.17 (on a scale of 1-9). NCLB disease severity scores exhibited significant genotypic variance and moderate-to-high heritability. From the six biparental populations, 23 QTLs were identified each explaining 2.7 to 15.8% of phenotypic variance. Collectively the detected QTLs explained 34.28, 51.37, 41.12, 12.46, 12.11 and 14.66% of the total phenotypic variance in DH populations 1, 2, 3 and F3 populations 4, 5 and 6, respectively. GWAS, using 337,110 high-quality SNPs, identified 15 marker-trait associations and several putative candidate genes linked to NCLB resistance in maize. Joint linkage association mapping (JLAM) identified 37 QTLs for NCLB resistance. Using linkage mapping, JLAM, and GWAS, several QTLs were identified within the genomic region spanning 4 to 15 Mbp on chromosome 2. This genomic region represents a promising target for enhancing NCLB resistance via marker-assisted breeding. Genome-wide predictions revealed moderate correlations with mean values of 0.45, 0.44, 0.55 and 0.42 for within GWAS panel, DH pop1, DH pop2 and DH pop3, respectively. Prediction by incorporating marker-by-environment interactions did not show much improvement. Overall, our findings indicate that NCLB resistance is quantitative in nature and is controlled by few major effect and many minor effect QTLs. Genomic regions that consistently detected across mapping approaches and populations should be prioritized in improving NCLB resistance, while genome-wide prediction results can help further to incorporate most of the major- and minor-effect genes. This study contributes to a deeper understanding of the genetic and molecular mechanisms driving maize resistance to NCLB.