Introgression of QTL Hotspot Regions Enhances Grain Yield and Maize Lethal Necrosis Resistance in Elite Maize Lines

Maize lethal necrosis (MLN) poses a severe threat to maize production in eastern and southern Africa, causing significant yield losses. In this study, marker-assisted backcrossing (MABC) was used to introgress major-effect MLN resistance Quantitative Trait Loci (QTL) located on chromosomes 3 and 6 into 14 elite but MLN-susceptible CIMMYT maize lines belonging to heterotic groups A and B. Ten Kompetitive Alelle Specific PCR (KASP) SNP markers closely linked to three validated QTL-hotspot regions were applied for foreground selection, with at least two hotspots polymorphic across all donor–recipient combinations. Foreground and background selection enabled fast tracking of MLN resistance alleles and recovery of near-recurrent parent genomes. The resulting BC₄F₂ introgressed lines exhibited markedly reduced MLN severity under artificial inoculation, with several lines showing a 50% reduction relative to their recurrent parents. Testcrosses of these lines demonstrated yield advantages of 2–4 t/ha under MLN pressure compared with original parental lines, while maintaining comparable performance under optimum conditions. Notably, introgressed derivatives of CML312, CML539, and CZL052 displayed both enhanced MLN resistance and superior yield performance, with CZL052-derived testcrosses achieving nearly two-fold yield gains under severe MLN stress. Importantly, equivalence trials confirmed that MLN resistance was improved without compromising resistance to gray leaf spot, turcicum leaf blight, or common rust. These findings validate the effectiveness of QTL-based conversion for enhancing MLN resistance in elite breeding lines and demonstrate the potential of these improved lines as robust parental sources for developing MLN-resilient hybrids adapted to eastern and southern Africa.