Genomic dissection of stable meta-quantitative trait loci and candidate genes enabling durable disease and insect resistance in maize to safeguard food production.
BACKGROUND Maize is a globally important cereal crop that supports food and nutritional security and sustains livelihoods through its use as food, feed, and industrial raw material. However, maize productivity is severely constrained by destructive diseases and insect pests. Breeding for durable resistance is challenging due to the quantitative, polygenic, and environment-sensitive nature of these traits. To refine the genomic basis of resistance and identify robust breeding targets, a comprehensive meta-quantitative trait loci (M-QTL) analysis was conducted by integrating 528 quantitative trait loci (QTLs), comprising 368 disease-resistant and 160 insect-resistance QTLs. RESULTS The collected QTLs were consolidated into 74 stable M-QTLs, including 31 disease-specific (DI-MQTLs), 23 insect-specific (IN-MQTLs), and 20 co-localized M-QTLs (PL-MQTLs) conferring combined resistance to both stresses. Confidence intervals (CIs) were reduced by an average of 70.6% for disease-related and 51.2% for insect-related loci, with the identified M-QTLs showing a mean phenotypic variance explained (PVE) of 14.6%. Several PL-MQTLs, including PL-MQTL4.1 (CI = 2.91 cM; PVE = 23.0%) and PL-MQTL4.2 (CI = 0.84 cM; PVE = 23.1%), emerged as highly stable resistance hotspots. A total of 1884 candidate genes were identified, including those encoding NBS-LRR receptors, receptor-like kinases, transcription factors (WRKY, MYB, NAC, and AP2/ERF), peroxidases, cytochrome P450s, and benzoxazinoid-pathway genes. Key components of the salicylic acid (SA) and jasmonic acid (JA) signaling pathways co-localized within PL-MQTL regions, suggesting a mechanistic basis for broad-spectrum resistance. CONCLUSION The identified stable M-QTLs and prioritized candidate genes provide robust genomic resources for marker-assisted breeding, genomic prediction, and genome-editing approaches, thereby accelerating the development of durable, broad-spectrum disease- and insect-resistant maize cultivars. © 2026 Society of Chemical Industry.