Multi-Omics Analysis of White Leaf Spot in Maize Resistance: Integrated GWAS, BSA-Seq, and RNA-Seq Identifies Candidate Genes and Facilitates Germplasm Evaluation

Abstract

The epidemic expansion of maize white leaf spot (WLS) is a substantial threat to the secure and sustained production of maize. Given its diversity and strong environmental adaptability, WLS has the potential to emerge as a globally prevalent disease affecting maize crops. A detailed exploration of genetic segments and genes that are significantly associated with resistance to WLS in maize, an analysis of the genetic mechanisms underlying maize’s response to this disease, as well as the identification and development of resistant germplasm resources and their promotion and application, are of great practical significance for ensuring the safe production of maize. In this study, a genome-wide association study (GWAS) of 11 related traits in 141 maize accessions was conducted, and a total of 1174 significant single-nucleotide polymorphism (SNP) sites were identified. BSA-Seq (Bulked Segregant Analysis Sequencing) identified 6319 sites and 79 candidate genes. Through comprehensive analysis of GWAS and RNA-Seq data, a total of 13 candidate genes associated with maize white spot resistance, including Zm00001eb093900 and Zm00001eb078490, were identified. This study systematically explored genetic regions and genes significantly linked to white spot resistance in maize, thereby providing novel genetic resources for future molecular design-based breeding and improvement of resistance traits. Furthermore, by correlating field disease incidence with the expression of immune response-related gene products, we developed a rapid evaluation system for maize WLS resistance, in which soil plant analysis development (SPAD) value, Fm, SSC, and POD served as key indicators. Using this system, 5 immune germplasm resources such as QB2229 and NP5366 and 89 highly resistant materials such as QB1923 and Chang7-2 were identified. The accurate evaluation of maize WLS resistance will provide essential resistance sources for subsequent breeding programs. RNA-Seq analysis revealed that systemic acquired resistance to maize WLS involves key pathways, including phenylpropanoid metabolism, as well as the synthesis of secondary metabolites such as flavonoids and glutathione. Further analysis of race-specific resistance indicated that the response of highly resistant maize varieties to WLS is primarily characterized by the accumulation of defense-related substances and enhanced activity across multiple energy metabolism pathways. In contrast, highly susceptible maize lines exhibited more pronounced enrichment in hormone signaling, the mitogen-activated protein kinase (MAPK) signaling pathway, and the metabolism of various amino acids.