Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred lines.

BACKGROUND: Northern corn leaf blight (NCLB) is a foliar disease in maize caused by the fungus Setosphaeria turcica, which severely impacts maize production. Genetic studies can help mitigate the effects of NCLB by developing maize resistant varieties and enhancing overall crop yield. RESULTS: In this study, a multi-parent population (MPP) was constructed using two temperate maize inbred lines (Zheng58 and HuangC) and one subtropical inbred line (AN20) as the female parents, with the elite temperate maize inbred line Ye107 as the common male parent. The MPP consisted of three recombinant inbred line (RIL) subpopulations, comprising a total of 529 F(8) RILs. Genotyping-by-sequencing (GBS) generated 549,531 single nucleotide polymorphisms (SNPs), which were used for genome-wide association studies (GWAS). GWAS analysis identified 14 SNPs significantly associated with NCLB resistance. Candidate genes were screened within a 100 Kb region upstream and downstream of the significant SNPs, identifying two novel candidate genes, Zm00001d034918 and Zm00001d024406, that regulate NCLB resistance in maize. These genes encode proteins involved in energy metabolism and protein interactions, both of which play key roles in maize defense responses against NCLB. qRT-PCR results confirmed that after artificial inoculation with Setosphaeria turcica, both genes were significantly upregulated in the parental line Zheng58. CONCLUSIONS: This study identifies two candidate genes associated with NCLB resistance through a genome-wide association analysis using 529 recombinant inbred lines evaluated across subtropical and tropical environments. The candidate genes were further validated through preliminary qRT-PCR analysis. These findings provide valuable genomic resources for breeding NCLB-resistant maize varieties and enhances our understanding of the genetic mechanisms underlying NCLB resistance in maize.