Transcriptomics-assisted quantitative trait locus fine mapping for the identification of a gray leaf spot resistance gene ZmEGH in maize

By integrating QTL fine-mapping with transcriptomic analysis, we identified Zm00001d053733 (ZmEGH)within a 157.4 kb genomic interval as a hub gene in a disease-resistance co-expression network and a candidate genepotentially involved in gray leaf spot resistance in maize.

Gray leaf spot is a globally significant fungal foliar disease of maize, and resistance to GLS is a typical quantitative trait governed by a complex genetic architecture. In this study, multi-generation populations derived from the highly resistant inbred line T32 and the highly susceptible inbred line J51 were used for genetic analysis. High-density linkage mapping followed by fine mapping identified a major quantitative trait locus (QTL), designated qGLS4, on chromosome 4, which was delimited to a 157.4 kb physical interval. To further identify candidate genes, RNA-seq data were generated before and after pathogen inoculation from the two parental lines and their backcross-derived populations. Weighted gene co-expression network analysis (WGCNA) was conducted to identify modules associated with the disease index, enabling the screening of ten candidate genes within the fine-mapped region. The brown module exhibited a strong positive correlation with disease index. Within the QTL interval, Zm00001d053733 (ZmEGH) was identified as a hub gene in this module and showed pathogen-induced expression specifically in resistant genotypes. Notably, ZmEGH expression was significantly up-regulated in the highly resistant parent T32 and was enriched in the plant–pathogen interaction pathway, further supporting its candidacy as a key potential underlying GLS resistance.