Integrated transcriptomic and BSA-seq analyses identify novel QTL and candidate genes for stay-green in maize

Abstract

The stay-green trait is crucial for enhancing maize yield and stress tolerance, yet its genetic basis in new germplasm remains underexplored. This study aimed to dissect the molecular mechanisms underlying stay-green in the inbred line T01 using an integrated approach. We constructed an F₂:₃ population from T01 and the non-stay-green line Mo17, and combined BSA-seq to map candidate loci, RNA-seq at three developmental stages to profile transcriptomic dynamics, and WGCNA to identify co-expression networks. BSA-seq mapped two candidate QTL regions on chromosomes 5 and 9, with the former representing a potentially novel locus. Transcriptomic analysis revealed stage-specific regulation, with enrichment in reactive oxygen species metabolism, photosynthesis, and chloroplast maintenance at 10, 20, and 30 days after pollination (DAP), respectively. WGCNA identified six hub genes functionally involved in transcriptional regulation, ROS scavenging, and photosynthesis. Notably, three genes ( ZmFSD3 , ZmWRKY62 , and ZmNAC29 ) were located within BSA-defined intervals and supported by WGCNA analysis, with their expression patterns validated by RT-qPCR. Our findings reveal a complex, multi-pathway regulatory network in which WRKY and NAC transcription factors are highly connected candidate nodes. This provides new genetic resources and a theoretical basis for molecular breeding of stay-green maize.