qSCR4.05 and qSCR4.08, two QTLs on chromosome 4 are associated with resistance to southern corn rust in maize

Southern corn rust (SCR), caused by the fungal pathogen Puccinia polysora, is one of the most serious threats to maize production. Identification of stable QTLs is a prerequisite in maize resistance breeding programs. Bulked Segregant RNA-Seq (BSR-Seq) and QTL mapping are two effective approaches to detect genomic regions responsible for traits of interest. In the present study, BSR-Seq analysis and QTL mapping were used to detect the genomic regions/QTLs associated with the resistance to SCR. By using BSR-Seq analysis, totally 2 and 3 genomic regions were detected in F2 and BC1 populations, respectively. By using QTL mapping analysis, 3 resistance QTLs (qSCR3.02/03, qSCR4.05 and qSCR4.08) were identified in F2:3 population. Among them, qSCR4.05 and qSCR4.08 overlapped with the regions detected by using BSR-Seq method. Moreover, the two QTLs were further validated by using near isogenic lines. The identification of the two stable QTLs (qSCR4.05 and qSCR4.08) lay the foundation for further application in resistance breeding programs. •QTLs for resistance to southern corn rust were analyzed via BSR-seq and QTL mapping analysis in maize.•qSCR4.05 and qSCR4.08 are stable QTLs detected via BSR-seq and QTL mapping analysis.•The resistance effects of the two stable QTLs were validated via near isogenic lines.