Mapping Genomic Regions and Identification of Candidate Genes Implicated in Resistance to Southern Corn Rust (SCR) Disease Caused by <i>Puccinia polysora</i> in Maize ( <i>Zea mays</i> )

Southern corn rust (SCR) disease caused by Puccinia polysora is emerging as a potential production constraint in maize. To effectively manage the disease, development and deployment of resistant cultivars to SCR is crucial with minimal effects on the environment. Under these premises, quantitative trait loci (QTLs) for resistance to SCR were detected by using mean disease severity data under artificial epiphytotic conditions across three locations from four doubled haploid (DH) populations, namely, PL#09 × PL#07 (MP1), PL#08 × PL#07 (MP2), PL#08 × PL#15 (MP3), and PL#18 × PL#15 (MP4). The DH populations were genotyped employing 392, 371, 378, and 253 polymorphic single nucleotide polymorphism markers, respectively. Inclusive composite interval mapping was performed to detect significant QTL, QTL × QTL, and QTL × location interaction effects. The QTL identified in the linkage group 2 (qSCR-2-1) was common across three locations and two DH populations derived from the cross PL#09 × PL#07 and PL#08 × PL#07, and percent phenotypic variation explained by this QTL was 12.99 and 13.57%. Similarly, another major QTL on chromosome 10 (qSCR-10-1) was found to be consistent across three locations in DH mapping population 3 (PL#08 × PL#15) for SCR resistance with phenotypic variation explained as 17.64%. The QTL on chromosome 10 harbored the candidate genes Zm00025ab420970, Zm00001d023311, Zm00001d023265, and Zm00001d023267 implicated in disease resistance. A total of 2, 8, and 10 epistatic QTLs present on different chromosomes were detected in MP1, MP2, and MP3. The percent phenotypic variation explained by the epistatic QTLs on different chromosomes ranged from 4.47 to 4.92%, 1.68 to 5.17%, and 0.62 to 1.26% in MP1, MP2, and MP3, respectively.