High-density mapping for gray leaf spot resistance using two related tropical maize recombinant inbred line populations

Gray leaf spot (GLS) caused by Cercospora zeae-maydis or Cercospora zeina is one of the devastating maize foliar diseases worldwide. Identification of GLS-resistant quantitative trait loci (QTL)/genes plays an urgent role in improving GLS resistance in maize breeding practice. Two groups of recombinant inbred line (RIL) populations derived from CML373 × Ye107 and Chang7-2 × Ye107 were generated and subjected to genotyping-by-sequencing (GBS). A total of 1,929,222,287 reads in CML373 × Ye107 (RIL-YCML) and 2,585,728,312 reads in Chang7-2 × Ye107 (RIL-YChang), with an average of 10,961,490 (RIL-YCML) and 13,609,096 (RIL-YChang) reads per individual, were got, which was roughly equal to 0.70-fold and 0.87-fold coverage of the maize B73 RefGen_V4 genome for each F7 individual, respectively. 6418 and 5139 SNP markers were extracted to construct two high-density genetic maps. Comparative analysis using these physically mapped marker loci demonstrated a satisfactory colinear relationship with the reference genome. 11 GLS-resistant QTL have been detected. The individual QTL accounted for 1.53–24.00% of the phenotypic variance explained (PVE). The new consensus QTL (qYCM-DS3-3/qYCM-LT3-1/qYCM-LT3-2) with the largest effect was located in chromosome bin 3.05, with an interval of 2.7 Mb, representing 13.08 to 24.00% of the PVE. Further gene annotation indicated that there were four candidate genes (GRMZM2G032384, GRMZM2G041415, GRMZM2G041544, and GRMZM2G035992) for qYCM-LT3-1, which may be related to GLS resistance. Combining RIL populations and GBS-based high-density genetic maps, a new larger effect QTL was delimited to a narrow genomic interval, which will provide a new resistance source for maize breeding programs.