Comparative QTL mapping of resistance to Ustilago maydis across four populations of European flint-maize

We mapped and characterized quantitative trait loci (QTLs) for resistance to Ustilago maydis and investigated their consistency across different flint-maize populations. Four independent populations, comprising 280 F-3 lines (A x B-I), 120 F-5 lines (A x B-II), 131 F-4 lines (A x C) and 133 F-4 lines (C x D), were produced from four European elite flint inbreds (A, B, C, D) and genotyped at 89, 151, 104, and 122 RFLP marker loci, respectively. All F-n lines were evaluated in field trials with two replications in five German environments. Genotypic variances were highly significant for the percentage of U. maydis infected plants (UST) in all populations, and heritabilities exceeded 0.69. Between five and ten QTLs were detected in individual populations by composite interval mapping, explaining between 39% and 58% of the phenotypic variance. These 19 different QTLs were distributed over all ten chromosomes without any clustering on certain chromosomes. In most cases, gene action was dominant or overdominant. Fourteen pairs of the detected QTLs for UST displayed significant digenic epistatic interactions, but only two of them did so after arcsin root UST/100 transformation. Significant QTL x environment interactions occurred frequently. Between two to four QTLs were common between pairs of populations. Population C x D was also grown in Chartres, a location with a high U. maydis incidence. Two out of six QTLs identified for Chartres were in common with QTLs detected across five German environments for Cx D. Consequently, marker-assisted or phenotypic selection based on results from natural infection seem to be suitable breeding strategies for improving the resistance of maize to U. maydis.