Identification of QTLs for grain yield and grain-related traits of maize (Zea mays L.) using an AFLP map, different testers, and cofactor analysis

We exploited the AFLP(R)(1) technique to map and characterise quantitative trait loci (QTLs) for grain yield and two grain-related traits of a maize s egregating population. Two maize elite inbred lines were crossed to produce 229 F-2 individuals which were genotyped with 66 RFLP and 246 AFLP marker loci. By selfing the F-2 plants 229 F-3 lines were produced and subsequentl y crossed to two inbred testers (T1 and T2). Each series of testcrosses was evaluated in field trials for grain yield, dry matter concentration, and t est weight. The efficiency of generating AFLP markers was substantially hig her relative to RFLP markers in the same population, and the speed at which they were generated showed a great potential for application in marker-ass isted selection. AFLP markers covered linkage group regions left uncovered by RFLPs; in particular at telomeric regions, previously almost devoided of markers. This increase of genome coverage afforded by the inclusion of the AFLPs revealed new QTL locations for all the traits investigated and allow ed us to map telomeric QTLs with higher precision. The present study has al so provided an opportunity to compare simple (SIM) and composite interval m apping (CIM) for QTL analysis. Our results indicated that the method of CIM employed in this study has greater power in the detection of QTLs, and pro vided more precise and accurate estimates of QTL positions and effects than SIM. For all traits and both testers we detected a total of 36 QTLs, of wh ich only two were in common between testers. This suggested that the choice of a tester for identifying QTL alleles for use in improving an inbred is critical and that the expression of QTL alleles identified may be tester-sp ecific.