QTL identification of kernel composition traits with popcorn using both F2:3 and BC2F2 populations developed from the same cross

Abstract Quantitative trait loci (QTL) influencing three main kernel composition traits, starch, protein and oil concentrations, in unselected F 2:3 and selected BC 2 F 2 maize populations derived from the same cross of a dent corn inbred Dan232 × an elite popcorn inbred N04 under the same conditions were detected. Four and two QTL for starch, four and three QTL for protein, and four and one QTL for oil were detected in the two populations, respectively, with three QTL jointly detected. The proportion of phenotypic variation explained by a single QTL was 5.2–10.6%, 5.0–14.3%, and 6.2–8.5% for the three traits. Ten QTL had favorable alleles contributed by Dan232. Several QTL detected in this study had identical or similar chromosome regions to those previously identified with other maize germplasms. No QTL with opposite effects for kernel composition traits and popping characteristics were detected in the same or near marker intervals. This reflected that some QTL detected in this study seemed to contribute to trait variation in a diverse array of maize populations and environments, and the opportunity existed for improving popcorn's nutritional quality while maintaining acceptable popping characteristics. Inconsistent broad sense heritability and trait correlation estimates were also observed in the two populations.