Quantitative Genetic Dissection of Shoot Architecture Traits in Maize: Towards a Functional Genomics Approach

Quantitative trait loci (QTL) affecting the total number of leaves made before flowering and the number of leaves below the uppermost ear (NLBE) were mapped and characterized using the intermated B73 × Mo17 recombinant inbred lines (IBMRILs) of maize (Zea mays L.). B73 and Mo17 typically make 20 and 17 leaves, 14 and 11 of which are below the ear. Total number of leaves and the number of leaves below the uppermost ear are ∼80% heritable in the IBMRILs, which show strongly transgressive phenotypic ranges of 15 to 24 and 10 to 18 leaves for these traits. B73 alleles at loci in chromosome bins 1.06, 3.06, 4.08, 8.04, 8.05, 9.07, and 10.04 increase leaf numbers, with all but the 3.06 QTL affecting both of these highly correlated traits (r = 0.86, p < 0.0001). Conservative QTL confidence intervals were computed and projected onto the draft maize genome sequence, revealing very narrow localizations (∼1 Mb) for four of the seven loci. More than 40% of the heritable variation for both traits is explained by an additive model, squarely accounting for the dramatic parental differences, but leaving the basis of the strong transgression unexplained. In addition, error rate control and confidence interval methods tailored for composite interval mapping are introduced, and their potential for improving QTL reporting is discussed.