An F1 population, derived from an intraspecific cross between two Alstroemeria aurea accessions, was used to map quantitative trait loci (QTL) involved in ornamental and morphological characteristics. One QTL for leaf length was mapped on linkage group three of both parents near marker E+ACCT/M+CGCA-I165 explaining 20% and 14.8% phenotypic variation. Two putative QTL were detected on leaf width on A002-3 and A002-6. One QTL and three putative QTL, involved in the leaf length/width ratio were identified accounting for 46.7% of the phenotypic variance in total. Significant interaction was observed between two QTL, S+AC/M+ACT-I162 and S+AC/M+AGA-I465 in a two-way analysis of variance (ANOVA). For the main color of the flower one QTL and putative QTL accounted for up to 60% of phenotypic variance suggesting simple genetic control of flower color. A two-way ANOVA of these QTL suggested an epistatic interaction. A QTL was detected for color of the inner side of outer lateral tepal with 26.5% of the phenotypic variance explained. This QTL was also associated with main color of the flower just below the 95% threshold value. Two QTL were detected with the Kruskal-Wallis test for the tip color of inner lateral tepal near QTL for other flower color traits. Consequently flower color traits were significantly correlated. A QTL and a putative QTL for the flower size was mapped near marker E+ACCG/M+CGCT-I193 and E+ACCG/M+CGCG-197, respectively. One putative QTL was detected for the stripe width of the inner lateral tepal.
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