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The genus Alstroemeria L. is endemic in South America, mainly in Chile and Brazil. Crossing barriers of mainly postfertilization origin hampered widely inter-specific hybridization. Culturing the ovules 2 days after pollination in an hormone-free MS medium with 9% saccharose for 6 weeks and hereafter transfer to a MS medium with 3% saccharose gives germination of the fertilized ovules. In a diallel cross with 5 Chilean and 2 Brazilian species 39 combinations failed, whereas after early ovule culture hybrid plants were obtained in 27 of the incongruous combinations. The rate of success varied between 0.4%–22.5% depending on the species combination. The hybrids were tested in in vitro stage for their true hybridity using isozyme analysis and/or genomic in situ hybridization of chromosomes (GISH). This method can easily be applied in hybrids between Chilean and Brazilian species. Backcrosses were made using the ovule culture again and in the combination (A. aurea × A. inodora) × A. inodora plants were obtained although the pollen fertility was very low (1%–5%). By using species-specific repetitive probes in in situ hybridization (FISH) chromosome specific patterns were obtained enabling us characterizing the backcross hybrids for their chromosome constitution. By this method we can identify our breeding material for special traits linked with identified chromosomes.
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.