We have evaluated the regeneration ability of leaf and root explants in 26 natural populations with the aim of analyzing the naturally occurring variation of Arabidopsis in vitro shoot and root organogenesis. All the accessions have been used as parental lines of available or under construction recombinant inbred lines (RILs) under construction. Phenotypic differences found between Ler and Cvi ecotypes were mapped in a population of 162 RILs. Several involved quantitative trait loci (QTL) have been identified. The analysis of near isogenic lines (NILs) would allow us to assign the effect of the QTLs identified and also possible candidate genes will be tested among those already described in the literature mapping into those regions.