Population analyzed during the experiments originated from a cross between 90-HAF-01 (S.tuberosum1) and 90-HAG-15 (S.tuberosum2xS.sparsipilum), which was previously evaluated for total glycoalkaloid content (TGA)1. Responses of stomatal conductance to different combinations of light, humidity, CO2 concentration on leaf surface as well as temperature were analyzed and their consequences on water use efficiency were evaluated during the climate chamber experiments in 2010 and 2011. We have previously participated in development of a de novo sequence-based alternative to positional cloning (SHOREMap)2. Here we employ a new method that allows QTL mapping exclusively from genomic sequence reads and a single reference genome sequence3. The procedure was applied to the population for which the low and high WUE groups in respect to dry matter / water use and photosynthesis / transpiration were identified. Four bulks (two of high and two of low WUE) and the parents were subsequently sequenced to ~30x coverage. Non-random distribution of sequence read-based polymorphisms between the WUE pools and the parental pool delimited highly resolved regions on several chromosomes. Within these regions candidate genes were found, namely glutamate ammonia ligase and proline synthase, that are presently being analyzed. 1. Sorensen, K.K. et al. Theor Appl Genet (2008). 2. Schneeberger, K. et al. Nature Methods 6: 550-551 (2009). 3. The potato genome sequencing consortium, Nature 475: 189-195 (2011).