Short read whole genome sequencing of the transgenic early flowering apple T1190 and its none-transgenic mother line PinS using DNA of in vitro plants

Rapid cycle breeding in apple (Malus domestica Borkh.) is based on the use of the transgenic early-flowering apple line T1190 as crossbred parents to facilitate the shortening of breeding programs aimed at introgression of genes originating from wild apple species. The transgenic apple T1190 expressing the BpMADS4 gene of silver birch originated from the non-transgenic genotype PinS, a F1-offspring of the apple cultivars 'Pinova' and 'Idared'. Seedlings carrying BpMADS4 have a juvenility phase of few weeks, this allowing a cross per year. T1190 and PinS were sequenced with Illumina short-read sequencing using DNA isolated from in vitro grown plantlets of these two genotypes. Whole genome sequencing resulted in ~650 Mio. raw reads and ~626 Mio trimmed reads per genotype. The data sets of PinS and T1190 correspond to a 138x-fold (T1190) and 123-fold (PinS) theoretical mean coverage of the GDDH13 reference genome sequence each. Mapping of each data set against the GDDH13 genome sequence resulted in a sequence coverage of ~86% (~98% without stretches of “N”) of the reference genome.