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. Genome sequences of T1190 and PinS (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.

苹果（Malus domestica Borkh.）的快速循环育种，以转基因早花苹果株系T1190作为杂交亲本，旨在缩短以渐渗野生苹果属物种基因为目标的育种项目周期。表达白桦BpMADS4基因的转基因苹果株系T1190源自非转基因基因型PinS，而PinS是苹果品种'Pinova'与'Idared'的F1后代。携带BpMADS4基因的实生苗童期仅为数周，因此每年可完成一次杂交。本研究以这两个基因型的组培苗提取的DNA为材料，采用Illumina短读长测序技术（Illumina short-read sequencing）对T1190与PinS进行全基因组测序。每个基因型产出约6.5亿条原始读段与约6.26亿条过滤后读段。PinS与T1190的测序数据相对于GDDH13参考基因组序列的理论平均覆盖度分别为138倍（T1190）与123倍（PinS）。将两组测序数据比对至GDDH13参考基因组后，参考基因组的序列覆盖度约为86%（若排除"N"碱基连续区域则可达约98%）。