An RNA-Seq analysis of the pear (Pyrus communis L.) transcriptome, with a focus on genes associated with dwarf

Dwarfing rootstocks, such as that of the Chinese pear variety ‘Zhongai 1’, are an important resource in modern fruit production. An RNA-Seq analysis of ‘Zhongai 1’ and its progenitor non-dwarfing variety ‘Jinxiang’ revealed a set of 234 genes which were differentially transcribed in the two varieties. Among the differentially transcribed gene set were some potential candidates for the dwarf trait: one encoded a gibberellin 3-beta-dioxygenase, four encoded auxin-associated proteins, one encoded LRR receptor-like serine/threonine-protein kinase, four encoded cytochrome P450s, two encoded enzymes involved in abscisic acid synthesis, three were ethylene-responsive transcription factors, six were moisture status related proteins, two were NAC and four WRKY transcription factors. The assessment of transcript abundance derived by the RNA-Seq analysis was validated using quantitative real time PCR for ten of the differentially transcribed genes. The transcript levels of these genes in other dwarf and non-dwarf varieties were also analyzed by the qPCR, but no completely consistent regularity was found. The concentration of some phytohormones (GA3, IAA and ABA) was also determined, the results accorded with the transcript levels of some related genes in some varieties, but did not accord in all the survey varieties.