Identification of differentially expressed genes using digital gene expression profiles in Pyrus pyrifolia Nakai cv. Hosui bud release following early defoliation

“Returning bloom” is a major problem in the warm pear-producing regions during autumn–winter after the pear harvest and can cause tremendous pear production losses in the following year. The molecular mechanism causing this phenomenon is a mystery. We used high-throughput tag-sequencing (tag-seq) technology to analyze the gene expression profiling of pear (Pyrus pyrifolia Nakai) floral buds at three time points for completely defoliated plants after harvest. A total of 13.2–15.8 million reads were obtained for each of the six libraries, and approximately 61.81–67.11 % were mapped to Pyrus bretschneideri Rehd. genome sequences. A total of 2713 differentially expressed genes, categorized into 35 functional groups, were associated with 251 Kyoto Encyclopedia of Genes and Genomes pathways. Gene Ontology and pathway enrichment analysis showed differentially expressed genes linked to photosynthesis, hormone/signaling, and carbohydrate biosynthesis and metabolism. Six differentially expressed genes were selected for quantitative real-time PCR analysis, and the expression patterns were consistent with the tag-seq results. We concluded that bud release after artificial defoliation required compensatory mechanisms, which induce genes specifically expressed in association with the process of photosynthesis, endogenous hormones, carbohydrate, and reactive oxygen species. The differential expressions of genes found in pear tree defoliated by hand should play important roles in the reversion phase from paradormancy back to growth.