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

  • Quan-jun Zhang
  • Shu-tian Tao
  • Meng Li
  • Xiao-xiao Qi
  • Jun Wu
  • Hao Yin
  • Jia-lin Deng
  • Shao-ling Zhang
Original Paper
Part of the following topical collections:
  1. Gene Expression


“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.


Hosui Bud release Returning bloom Digital gene expression (DGE) Differentially expressed genes 



This work was supported by the National High-tech R&D Program of China (863 Program, Grant Nos. 2011AA10020602 and 2013AA102606-02), the National Natural Science Foundation of China (Grant Nos. 31230063, 31301748, 31171936 and 31471839), the Doctoral Fund of Ministry of Education of China (20110097110029), and the Applied and Basic Research Project Fund of the Department of Science and Technology of Sichuan Province (2015JY0233).

Data archiving statement

Gene sequences of pear were obtained from the Pear Genome Project website (

Raw sequencing reads were deposited in the Sequence Read Archive (SRA) database in NCBI under the accession number of PRJNA248562 (

Supplementary material

11295_2015_858_MOESM1_ESM.doc (29 kb)
Supplementary Table 1 List of primers used for quantitative reverse transcription-PCR analysis (DOC 29 kb)
11295_2015_858_MOESM2_ESM.xls (512 kb)
Supplementary Table 2 Pathway enrichment analysis of expressed genes. BLASTing against KEGG database indicated that expressed genes were involved in 251 pathways (XLS 511 kb)
11295_2015_858_MOESM3_ESM.xls (55 kb)
Supplementary Table 3 List of pathway enriched differentially expressed genes in complete defoliation treatments. These genes are related to photosynthesis, carbohydrate metabolism and plant hormone signal transduction (XLS 55 kb)
11295_2015_858_MOESM4_ESM.xls (384 kb)
Supplementary Table 4 List of time course genes (Top 100 genes of BD7, BD17, BD27) differentially expressed (XLS 384 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Quan-jun Zhang
    • 1
    • 2
  • Shu-tian Tao
    • 1
  • Meng Li
    • 1
  • Xiao-xiao Qi
    • 1
  • Jun Wu
    • 1
  • Hao Yin
    • 1
  • Jia-lin Deng
    • 2
  • Shao-ling Zhang
    • 1
  1. 1.College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm EnhancementNanjing Agricultural UniversityNanjingChina
  2. 2.Horticultural Research Institute of Sichuan Academy of Agricultural Sciences, Key Laboratory of Horticultural Crops, Biology and Germplasm Enhancement in Southwest RegionsMinistry of AgricultureChengduChina

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