, Volume 241, Issue 6, pp 1363–1379 | Cite as

Proteome analysis of pear reveals key genes associated with fruit development and quality

  • Jia Ming Li
  • Xiao San Huang
  • Lie Ting Li
  • Dan Man Zheng
  • Cheng Xue
  • Shao Ling Zhang
  • Jun WuEmail author
Original Article


Main conclusion

Comparative and association analyses of the proteome and transcriptome for pear fruit development were conducted for the first time in this study.

Pear fruit development involves complex physiological and biochemical processes, but there is still little knowledge available at proteomic and transcriptomic levels, which would be helpful for understanding the molecular mechanisms of fruit development and quality in pear. In our study, three important stages, including early development (S4-22), middle development (S6-27), and near ripening (S8-30), were investigated in ‘Dangshansuli’ by isobaric tags for relative and absolute quantitation (iTRAQ) labeling technology, identifying a total of 1,810 proteins during pear fruit development. The association analysis of proteins and transcript expression revealed 1,724, 1,722, and 1,718 associated proteins identified in stages S4-22, S6-27, and S8-30, respectively. A total of 237, 318, and 425 unique proteins were identified as differentially expressed during S4-22 vs S6-27, S6-27 vs S8-30, S4-22 vs S8-30, respectively, and the corresponding correlation coefficients of the overall differentially expressed proteins and transcripts data were 0.6336, 0.4113, and 0.7049. The phenylpropanoid biosynthesis pathway, which is related to lignin formation of pear fruit, was identified as a significantly enriched pathway during early stages of fruit development. Finally, a total of 35 important differentially expressed proteins related to fruit quality were identified, including three proteins related to sugar formation, seven proteins related to aroma synthesis, and sixteen proteins related to the formation of lignin. In addition, qRT-PCR verification provided further evidence to support differentially expressed gene selection. This study is the first to reveal protein and associated mRNA variations in pear during fruit development and quality conformation, and identify key genes and proteins helpful for future functional genomics studies, and provides gene resources for improvement of pear quality.


Pear Fruit development Proteomic Transcriptomic Differential expression 



Day after full blooming,


Isobaric tags for relative and absolute quantitation


Strong cation exchange


High pressure liquid chromatography


Automatic gain control


High-energy collision dissociation


Kyoto encyclopedia of genes and genomes


Gene ontology


Cluster of orthologous groups of proteins






4-coumarate-CoA ligase


Cinnamoyl-CoA reductase






Hydroxycinnamoyl transferase


Major facilitator super family transporter



The work was financially supported by the National Science Foundation of China (31171928), Ministry of Education Program for New Century Excellent Talents in University (NCET-13-0864), and the Earmarked Fund for China Agriculture Research System (CARS-29).

Supplementary material

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Supplementary material 1 (TIFF 4067 kb)
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Supplementary material 3 (DOC 158 kb)
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Supplementary material 4 (XLS 1734 kb)
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Supplementary material 5 (XLS 141 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2015

Authors and Affiliations

  • Jia Ming Li
    • 1
  • Xiao San Huang
    • 1
  • Lie Ting Li
    • 1
  • Dan Man Zheng
    • 2
  • Cheng Xue
    • 1
  • Shao Ling Zhang
    • 1
  • Jun Wu
    • 1
    Email author
  1. 1.State Key Laboratory of Crop Genetics and Germplasm Enhancement, Centre of Pear Engineering Technology ResearchNanjing Agricultural UniversityNanjingChina
  2. 2.Roy J. Carver Biotechnology CenterUniversity of Illinois Urbana-ChampaignUrbanaUSA

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