Molecular Breeding

, 39:1 | Cite as

Candidates responsible for dwarf pear phenotype as revealed by comparative transcriptome analysis

  • Yuxiong Xiao
  • Caihong WangEmail author
  • Yike Tian
  • Shaolan Yang
  • Junling Shen
  • Qianqian Liu
  • Haiyue Zhang


Dwarfism is an important character in fruit production for intensive cultivation and effective orchard management. We previously located a single dominant gene at a narrow region on scaffold00074 of pear based on simple sequence repeat markers. To identify the gene and fully understand the different developmental processes, we conducted a transcriptomic analysis of the young apical stem between dwarf and standard pears. A total of 2170 differentially expressed genes (DEGs), of which 987 were down-regulated and 1183 were up-regulated, were determined. These DEGs were mainly involved in ribosome biogenesis, phenylpropanoid biosynthesis, photosynthesis, porphyrin and chlorophyll metabolism and DNA replication. Subsequently, a classical arabinogalactan protein 7-like gene (PCP021014) and a protein WVD2-like 7 gene (PCP021015) were identified as the most likely candidates for the PcDw locus on the basis of the DEGs and annotation of scaffold00074. Furthermore, we performed qRT-PCR to validate the expression patterns of 12 DEGs associated with the dwarf character. Our results provide a systemic viewpoint into the complex regulatory networks between the dwarf and standard pear phenotypes.


Pear Dwarf Phenotype Transcriptome DEG PcDw 


Funding information

This study was supported by the National Natural Science Foundation of China (31372049) and the Funds for Modern Agricultural Industry Technology System in Shandong Province, China (SDAIT-06-06).

Compliance with ethical standards

Conflict of interest

The authors declare that we have no conflict of interest.

Supplementary material

11032_2018_907_MOESM1_ESM.docx (1.5 mb)
Online Resource 1 Phenotype of dwarf and standard pears. (DOCX 1507 kb)
11032_2018_907_MOESM2_ESM.xlsx (2.8 mb)
Online Resource 2 Expression values (FPKM values) of all annotated genes in Pyrus communis (XLSX 2845 kb)
11032_2018_907_MOESM3_ESM.xls (91 kb)
Online Resource 3 DEGs between dwarf and standard pears (XLS 91 kb)
11032_2018_907_MOESM4_ESM.xlsx (263 kb)
Online Resource 4 GO annotation of DEGs between dwarf and standard pears (XLSX 263 kb)
11032_2018_907_MOESM5_ESM.xlsx (12 kb)
Online Resource 5 GO enrichment of DEGs between dwarf and standard pears (XLSX 11 kb)
11032_2018_907_MOESM6_ESM.xlsx (9 kb)
Online Resource 6 KEGG enrichment of DEGs between dwarf and standard pears (XLSX 8 kb)
11032_2018_907_MOESM7_ESM.docx (303 kb)
Online Resource 7 KEGG maps of enriched KEGG pathways of DEGs between dwarf and standard pears (DOCX 303 kb)
11032_2018_907_MOESM8_ESM.xlsx (31 kb)
Online Resource 8 Differentially expressed transcription factor genes between dwarf and standard pears (XLSX 31 kb)
11032_2018_907_MOESM9_ESM.docx (13 kb)
Online Resource 9 Primer sequences for qRT-PCR testing in this study (DOCX 12 kb)
11032_2018_907_MOESM10_ESM.doc (61 kb)
Online Resource 10 Genes identified on scaffold00074 (DOC 61 kb)
11032_2018_907_MOESM11_ESM.docx (13 kb)
Online Resource 11 Differential expressed genes in scaffold00074 (DOCX 12 kb)


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Copyright information

© Springer Nature B.V. 2018

Authors and Affiliations

  1. 1.College of HorticultureQingdao Agricultural UniversityQingdaoChina
  2. 2.Qingdao Key Laboratory of Genetic Improvement and Breeding in Horticultural PlantsQingdaoChina

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