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

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.