Comparison of the transcriptomic analysis between two Chinese white pear (Pyrus bretschneideri Rehd.) genotypes of different stone cells contents

Jinyun Zhang; Xi Cheng; Qing Jin; Xueqiang Su; Manli Li; Chongchong Yan; Xiaoyu Jiao; Daihui Li; Yi Lin; Yongping Cai

doi:10.1371/journal.pone.0187114

Comparison of the transcriptomic analysis between two Chinese white pear (Pyrus bretschneideri Rehd.) genotypes of different stone cells contents

PLoS One. 2017 Oct 31;12(10):e0187114. doi: 10.1371/journal.pone.0187114. eCollection 2017.

Authors

Jinyun Zhang^{1

2}, Xi Cheng¹, Qing Jin¹, Xueqiang Su¹, Manli Li¹, Chongchong Yan², Xiaoyu Jiao¹, Daihui Li¹, Yi Lin¹, Yongping Cai¹

Affiliations

¹ School of Life Science, Anhui Agricultural University, Hefei, China.
² Horticultural Institute, Anhui Academy of Agricultural Sciences, Hefei, Anhui, China.

Abstract

Stone cell content is thought to be one of the key determinants for fruit quality in pears. However, the molecular mechanism of stone cell development remains poorly understood. In this study, we found that the stone cell clusters (SCCs) distribution and area in 'Dangshan Su' (with abundant stone cells) were higher as compared to 'Lianglizaosu' (low stone cell content bud sport of 'Dangshan Su') based on the histochemical staining, and the correlations of lignin content with stone cell content and SCC area was significant. The fruits of 'Dangshan Su' and 'Lianglizaosu' at three different developmental stages (23 and 55 days after flowering and mature) were sampled for comparative transcriptome analysis to explore the metabolic pathways associated with stone cell development. A total of 42444 unigenes were obtained from two varieties, among which 7203 differentially expressed genes (DEGs) were identified by comparison of the six transcriptomes. Specifically, many DEGs associated with lignin biosynthesis were identified, including coumaroylquinate 3-monooxygenase (C3H), shikimate O-hydroxycinnamoyltransferase (HCT), ferulate 5-hydroxylase (F5H), cinnamyl alcohol dehydrogenase (CAD) and peroxidase (POD), as well as genes related to carbon metabolism, such as sorbitol dehydrogenase-like (SDH-like) and ATP-dependent 6-phosphofructokinase (ATP-PFK). At the peak of the stone cell content (55 days after flowering), the expression level of these genes in 'Dangshan Su' was significantly increased compared with 'Lianglizaosu', indicating that these genes were closely related to stone cell development. We validated the transcriptional levels of 33 DEGs using quantitative real-time polymerase chain reaction (qRT-PCR) analysis. The results were consistent with the transcriptome analysis, indicating the reliability of transcriptome data. In addition, subcellular localization analysis of three DEGs in lignin synthesis (PbC3H, PbF5H and PbPOD) revealed that these proteins are mainly distributed in the cell membrane and cytoplasm. These results provide new insights into the molecular mechanism of stone cell formation.

Publication types

Comparative Study

MeSH terms

Fruit / cytology*
Fruit / growth & development
Fruit / metabolism
Gene Expression Profiling
Gene Expression Regulation, Plant
Genetic Association Studies
Lignin / metabolism
Metabolic Networks and Pathways / genetics
Pyrus / genetics*
Pyrus / metabolism
Real-Time Polymerase Chain Reaction
Sequence Analysis, DNA

Substances

Lignin

Grants and funding

This work was supported by National Natural Science Foundation of China (http://www.nsfc.gov.cn/), Award Number 31640068 (Grant Recipient: Yongping Cai); and Postgraduate Student’s Innovation Fund of Anhui Agricultural University (http://yjsc.ahau.edu.cn/web/index.aspx), Graduate School of Anhui Agricultural University, Award Number 2017yjs-32 (Grant Recipient: Xi Cheng). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.