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Network Analysis of Differentially Expressed Genes across Four Sweet Orange Varieties Reveals a Conserved Role of Gibberellin and Ethylene Responses and Transcriptional Regulation in Expanding Citrus Fruits

  • Minghao Cao
  • Jian Zheng
  • Yihong Zhao
  • Zhiqiang Zhang
  • Zhi-Liang ZhengEmail author
Article

Abstract

Citrus represents the most important non-climacteric fruits and thus understanding transcriptional control during fruit development is important for improving fruit yield and quality. Compared to relatively intensive transcriptomic studies of ripening citrus fruits, much less is known regarding expanding fruits. To provide a systems view of hormone response and transcriptional regulation in citrus fruit development from Stage I (slow fruit growth) to Stage II (rapid growth), we re-analyzed the fruit transcriptomes which we previously collected from the sweet orange varieties, Newhall, Xinhui, Bingtang, and Succari (Citrus sinensis L. Osbeck). A total of 3145 genes were differentially expressed across all four varieties, indicating that they likely have conserved functions in orange fruit development. Using a gene coexpression network-based systems approach, we constructed the subnetworks respectively for gibberellin response, ethylene response, transcription factors and chromatin modifications. Analysis of these subnetworks has led to the identification of more than a dozen major hub genes, such as EXPA1, GASA1/14, ERF13, HB22, ATK1, and TOPII, which represent the most promising candidates for future functional characterization.

Keywords

Citrus Fruit development Gene coexpression network Hormone response Transcription and chromatin modification 

Abbreviations

DPA

Days post anthesis

ERF

Ethylene response factor

EXPA

Expansin

FDR

False discovery rate

GA

Gibberellin

GASA

GA-Stimulated in Arabidopsis

GO

Gene ontology

WGCNA

Weighted gene coexpression network analysis

Notes

Acknowledgements

This research was mainly supported by a grant from Chongqing Science and Technology Commission (Grant No. cstc2012gg-yyjsB80004).

Author Contributions

M.C., J. Z., Z.Z and Z.-L.Z. performed bioinformatic analyses, Y.Z. performed systems biology analysis, and all authors discussed the results. Y.Z. and Z.-L.Z. wrote the article.

Supplementary material

12042_2018_9213_MOESM1_ESM.pdf (43 kb)
Fig. S1 GA response subnetwork with all gene nodes shown. (PDF 42 kb)
12042_2018_9213_MOESM2_ESM.pdf (47 kb)
Fig. S2 Ethylene response subnetwork with all gene nodes shown. (PDF 47 kb)
12042_2018_9213_MOESM3_ESM.pdf (32 kb)
Fig. S3 Transcription factor gene subnetwork with all gene nodes shown. (PDF 32 kb)
12042_2018_9213_MOESM4_ESM.pdf (298 kb)
Fig. S4 Chromatin modification gene network with all gene nodes shown. (PDF 297 kb)
12042_2018_9213_MOESM5_ESM.xlsx (90 kb)
Table S1 List of 3145 commonly regulated genes in four sweet orange varieties and the result of GO enrichment analysis. (XLSX 89 kb)
12042_2018_9213_MOESM6_ESM.xlsx (61 kb)
Table S2 List of genes in the four subnetworks. (XLSX 61 kb)

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© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Plant Nutrient Signaling and Fruit Quality Improvement Laboratory, National Citrus Engineering Research Center, Citrus Research InstituteSouthwest UniversityChongqingChina
  2. 2.Department of Health Policy & Health Services ResearchBoston UniversityBostonUSA
  3. 3.Department of Biological Sciences, Lehman CollegeCity University of New YorkBronxUSA

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