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

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.