Abstract
Flowering is one of the important defining features of angiosperms. The initiation of flower development and the formation of different floral organs are the results of the interplays among numerous genes. But until now, just fewer genes have been found linked with flower development. And the functions of lots of genes of Arabidopsis thaliana are still unknown. Although, the quartet model successfully simplified the ABCDE model to elaborate the molecular mechanism by introducing protein-protein interactions (PPIs). We still don't know much about several important aspects of flower development. So we need to discriminate even more genes involving in the flower development. In this study, we identified seven differentially modules through integrating the weighted gene co-expression network analysis (WGCNA) and Support Vector Machine (SVM) method to analyze co-expression network and PPIs using the public floral and non-floral expression profiles data of Arabidopsis thaliana. Gene set enrichment analysis was used for the functional annotation of the related genes, and some of the hub genes were identified in each module. The potential floral organ morphogenesis genes of two significant modules were integrated with PPI information in order to detail the inherent regulation mechanisms. Finally, the functions of the floral patterning genes were elucidated by combining the PPI and evolutionary information. It was indicated that the sub-networks or complexes, rather than the genes, were the regulation unit of flower development. We found that the most possible potential new genes underlining the floral pattern formation in A. thaliana were FY, CBL2, ZFN3, and AT1G77370; among them, FY, CBL2 acted as an upstream regulator of AP2; ZFN3 activated the flower primordial determining gene AP1 and AP2 by HY5/HYH gene via photo induction possibly. And AT1G77370 exhibited similar function in floral morphogenesis, same as ELF3. It possibly formed a complex between RFC3 and RPS15 in cytoplasm, which regulated TSO1 and CPSF160 in the nucleus, to control the floral organ morphogenesis. This process might also be fine tuning by AT5G53360 in the nucleus.
Highlights
Flowering is one of the important defining features of angiosperms
It was confirmed by literature retrieval that the early flowering 3 (ELF3) of Arabidopsis was responsible for generation of circadian rhythm as well as for regulation of photoperiodic flowering (Zhao et al, 2012)
We need to discriminate even more genes involving in the flower development to better understand the molecular regulation mechanism of the floral pattern formation in A. thaliana
Summary
Flowering is one of the important defining features of angiosperms. Flowering is the most pivotal stage that interposes vegetative growth stage and fruiting stage during the development in the higher plants. Each flower starts from a small fraction of undifferentiated cell, and develops into a complex pattern structure while different organs precisely occupy different positions This process, named as the floral pattern formation, attracts growing attentions in recent years (Bemis et al, 2013). In 1991, the ABC model was proposed by Coen and Meyerowitz (1991) to elaborate the classification of homeotic genes, and to explain the mechanisms of how A, B, and C class genes forming the floral organs in the precise positions during flower development. Protein is the function executor of a gene From this point of view, a quartet model was proposed by Theissen et al, who presumed that the development of a specific floral organ was achieved by the formation of a single protein complex by both ACB transcription factors and SEPALLATA transcription factors (Theissen and Saedler, 2001). The quartet model successfully simplified the ABCDE model by introducing protein-protein interactions (PPIs)
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