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Open Access Research article

Genomic survey, expression profile and co-expression network analysis of OsWD40 family in rice

Yidan Ouyang1, Xiaolong Huang2, Zhanhua Lu3 and Jialing Yao2*

Author Affiliations

1 National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China

2 College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China

3 College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China

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BMC Genomics 2012, 13:100  doi:10.1186/1471-2164-13-100

Published: 20 March 2012

Abstract

Background

WD40 proteins represent a large family in eukaryotes, which have been involved in a broad spectrum of crucial functions. Systematic characterization and co-expression analysis of OsWD40 genes enable us to understand the networks of the WD40 proteins and their biological processes and gene functions in rice.

Results

In this study, we identify and analyze 200 potential OsWD40 genes in rice, describing their gene structures, genome localizations, and evolutionary relationship of each member. Expression profiles covering the whole life cycle in rice has revealed that transcripts of OsWD40 were accumulated differentially during vegetative and reproductive development and preferentially up or down-regulated in different tissues. Under phytohormone treatments, 25 OsWD40 genes were differentially expressed with treatments of one or more of the phytohormone NAA, KT, or GA3 in rice seedlings. We also used a combined analysis of expression correlation and Gene Ontology annotation to infer the biological role of the OsWD40 genes in rice. The results suggested that OsWD40 genes may perform their diverse functions by complex network, thus were predictive for understanding their biological pathways. The analysis also revealed that OsWD40 genes might interact with each other to take part in metabolic pathways, suggesting a more complex feedback network.

Conclusions

All of these analyses suggest that the functions of OsWD40 genes are diversified, which provide useful references for selecting candidate genes for further functional studies.

Keywords:
Oryza sativa; Expression profiles; Microarray; WD40 gene; Co-expression network