title: The rice B-box zinc finger gene family: genomic identification, characterization, expression profiling and diurnal analysis.
abstract: BACKGROUND
  The B-box (BBX) -containing proteins are a class of zinc finger proteins that contain one or two B-box domains and play important roles in plant growth and development. The Arabidopsis BBX gene family has recently been re-identified and renamed. However, there has not been a genome-wide survey of the rice BBX (OsBBX) gene family until now.
  
  
  RESULTS
  In this study, we identified 30 rice BBX genes through a comprehensive bioinformatics analysis. Each gene was assigned a uniform nomenclature. We described the chromosome localizations, gene structures, protein domains, phylogenetic relationship, whole life-cycle expression profile and diurnal expression patterns of the OsBBX family members. Based on the phylogeny and domain constitution, the OsBBX gene family was classified into five subfamilies. The gene duplication analysis revealed that only chromosomal segmental duplication contributed to the expansion of the OsBBX gene family. The expression profile of the OsBBX genes was analyzed by Affymetrix GeneChip microarrays throughout the entire life-cycle of rice cultivar Zhenshan 97 (ZS97). In addition, microarray analysis was performed to obtain the expression patterns of these genes under light/dark conditions and after three phytohormone treatments. This analysis revealed that the expression patterns of the OsBBX genes could be classified into eight groups. Eight genes were regulated under the light/dark treatments, and eleven genes showed differential expression under at least one phytohormone treatment. Moreover, we verified the diurnal expression of the OsBBX genes using the data obtained from the Diurnal Project and qPCR analysis, and the results indicated that many of these genes had a diurnal expression pattern.
  
  
  CONCLUSIONS
  The combination of the genome-wide identification and the expression and diurnal analysis of the OsBBX gene family should facilitate additional functional studies of the OsBBX genes.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Jianyan
authors.initials: J
authors.lastname: Huang
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Zhao
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Weng
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
mesh_terms: D000040:Abscisic Acid / Q000502:physiology; D000595:Amino Acid Sequence; D002874:Chromosome Mapping; D032461:Chromosomes, Plant / Q000235:genetics; D002940:Circadian Rhythm; D016384:Consensus Sequence; D004742:Enhancer Elements, Genetic; D020440:Gene Duplication; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D010802:Phylogeny; D010937:Plant Growth Regulators / Q000502:physiology; D010940:Plant Proteins / Q000235:genetics*; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D014157:Transcription Factors / Q000235:genetics*; D059467:Transcriptome; D016335:Zinc Fingers / Q000235:genetics
chemical_list: D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors; D000040:Abscisic Acid