The rice B-box zinc finger gene family: genomic identification, characterization, expression profiling and diurnal analysis

PLoS One. 2012;7(10):e48242. doi: 10.1371/journal.pone.0048242. Epub 2012 Oct 31.

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.

Methodology/principal findings: 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/significance: 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Abscisic Acid / physiology
  • Amino Acid Sequence
  • Chromosome Mapping
  • Chromosomes, Plant / genetics
  • Circadian Rhythm
  • Consensus Sequence
  • Enhancer Elements, Genetic
  • Gene Duplication
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant
  • Genes, Plant*
  • Genome, Plant
  • Molecular Sequence Annotation
  • Molecular Sequence Data
  • Oligonucleotide Array Sequence Analysis
  • Oryza / genetics*
  • Oryza / metabolism
  • Oryza / physiology
  • Phylogeny
  • Plant Growth Regulators / physiology
  • Plant Proteins / genetics*
  • Protein Structure, Tertiary
  • Sequence Homology, Amino Acid
  • Transcription Factors / genetics*
  • Transcriptome
  • Zinc Fingers / genetics

Substances

  • Plant Growth Regulators
  • Plant Proteins
  • Transcription Factors
  • Abscisic Acid

Grant support

This work was supported by grants from the National 863 Project (2012AA100103) and the National Natural Science Foundation of China (30921091). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.