Genome-wide analysis of endosperm-specific genes in rice

Abstract

The endosperm of the cereal crop is an important nutrient source for humans. It also acts as a critical integrator of plant seed growth and development. Despite its importance, the comprehensive understanding in regulating of endosperm development in rice remains elusive. Here, we performed a genomic survey comprising the identification and functional characterization of the endosperm-specific genes (OsEnS) in rice using Affymetrix microarray data and Gene Ontology (GO) analysis. A total of 151 endosperm-specific genes were identified, and the expression patterns of 13 selected genes were confirmed by qRT-PCR analysis. Promoter regions of the endosperm-specific expression genes were analyzed by PLACE Signal Scan Search. The results indicated that some motifs were involved in endosperm-specific expression regulation, and some cis-elements were responsible for hormone regulation. The bootstrap analysis indicated that the RY repeat (CATGCA box) was over-represented in promoter regions of endosperm-specific expression genes. GO analysis indicated that these genes could be classified into 12 groups, namely, transcription factor, stress/defense, seed storage protein (SSP), carbohydrate and energy metabolism, seed maturation, protein metabolism, lipid metabolism, transport, cell wall related, hormone related, signal transduction, and one unclassified group. Taken together, our results provide informative clues for further functional characterization of the endosperm-specific genes, which facilitate the understanding of the molecular mechanism in rice endosperm development.

Keywords: 1-Naphthaleneacetic acid; ABA; Abscisic acid; BAC; Bacterial artificial chromosomes; Basic leucine zipper; Cis-element; DAP; DNA binding with one finger; DOF; Days after pollination; Endosperm-specific expression; Endosperm-specific gene; Expression profile; FAA; Formalin–acetic acid–alcohol; GA; GO; Gene ontology; Genome; Gibberellin; IAA; Indole acid; KD; KEGG; KT; Knock-down; Kyoto Encuclopedia of Genes and Genomes; LEA; Late embryogenesis abundant; NAA; Non-redundant; ORF; Open reading frame; OsEns gene; PAC; PCD; Phage artificial chromosome; Programmed cell death; RNA interference; RNAi; Real-time quantitative polymerase chain reaction; Rice; SSP; Seed storage protein; TF; Transcription factor; bZIP; kinetin; nr; qRT-PCR.