Genome-Wide Analysis of Endosperm-Specific Genes in Rice

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 GO analysis of the endosperm-specific genes (OsEnS) in rice using Affymetrix microarray data on CREP. In total, we identified 151 genes that showed tissue specific expression in rice endosperm. qRT-PCR analysis of 13 randomly selected genes from the 151 genes have confirmed their endosperm-specific expression. 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 RY repeat (CATGCA box) was over-represented in promoter regions of endosperm-specific expression genes. Gene Ontology analysis indicated that those genes could be classified into 11 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.