In silico analysis of expression data for identification of genes involved in spatial accumulation of calcium in developing seeds of rice

• Published in: Omics (Larchmont, N.Y.) Vol. 16; no. 7-8; p. 402
• Main Authors: Goel, Anshita, Gaur, Vikram S, Arora, Sandeep, Gupta, Sanjay, Kumar, Anil
• Format: Journal Article
• Language: English
• Published: United States 01.07.2012
• Subjects: Analysis of Variance; Antiporters - genetics; Antiporters - metabolism; Base Sequence; Calcium - metabolism; Calcium Channels - genetics; Calcium Channels - metabolism; Calcium-Transporting ATPases - genetics; Calcium-Transporting ATPases - metabolism; Computer Simulation; Gene Expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Germination - genetics; High-Throughput Nucleotide Sequencing; Models, Genetic; Oligonucleotide Array Sequence Analysis; Oryza - genetics; Oryza - growth & development; Oryza - metabolism; Plant Proteins - genetics; Plant Proteins - metabolism; Principal Component Analysis; Regulatory Sequences, Nucleic Acid; Seeds - genetics; Seeds - growth & development; Seeds - metabolism
• ISSN: 1557-8100
• DOI: 10.1089/omi.2012.0004

The calcium (Ca(2+)) transporters, like Ca(2+) channels, Ca(2+) ATPases, and Ca(2+) exchangers, are instrumental for signaling and transport. However, the mechanism by which they orchestrate the accumulation of Ca(2+) in grain filling has not yet been investigated. Hence the present study was designed to identify the potential calcium transporter genes that may be responsible for the spatial accumulation of calcium during grain filling. In silico expression analyses were performed to identify Ca(2+) transporters that predominantly express during the different developmental stages of Oryza sativa. A total of 13 unique calcium transporters (7 from massively parallel signature sequencing [MPSS] data analysis, and 9 from microarray analysis) were identified. Analysis of variance (ANOVA) revealed differential expression of the transporters across tissues, and principal component analysis (PCA) exhibited their seed-specific distinctive expression profile. Interestingly, Ca(2+) exchanger genes are highly expressed in the initial stages, whereas some Ca(2+) ATPase genes are highly expressed throughout seed development. Furthermore, analysis of the cis-elements located in the promoter region of the subset of 13 genes suggested that D of proteins play essential roles in regulating the expression of Ca(2+) transporter genes during rice seed development. Based on these results, we developed a hypothetical model explaining the transport and tissue specific distribution of calcium in developing cereal seeds. The model may be extrapolated to understand the mechanism behind the exceptionally high level of calcium accumulation seen in grains like finger millet.