In Silico Analysis of Expression Data for Identification of Genes Involved in Spatial Accumulation of Calcium in Developing Seeds of Rice

Abstract

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 Dof 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.

Ca2+/Cation Antiporters (CaCA): Identification, Characterization and Expression Profiling in Bread Wheat (Triticum aestivum L.)

“…The majority of TaCAX genes were highly expressed in grain except TaCAX3 group genes, which were highly expressed in root and stem (Figure 6A). The high expression of CAX genes is also reported in seed of rice and Arabidopsis (Goel et al, 2012; Bickerton and Pittman, 2015). …”

Calcium Biofortification: Three Pronged Molecular Approaches for Dissecting Complex Trait of Calcium Nutrition in Finger Millet (Eleusine coracana) for Devising Strategies of Enrichment of Food Crops

“…Our preliminary study based on rice Ca sensor and transporter data suggests that Ca transporters (especially Ca Exchanger) are the main Ca transporting proteins that pump Ca inside seed. Based on the structural and expression analysis of the calcium transporter genes and available data in literature, a hypothetical model for accumulation of calcium in the cereal grains was proposed (Goel et al, 2011, 2012). The nine calcium transporter genes identified through the analysis of rice MPSS and microarray data were tested and one calcium ATPase and one calcium exchanger was found to be highly expressed in high seed calcium finger millet genotype.…”

“…S1 (booting), S2 (spike emergence), S3 (pollination), S4 (Grain filling or milky) and S5 (seed maturation). (Adapted from Goel et al, 2012). …”

CAX‐ing a wide net: Cation/H+ transporters in metal remediation and abiotic stress signalling

“…Likewise, in silico expression analyses has revealed that CAX genes are highly expressed in the initial stages of seed development in rice (Goel et al . 2012). This suggests that enhanced expression of CAX genes may improve rice varieties (Kim et al .…”