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Genome-wide identification, expression profiling, and network analysis of calcium and cadmium transporters in rice (Oryza sativa L.)

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Abstract

Calcium (Ca) and cadmium (Cd) are transition metals coexisting in the ecosystem. Ca is indispensable for the growth and development of plants as well as animals, while Cd is regarded as a toxic heavy metal for the living system. The transportation of Cd in the biological systems often used the pathways of Ca because of chemical similarities. High concentrations of cadmium replace Ca, Mn, and Zn from their respective metalloprotein sites and strongly associated with them. Replaced minerals from their metalloprotein sites are often released as an oxidative ion that is detrimental to it. The common transportation mechanism of Ca and Cd is implicit in the role of common and similar transporters for transporting them in plants. Thus, our study was done to identify the transporters for Ca and Cd and characterize them for similarity in terms of cotransportation system. A profile-based search program identified 44 transporters genes for Ca transportation and 70 genes for cadmium transportation. They were categorized into different groups based on the presence of signature motifs and domains. Identified transporters were characterized for genomic distribution, gene structure, annotation, conserved signature motifs, and domain. Further, cis motif analysis, heat map, gene ontology, and protein–protein interaction were conducted for Ca and Cd transporter genes. In silico expression showed Os05g0319800-1304 and Os0319800-6065 transporter genes were overexpressed for Ca and Os07g00232800-40298 and Os07g00384500-25924 transporter genes overexpressed for Cd transporter. These genes could be used as a candidate genes for enhancing the Ca concentration with reduced Cd content in rice using biotechnological approaches. Twenty-seven genes were found as the common transporters for Ca and Cd. Both active and passive transporter mechanisms act as cotransporters for Ca and Cd. The common signature motifs and domains can be targeted for the characterization of cotransporters of different minerals.

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All the data generated have been given in the manuscript.

Abbreviations

NCBI:

National Centre for Biotechnology Information

SMART:

Simple modular architecture research tools

MEME:

Multiple Em for motif elicitation

KDa:

Kilo Dalton

RPKM:

Read per kilobase million

DEG:

Differentially expressed genes

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Acknowledgements

Authors are thankful to the Department of Agricultural Biotechnology and Molecular Biology for providing facilities and infrastructure to perform the mentioned work.

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Authors and Affiliations

  1. Department of Agricultural Biotechnology and Molecular Biology, CBS&H, RPCAU-Pusa, Samastipur, India

    Shubham Kothari, V. K. Sharma & Sarita Kumari

  2. Department of Seed Science and Technology, PGCA, RPCAU-Pusa, Samastipur, India

    Sumeet Kumar Singh

  3. Centre for Advanced Studies on Climate Change, RPCAU-Pusa, Samastipur, India

    Ashutosh Singh

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  1. Shubham Kothari
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  2. V. K. Sharma
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Correspondence to Sarita Kumari.

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Communicated by P. Stephen Baenziger.

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Kothari, S., Sharma, V.K., Singh, A. et al. Genome-wide identification, expression profiling, and network analysis of calcium and cadmium transporters in rice (Oryza sativa L.). CEREAL RESEARCH COMMUNICATIONS (2024). https://doi.org/10.1007/s42976-024-00492-9

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