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Rice Male Gamete Expression Database (RMEDB): A Web Resource for Functional Genomic Studies of Rice Male Organ Development

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Abstract

Oryza sativa (rice) is an economically important crop, which is valued as a staple food source and as genetic model for cereals. Rice production needs to increase substantially to meet the growing global demand. Genetic studies have indicated that anther and pollen development genes can be used as targets to improve yield. Although several genes related to male organ developmental pathways have been characterized, the complete signaling network remains unclear. We used publicly available anther and pollen development transcriptome datasets to identify candidates for functional genomics studies. In addition, we newly generated RNA-Seq data for anther, anther wall and pollen samples with leaf sheath as control to provide the expression data for genes that are not covered by microarray technologies in rice. We constructed a platform, the rice male gamete expression database (RMEDB), comprising microarray and RNA-Seq based 188 transcriptome samples across diverse rice tissues and developmental stages of O. sativa japonica and O. sativa indica. Meta-expression analysis identified genes expressed at specific stages of anther or pollen developments. The functionalities in RMEDB database (http://ricephylogenomics-khu.org/RMEDB/home.php) can serve to identify candidates in male organ development for functional genomic studies of rice.

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Data Availability

All newly generated RNASeq raw reads are deposited in ArrayExpress. Mature anther, anther wall and pollen samples are provided under accession number E-MTAB-7974. Leaf sheath data is deposited under accession number E-MTAB-8353.

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Acknowledgements

This work was supported by grants from the Next-Generation BioGreen 21 Program (PJ01366401 to KHJ and PJ01369001 to SKP), the Rural Development Administration, Republic of Korea.

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Author notes

  1. Anil Kumar Nalini Chandran and Woo-Jong Hong are equally contributed.

Authors and Affiliations

  1. Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin, 17104, Republic of Korea

    Anil Kumar Nalini Chandran, Woo-Jong Hong, Balachandran Abhijith, Yu-Jin Kim & Ki-Hong Jung

  2. School of Applied Biosciences, Kyungpook National University, Daegu, 41566, Republic of Korea

    Jinwon Lee & Soon Ki Park

Authors
  1. Anil Kumar Nalini Chandran
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  2. Woo-Jong Hong
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  3. Balachandran Abhijith
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  4. Jinwon Lee
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  5. Yu-Jin Kim
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  6. Soon Ki Park
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Contributions

AKNC, SKP, and KHJ designed the research. AKNC, AB, WJH, JWL and YJK performed the experiments and analyzed the data. AKNC, SKP, and KHJ wrote the manuscript.

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Correspondence to Soon Ki Park or Ki-Hong Jung.

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The author(s) declare no competing interest.

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Chandran, A.K.N., Hong, WJ., Abhijith, B. et al. Rice Male Gamete Expression Database (RMEDB): A Web Resource for Functional Genomic Studies of Rice Male Organ Development. J. Plant Biol. 63, 421–430 (2020). https://doi.org/10.1007/s12374-020-09267-1

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  • DOI: https://doi.org/10.1007/s12374-020-09267-1

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