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KMID : 0368420200630060421
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Journal of Plant Biology
2020 Volume.63 No. 6 p.421 ~ p.430
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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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Chandran Anil Kumar Nalini
Hong Woo-Jong
Abhijith Balachandran
Lee Jin-Won
Kim Yu-Jin
Park Soon-Ki
Jung Ki-Hong
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Abstract
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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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KEYWORD
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Database, Functional genomics, Male development, Meta-expression, Rice
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