Rice Male Gamete Expression Database (RMEDB): A Web Resource for Functional Genomic Studies of Rice Male Organ Developme
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TECHNICAL REPORT
Rice Male Gamete Expression Database (RMEDB): A Web Resource for Functional Genomic Studies of Rice Male Organ Development Anil Kumar Nalini Chandran1 · Woo‑Jong Hong1 · Balachandran Abhijith1 · Jinwon Lee2 · Yu‑Jin Kim1 · Soon Ki Park2 · Ki‑Hong Jung1 Received: 18 March 2020 / Revised: 8 May 2020 / Accepted: 6 July 2020 © Korean Society of Plant Biologist 2020
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 (https:// ricephylogenomics-khu.org/RMEDB/home.php) can serve to identify candidates in male organ development for functional genomic studies of rice. Keywords Database · Functional genomics · Male development · Meta-expression · Rice
Introduction Over the past decades, Oryza sativa (rice) has emerged as a model crop for genetic and functional genomic studies of the family Poaceae. This trend has been established because Anil Kumar Nalini Chandran and Woo-Jong Hong are equally contributed. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s12374-020-09267-1) contains supplementary material, which is available to authorized users. * Soon Ki Park [email protected] * Ki‑Hong Jung [email protected] 1
Graduate School of Biotechnology and Crop Biotech Institute, Kyung Hee University, Yongin 17104, Republic of Korea
School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
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of the favorable genomic features of rice as well as the fact that it is the major nutrient source for more than half of the world’s population (Li et al. 2018). In the wake of growing global population, rice productivity needs to increase substantially. Among several factors, rice grain yield is highly influenced by pollen tube growth and function (Li et al. 2013). Previously, abnormalities in anther or pollen development have been shown to result in male sterility or yield reduction (Zhang e
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