title: RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression.
abstract: MicroRNAs (miRNAs) are known to play critical roles in plant development and stress-response regulation, and they frequently display multi-targeting characteristics. The control of defined rice phenotypes occurs through multiple genes; however, evidence demonstrating the relationship between agronomic traits and miRNA expression profiles is lacking. In this study, we investigated eight yield-related traits in 187 local rice cultivars and profiled the expression levels of 193 miRNAs in these cultivars using microarray analyses. By integrating the miRBase database, the rice annotation project database, and the miRanda and psRNATarget web servers, we constructed a database (RiceATM) that can be employed to investigate the association between rice agronomic traits and miRNA expression. The functions of this platform include phenotype selection, sample grouping, microarray data pretreatment, statistical analysis and target gene predictions. To demonstrate the utility of RiceATM, we used the database to identify four miRNAs associated with the heading date and validated their expression trends in the cultivars with early or late heading date by real-time PCR. RiceATM is a useful tool for researchers seeking to characterize the role of certain miRNAs for a specific phenotype and discover potential biomarkers for breeding or functional studies.Database URL: http://syslab3.nchu.edu.tw/rice/.
authors.affiliation: Institute of Biomedical Sciences.
authors.forename: Wei-Ting
authors.initials: WT
authors.lastname: Liu
authors.affiliation: Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.
authors.forename: Chia-Chun
authors.initials: CC
authors.lastname: Yang
authors.affiliation: Chiayi Branch Station, Tainan District Agricultural Research and Extension Station, Council of Agriculture, Chiayi, Taiwan.
authors.forename: Rong-Kuen
authors.initials: RK
authors.lastname: Chen
authors.affiliation: Taiwan Agricultural Research Institute, Taichung, Taiwan.
authors.forename: Woei-Shyuan
authors.initials: WS
authors.lastname: Jwo
authors.affiliation: Kaohsiung District Agricultural Research and Extension Station, Council of Agriculture, Kaohsiung, Taiwan.
authors.forename: Chih-Wen
authors.initials: CW
authors.lastname: Wu
authors.affiliation: Taitung District Agricultural Research and Extension Station, Council of Agriculture, Taitung, Taiwan.
authors.forename: Wen-Yen
authors.initials: WY
authors.lastname: Ting
authors.affiliation: Hualien District Agricultural Research and Extention Station, Council of Agriculture, Hualien, Taiwan.
authors.forename: Dah-Pyng
authors.initials: DP
authors.lastname: Shung
authors.affiliation: Institute of Biomedical Sciences jwchen@dragon.nchu.edu.tw.|Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung, Taiwan.
authors.forename: Chun-Chi
authors.initials: CC
authors.lastname: Liu
authors.affiliation: Institute of Biomedical Sciences jwchen@dragon.nchu.edu.tw.|Institute of Molecular Biology, National Chung Hsing University, Taichung, Taiwan.|Agricultural Biotechnology Center, National Chung Hsing University, Taichung, Taiwan and.|Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung, Taiwan.
authors.forename: Jeremy J W
authors.initials: JJ
authors.lastname: Chen
mesh_terms: D018556:Crops, Agricultural / Q000235:genetics / Q000378:metabolism; D030541:Databases, Genetic; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D035683:MicroRNAs / Q000096:biosynthesis / Q000235:genetics; D058977:Molecular Sequence Annotation; D012275:Oryza / Q000235:genetics / Q000378:metabolism; D040641:Quantitative Trait Loci; D018749:RNA, Plant / Q000096:biosynthesis / Q000235:genetics; D012984:Software
chemical_list: D035683:MicroRNAs; D018749:RNA, Plant