Functional genomic study in cereals requires an establishment of efficient transformation systems platform. Major QTLs have been identified in IRRI breeding programs; the gene validation platform enhances and facilitates input for breeding or genetic engineering of new rice varieties. Our aims are: 1) Development of gene-based marker system, to identify candidate genes in the QTL underlying a trait and 2) Elucidation of gene function. Capacity to do large-scale transformation of different rice varieties using Agrobacterium mediated with high efficiency at IRRI has been established. We obtain efficiency for japonica varieties in the range of 90-100% and elite indica variety IR64 in the range of 25-40%. Target–specific silencing using RNAi (Weil 2003) and amiRNAs (Warthmann 2008) and overexpression of genes are powerful tools for identifying and validating new and desired trait target genes. Using the Gene Validation Platform, transgenic plants over-expressing or silencing the candidate genes were developed, to validate/identify the gene function for the following: anaerobic germination tolerance (Septiningsih E, et. al.), rice spherical tungro virus resistance (Choi et. al.) and phosphate soil deficiency involving the major QTL for phosphate uptake Pup1 (Heuer et. al.), and drought tolerance involving major QTL 12.1 (Kohli, et. al.). This platform has also been used for temporal and spatial promoter studies.