Significance Although recent advances in next-generation sequencing have facilitated the construction of whole genomes from hundreds of organisms, considerable barriers still restrict the functional understanding of the genes that they contain. An initial prerequisite for such an understanding is the availability of high-quality gene libraries (ORFeomes) amenable to high-throughput functional experiments. Here we develop a massively parallel next-generation sequencing method, PLATE-seq, and leverage the method to construct an ORFeome for rice, providing a toolkit for systematic functional study in an agricultural species. To demonstrate the utility of these resources, we present a map of rice protein–protein interactions.