Int J Biol Sci 2011; 7(1):28-40. doi:10.7150/ijbs.7.28

Research Paper

Functional Genomics of Rice Pollen and Seed Development by Genome-wide Transcript Profiling and Ds Insertion Mutagenesis

Shu-Ye Jiang, Srinivasan Ramachandran

Rice Functional Genomics Group, Temasek Life Sciences Laboratory, 1 Research Link, Singapore 117604

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Jiang SY, Ramachandran S. Functional Genomics of Rice Pollen and Seed Development by Genome-wide Transcript Profiling and Ds Insertion Mutagenesis. Int J Biol Sci 2011; 7(1):28-40. doi:10.7150/ijbs.7.28. Available from

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Rice pollen and seed development are directly related to grain yield. To further improve rice yield, it is important for us to functionally annotate the genes controlling pollen/seed development and to use them for rice breeding. Here we first carried out a genome-wide expression analysis with an emphasis on genes being involved in rice pollen and seed development. Based on the transcript profiling, we have identified and functionally classified 82 highly expressed pollen-specific, 12 developing seed-specific and 19 germinating seed-specific genes. We then presented the utilization of the maize transposon Dissociation (Ds) insertion lines for functional genomics of rice pollen and seed development and as alternative germplasm resources for rice breeding. We have established a two-element Activator/Dissociation (Ac/Ds) gene trap tagging system and generated around 20,000 Ds insertion lines. We have subjected these lines for screens to obtain high and low yield Ds insertion lines. Some interesting lines have been obtained with higher yield or male sterility. Flanking Sequence Tags (FSTs) analyses showed that these Ds-tagged genes encoded various proteins including transcription factors, transport proteins, unknown functional proteins and so on. They exhibited diversified expression patterns. Our results suggested that rice could be improved not only by introducing foreign genes but also by knocking out its endogenous genes. This finding might provide a new way for rice breeder to further improve rice varieties.

Keywords: Activator/Dissociation (Ac/Ds), flanking sequence tags, gene trap, germplasm, grain yield, Pollen and seed development