Genomic and Epigenomic Changes in Rice T-DNA Transformation

Agrobacterium-mediated transformation is a well-established method for the integration of T-DNA into rice genome. During transformation, the genomic and epigenomic changes such as DNA methylation and copy number variations are still unclear. Our goal is to exam DNA methylation and copy number variation changes during rice transformation. In this project we have rice calli prepared in 4 different treatments in transformation protocol in order to identify the effect of individual treatment. We collected their leaf samples for whole genome bisulfite sequencing (WGBS). We compared these four libraries with wild type rice data available from GEO SRR618545. The bisulfited converted are trimmed to remove low quality sequences, and aligned and processed by BS-Seekers2.

In our preliminary result, we found particular treatments on calli show a greater changes of global methylation levels than others, that are consistent with the previous study. The data shows that CG and CHH sites tend to be hyper-methylated in treated calli and these changes are revealed in differentially methylated regions. We also identified genomic regions that show copy number variation; suggesting the genomic impact from T-DNA transformation. These regions may be served as amplification/deletion hot spots during transformation where genes in these genes are likely to be affected., We performed the first detailed analysis of rice methylomes in rice transformation with different conditions, and the result can greatly improve our understanding of the transformation impact on rice epigenome.