Pipeline for Detection of Mutations from Whole-Genome Sequence Data of Rice

The technology of next-generation sequencing (NGS) is enables to obtain the whole-genome sequence of individual plant. For the improvement of crops, especially for the marker assisted breeding, discovery of DNA markers is essential. The efficient method to detect polymorphism from the NGS data is required. We have developed 50,000 lines of regenerated rice for making mutant panel by Tos17 insertions. Half of mutant lines showed at least one phenotype. The difference of phenotype of regenerated plant is called ‘somaclonal variation’. To understand of the somaclonal variation, we sequenced some regenerated lines and analyzed the NGS data using the original pipeline for mutation detection. We found the mutation rate of regenerated rice is accelerated. We also found structural change of genome including a large segmental duplication, small deletions in addition to transposition of Tos17. We will describe the pipeline for detection of these mutations. The pipeline integrated into our web-based database system. Detected polymorphisms will be useful for functional analysis of rice genes. And also, our techniques for mutation detection will contribute for molecular breeding of crops.

Miyao, A., et al. (2012) Plant Cell Physiol. 53:256-264.