Vietnamese Rice Varieties Resequenced

Rice is the most important agricultural commodity of Vietnam, however climate change threatens rice production in Vietnam through increased risk of flooding, salinisation of the soils, periods of drought and newly emerging pests and pathogens. In order to aid the development of breeding lines which are resistant to these stresses, 36 traditional varieties have been selected for resequencing. Each line exhibits a desirable phenotype for tolerance to drought, salinity or submergence, resistance to pests (e.g. brown planthopper, blast and bacterial blight) or has high quality or yield potential. The lines are a mixture of indicas and tropical japonicas, and have been phenotyped for fifty agronomic traits, under field conditions in Vietnam.

These 36 lines have also been sequenced with the Illumina HiSeq 2000 to give 100bp paired-end reads, with an average depth of 30x per sample. The reads were aligned to the temperate japonica reference (Nipponbare) and the whole genome shotgun indica reference (93-11). Variants have been called against each of the references, and filtered to achieve a high confidence set of variants specific to the Vietnamese lines. A database containing these variants is under development to aid researchers and breeders in the improvement of stress-tolerant rice for Vietnam.