A Bioinformatics Workflow for Genetic Association Studies of Traits in Indonesian Rice

Asian rice is a staple food in Indonesia and worldwide, and its production is essential to food security. Cataloging and linking genetic variation in Asian rice to important traits, such as quality and yield, is needed in developing superior varieties of rice. We develop a bioinformatics workflow for quality control and data analysis of genetic and trait data for a diversity panel of 467 rice varieties found in Indonesia. The bioinformatics workflow operates using a back-end relational database for data storage and retrieval. Quality control and data analysis procedures are implemented and automated using the whole genome data analysis toolset, PLINK, and the [R] statistical computing language. The 467 rice varieties were genotyped using a custom array (717,312 genotypes total) and phenotyped for 12 traits in four locations in Indonesia across multiple seasons. We applied our bioinformatics workflow to these data and present prototype genome-wide association results for a continuous trait - days to flowering. Two genetic variants, located on chromosome 4 and 12 of the rice genome, showed evidence for association in these data. We conclude by outlining extensions to the workflow and plans for more sophisticated statistical analyses.