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
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Bioinformatics Research Group, Bina Nusantara University, Jakarta, Indonesia [email protected] http://www.binus.edu Indonesian Center for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor, Indonesia
Abstract. 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. Keywords: data analysis, workflow, agriculture genetics, genome-wide association study, bioinformatics, statistical genetics.
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Introduction
Indonesia is located in one of the most biodiverse regions in the world. Studying the biodiversity unique to this region for agriculturally important species can lead to crop and animal improvements. Oryza saliva or 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 to develop new varieties of rice with superior properties. The 389 Megabase (Mb) Asian rice genome consist of 12 chromosomes [1]. Throughout the genome, sequence variations called single-nucleotide polymorphism (SNP) are common. At these locations (or loci), the alternative nucleotides Linawati et al. (Eds.): ICT-EurAsia 2014, LNCS 8407, pp. 356–364, 2014. c IFIP International Federation for Information Processing 2014
A Bioinformatics Workflow for Genetic Association Studies
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are called alleles, and the two alleles from the paired chromosomes are called SNP genotypes. High-throughput genotyping and sequencing technologies have revolutionized agriculture genetics, allowing for genome-wide interrogation of thousands of SNPs. Recent research using these technologies, have focused on genome-wide genotyping of a rice diversity panel consisting of 413 varieties from 82 countries [2]. While this research has identified genetic regions associated with many complex traits, ther
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