Data construction

The data obtained from the rice GWAS employing 176 temperate japonica varieties included single nucleotide variants and phenotypic data for 7 traits (Yano et al., 2016). The low-quality bases and adapter sequences in each read were removed by using Trimmomatic 0.36 (Bolger et al. 2014). The reads were mapped to the IRGSP-1.0 Nipponbare reference genome (Kawahara et al. 2013) by BWA-mem (v0.7.15) with the default setting (Li and Durbin 2009), and local realignment was conducted by using GATK 3.7 (Van der Auwera et al. 2013). After removing PCR duplicates with Picard 2.9.0 (http://picard.sourceforge.net), the variants were called for each sample by using the GATK HaplotypeCaller and GenotypeGVCFs with the default setting. As a result, 822,655 SNPs were detected. The effect of each variant site was annotated by SnpEff (Cingolani et al. 2012). Rice genome annotation information from the RAP database (RAP-DB) (Sakai et al. 2013) and MSU release 7 (Kawahara et al. 2013) was used for the SnpEff analysis, and this information was included in the annotation track of TASUKE+. For the GWAS, VCF files were converted to a PLINK format file by using PLINK v1.9 (Purcell et al. 2007). After removing sites with a minor allele frequency of <0.05, 406,224 SNPs were retained, and data imputation was conducted using Beagle version 3.3.2 (Browning et al. 2011). Then, a GWAS was performed with the linear mixed model implemented in the Fast-LMM program (Lippert et al. 2011).

Citation

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