*3.2. Marker Coverage*

The sequencing data were mapped to the Nipponbare reference genome (IRGSP 1.0). After removing the SNPs with minor allele frequency (MAF) < 5% and missing data > 10%, 2,338,386 SNPs were left and employed for GWAS. The chromosome size varied from 22.8 Mb for chromosome 9 to 43.2 Mb for chromosome 1. These markers spanned a physical distance of 373 Mb, with an average density of 0.16 Kb per marker.
