Rice Genome Resequencing and RIL Analysis

We re-sequenced rice (Oryza sativa) lines Hitomebore and Moukoto and 249 RILs from their cross. First, genomic DNA was extracted from fresh leaves using Agencourt Chloropure Kit (Beckman Coulter, California, United States of America). Then, DNA was quantified using Invitrogen Quant-iT PicoGreen dsDNA Assay Kits (Thermo Fisher Scientific, Massachusetts, USA). For Hitomebore and Moukoto, library construction was performed using TruSeq DNA PCR-Free Library Prep Kit (Illumina, California, USA). These 2 libraries were sequenced using the Illumina NextSeq, HiSeq, and MiSeq platforms (Illumina, California, USA) for 75-bp, 150-bp, and 250/300-bp paired-end reads, respectively (S1 Table). For the 249 RILs, library construction was performed using house-made sequencing adapters and indices. These libraries were sequenced using the Illumina NextSeq platform for 75-bp paired-end reads (S1 Table). First, we removed adapter sequences using FaQCs v2.08 [127 (link)]. Then, we used PRINSEQ lite v0.20.4 [128 (link)] to remove low-quality bases with the option “-trim_left 5 -trim_qual_right 20 -min_qual_mean 20 -min_len 50.” In addition, 300-bp reads were trimmed to 200 bp by adding an option “-trim_to_len 200.”