2.3.1. Whole Genome Sequencing

The aboveground parts of KDML105, DH103, and CSSL104 rice plants were collected at fourteen days after germination. Rice genomic DNA was extracted using a Genomic DNA Mini Kit, 'Plant' (Geneaid, New Taipei City, Taiwan). Genomic DNA libraries were prepared for sequencing by using an Illumina genome analyzer (Illumina, San Diego, CA, USA) with Illumina HiSeq3000's protocol. For genome analyses, the sequence reads were classified into specific categories using the pipeline developed by Missirian et al. [16]. The rice genomic sequence from the Rice Genome Annotation Project database [17] was used as a reference genome [18] to map the sequence reads. The raw reads were submitted to GenBank at the NCBI under BioProject no. PRJNA659381. Bioinformatic tools were used to compare the genome of CSSL104 with the KDML105 rice genome to identify loci containing di fferent single nucleotide polymorphisms (SNPs). These loci may contribute to the drought-tolerance phenotypes of CSSL104. The genome comparison first started by discarding all SNPs shared by both CSSL104 and KDML105. The remaining di fferential SNPs were counted within a sliding window of 5000 background nucleotides. To visualize the chromosome plots with the marks of di fferent SNPs' loci, the window region containing more than 100 SNPs in CSSL104 with di fferent nucleotides from KDML105 was marked as a blue line on the chromosome plots. The analysis of the locations of SNPs in the candidate genes was analyzed.
