*4.4. DNA Extraction, Re-Sequencing, and SNP Calling*

The extraction of the genomic DNA of the two parents and each RIL was performed using a modified CTAB method [41]. Biomarker Technologies were used for the re-sequencing of the parents and RILs. The procedure was performed according to Jiang et al. [41]. The short read alignment was done as described by Li and Durbin [42]. Straining of the low-quality data was performed to produce better-quality mapping. The clean data were then aligned to the Nipponbare reference genome (Os-Nipponbare-Reference-IRGSP-1.0) [43] using the BWA software [42]. The calculations of the sequencing coverage and depth were performed through Samtools [44]. Then, the Genome Analysis Toolkit (GATK) was used to detect the SNPs with default parameters [45]. The accession number raw sequence data obtained in our study have been deposited in the NCBI Short Read Archive, with accession number PRJNA587802.
