**4. Materials and Methods**

#### *4.1. Plant Materials and Blast Isolates*

Rice cvs. 02428 and LXG were used to construct an F2 population to evaluate the segregation of blast disease reaction and for QTL mapping. Besides 02428 and LXG, a collection of 323 rice accessions consisting mainly of Chinese rice varieties or breeding materials were used for haplotype assessment in this study (Supplementary Table S2). The *M. oryzae* isolates CHNOS, Guy11, and KJ201 were kindly provided by Dr. Guo-Liang Wang (Department of Plant Pathology, Ohio State University, Ohio, USA), and isolates 2Y838-1, 501-3, IR16-1, RB6, and RB22 were collected from Fujian province, China.

#### *4.2. Rice Blast Inoculations*

Rice blast inoculations were carried out following a previously described spraying method [36]. Rice seedlings were grown in a greenhouse for about 12–14 days and were inoculated with *M. oryzae* spores at a concentration of 5 <sup>×</sup>105 spores mL<sup>−</sup>1. After inoculation, the seedlings were grown at 25 ◦<sup>C</sup> under high humidity for 4–5 days. Blast disease reactions were scored following a 0–5 scale (0–1: resistant, 2: moderately resistant, 3: moderately susceptible, 4–5: severely susceptible) [37].

#### *4.3. Bulking, DNA Extraction, and Whole-Genome Resequencing*

To understand the genetic basis of basal resistance to rice blast disease in 02428, a total of 626 F2 plants derived from a cross between 02428 and LXG were inoculated by RB22, and were investigated for the segregation of disease reaction. For bulked segregant analysis, about 10,000 individuals of the F2 population of 02428 × LXG were inoculated with the *M. oryzae* isolate RB22. About 126 highly resistant and 120 highly susceptible F2 individuals were screened to generate the ER and ES bulks, respectively. Both the ER and ES bulks were divided into two replicates, ER-1 (56 individuals) and ER-2 (70 individuals) for the ER bulk, and ES-1 (60 individuals) and ES-2 (60 individuals) for the ES bulk. The genomic DNAs of the four bulked samples were extracted and were mixed with equal amounts. DNA samples of the two parents, 02428 and LXG, and the four pools were subjected to whole-genome resequencing using the Illumina HiSeq X Ten platform, followed by standard paired-end 150 bp sequencing library construction protocols.
