*4.2. DNA Extraction and QTL Analysis*

Young leaves of each line were collected two weeks after transplant. The CTAB method was used in extracting the high-quality genomic DNA. The sequencing libraries were constructed on an Illumina HiSeq2500 platform (Illumina, Inc.; San Diego, CA, USA) according to the manufacturer's instructions. We aligned the sequence data to the reference genome (Nipponbare, http://rapdb.dna. affrc.go.jp/download/irgsp1.html/) using SOAP2 software [11]. To construct the genetic linkage map for QTL analysis, we combined the cosegregating SNP/InDel into bins via HighMap software [20]. A map containing 3652 bins and 1592.12 cM in length was constructed with an average of 304 bins on each chromosome. Twelve linkage groups corresponded to the 12 rice chromosomes. We observed the full collinearity between the genetic map and the rice genome, and the minimum value of the Spearman coefficient for chromosomes was 0.962 (Chr. 7). The HighMap software was used to construct a linkage map. The software constructs high-quality linkage map according to the maximum likelihood estimation method. We used the R/qtl (version: 1.44-9) software to conduct QTL analysis via a composite interval mapping (CIM) model. The significance thresholds were determined by 1000 permutations. The percentage of phenotypic variance calculation explained by each QTL was obtained according to the population variance within the mapping population. The details of the QTL analysis were described in our previous studies [21].

**Author Contributions:** Q.X., Z.X., and G.S. designed this study and contributed to the original concept of the project. Y.Y., M.Z., Y.C., and Y.L. performed most of the experiments. Z.L. and N.J. participated in crossing B.I.L. and Sasanishiki. Q.X. wrote the manuscript. All authors have read and agreed to the published version of the manuscript.

**Funding:** The National Key R&D Program of China (2017YFD0100500), and the Liaoning BaiQianWan Talents Program (2016921039) supported this study.
