*2.2. Genotyping*

Total genomic DNA for re-sequencing was extracted from young leaves according to the CTAB method. The 208 accessions were genotyped using the Illumina HiSeq 2000 (PE150) (50X) by Berry Genomics Corporation (https://www.berrygenomics.com/) (Beijing, China). The average sequencing depth of each accession genome was 50×. Reads were aligned to the Nipponbare RefSeq (IRGSP-1.0) using BWA-MEM (release 0.7.10). Then, the mapped reads were sorted and duplicated were removed

by Picard tools (http://broadinstitute.github.io/picard/). The variants for each accession were called by the GATK best practices (release 3.2-2).
