Following the publication of this article , it was brought to our attention that the NCBI Batch ID for the Nuclear GBS dataset was incorrectly cited in the ‘Availability of Data and Materials’ section. The correct NCBI Batch Submission ID is 1062455 (https://www. ncbi.nlm.nih.gov/projects/SNP/snp_viewBatch.cgi?sbid= 1062455). Links to the information are also available at https:// ricediversity.org/data/index.cfm More detailed citations for the Chloroplast SNP data are also now available (https://www.ncbi.nlm.nih.gov/nucleotide). The records can be retrieved from the nucleotide database by searching Entrez Nucleotide using the accession numbers below: * chloroplast_region1: KX556608 - KX556920 * chloroplast_region2: KX556921 - KX557233 * chloroplast_region3: KX556295 - KX556607 * chloroplast_region4: KX555982 - KX556294.