Data availability
The RNA-seq data, DAP-seq data and CUT&Tag-seq data have been deposited in the Genome Sequence Archive in the National Genomics Data Center (https://ngdc.cncb.ac.cn/, bioproject ID PRJCA031750). CHPO sequence data of Fig. 5g and Extended Data Fig. 10a–c are available from the Rice Annotation Project Database (RAP-DB) (https://rapdb.dna.naro.go.jp/), Pangenome Database of Wild and Cultivated Rice (RicePandb) (http://ricepandb.ncgr.ac.cn/) and the dataset associated with the published study ‘Multiple domestications of Asian rice’29 (https://doi.org/10.1038/s41477-023-01476-z). CHPO GCG allele data of Extended Data Fig. 10d–f are available from Rice Variation Map v.2.0 (https://ricevarmap.ncpgr.cn/). Geographical distribution information of varieties of Extended Data Fig. 10d–f is available from Rice Variation Map v.2.0 (https://ricevarmap.ncpgr.cn/) and Sandbox (https://sandbox.genesys-pgr.org). Soil temperature data of Extended Data Fig. 10d–f are available from the NOAA-CIRES-DOE 20th Century Reanalysis v.3 dataset provided by the NOAA Physical Sciences Laboratory, using the daily long-term mean soil temperature file tsoil.day.ltm.nc (https://psl.noaa.gov/data/gridded/data.20thC_ReanV3.html). Altitude data of Extended Data Fig. 10d–f are available from R package elevatr (https://cran.r-project.org/web/packages/elevatr/index.html). Soil nitrogen content data of Extended Data Fig. 10d–f are obtained from the Global Soil Dataset for Earth System Modeling (http://globalchange.bnu.edu.cn/research/soilw). Full version of all gels and blots are provided in Supplementary Fig. 1. Source data are provided with this paper.
