Selected candidate genes involved in nitrogen assimilation. (A) Nitrogen assimilation pathway. The gene OsAMT1;1 strongly selected in IndI is indicated in red, and genes significantly selected in IndII (OsNRT2.3, OsNAR2.2, OsNiR1, OsGS1;2, and OsGS1;3) are indicated in blue. (B–G) XP-CLR values near the selected candidates. The candidates are indicated by the green arrows. Detailed information on selected candidates participating in nitrogen assimilation, phosphorus uptake and translocation, and potassium transporters can be found in Dataset S6.