Fig. 1

The early flowering rice variety KitaakeX; a KitaakeX and selected sequenced rice varieties under long-day conditions. Scale bar = 10 cm; b Flowering time of KitaakeX and selected rice varieties under long-day conditions. DAG, days after germination. Asterisks indicate significant differences using the unpaired Student’s t-test (P < 0.0001); We used 18 KitaakeX, 30 Nipponbare, 16 93–11, 21 IR64, 20 Zhenshan97, 19 Minghui 63, and 15 Kasalath plants to measure heading date. c KitaakeX in the unweighted neighbor-joining tree comprising 3010 accessions of the 3 k rice genomes project and indicated varieties. It includes four XI clusters (XI-1A from East Asia, XI-1B of modern varieties of diverse origins, XI-2 from South Asia and XI-3 from Southeast Asia); three GJ clusters [primarily East Asian temperate (named GJ-tmp), Southeast Asian subtropical (named GJ-sbtrp) and Southeast Asian Tropical (named GJ-trp)]; and two groups for the mostly South Asian cA (circum-Aus) and cB (circum-Basmati) accessions, 1 group Admix (accessions that fall between major groups were classified as admixed) Branch length indicates the genetic distance between two haplotypes