Genetic differentiation of Oryza ruffipogon Griff. from Hainan Island and Guangdong, China Based on Hd1 and Ehd1 genes

► Most of the Oryza rufipogon individuals were heterozygous for Hd1 and Ehd1. ► Genetic diversity of Hainan island's O. rufipogon was richer than Guangdong. ► Differentiation of O. rufipogon did not occur due to geographic isolation. ► Different ecological niches impacted the genetic differentiation of O. rufipogon.