Abstract

Hybrid rice has achieved a significant leap in rice yield, but the low outcrossing rate of sterile lines limits hybrid seed production due to rice’s self-pollinating habits, constraining the further development and widespread adoption of hybrid rice. Stigma exsertion is a critical trait affecting outcrossing rate. Here we characterize a rice mutant, high exsertion rate1 ( her1 ), characterized by enlarged stigma and enhanced stigma exsertion. HER1 encodes a SET domain-containing protein that binds to histone H3 at methylated lysine 9 and regulates H3K9me2 levels. Loss of function of HER1 results in reduced H3K9me2 levels in her1 , increasing the transcription of Downstream2 ( DS2 ), which positively controls stigma size. Using the loss-of-function allele of her1 , we develop a high-exsertion male-sterile line herA , which increases hybrid seed production by more than 20% in field conditions, substantiating the breeding value of HER1 in hybrid seed production.