Abstract
The functional stay-green trait is a major goal of rice breeding. Here, we cloned OsSCE1a encoding SUMO-conjugating enzyme from Yuanjiang common wild rice, which simultaneously regulates the functional stay-green trait and growth duration. Low expression or knocking out OsSCE1a corresponded to increased chlorophyll content, photosynthetic competence, N use efficiency and a shortened growth period without affecting yield. A natural MITE-transposon insertion/deletion in the OsSCE1a promoter is the functional variation that regulates these traits. OsSCE1a was selected during evolution and shows significant variation between indica and japonica rice. OsNAC2 interacts with the MITE to enhance OsSCE1a expression. Genetic manipulation of OsSCE1a revealed its potential for rice improvement. OsSCE1a-mediated SUMOylation of OsGS2 suppresses GS (involved in N assimilation) enzyme activity. OsSCE1a also regulates growth duration by SUMOylating the transcription factor such as OsGBP1, which regulates the expression of the key heading gene Ghd7. Our findings shed light on the role of SUMOylation in crops and provide a strategy for increasing agricultural productivity.