Natural variation in the <i>HAN1</i> gene confers chilling tolerance in rice and allowed adaptation to a temperate climate

Abstract

Rice (<i>Oryza sativa</i> L.) is a chilling-sensitive staple crop that originated in subtropical regions of Asia. Introduction of the chilling tolerance trait enables the expansion of rice cultivation to temperate regions. Here we report the cloning and characterization of <i>HAN1</i>, a quantitative trait locus (QTL) that confers chilling tolerance on temperate <i>japonica</i> rice. <i>HAN1</i> encodes an oxidase that catalyzes the conversion of biologically active jasmonoyl-L-isoleucine (JA-Ile) to the inactive form 12-hydroxy-JA-Ile (12OH-JA-Ile) and fine-tunes the JA-mediated chilling response. Natural variants in <i>HAN1</i> diverged between <i>indica</i> and <i>japonica</i> rice during domestication. A specific allele from temperate <i>japonica</i> rice, which gained a putative MYB cis-element in the promoter of <i>HAN1</i> during the divergence of the two <i>japonica</i> ecotypes, enhances the chilling tolerance of temperate <i>japonica</i> rice and allows it to adapt to a temperate climate. The results of this study extend our understanding of the northward expansion of rice cultivation and provide a target gene for the improvement of chilling tolerance in rice.