Vitamin E-Vitamin K1 Sub-Network in Chloroplast is Revealed as the Core for Rice Chilling Tolerance Divergence by Integrated Global Analysis

Abstract

Rice, a staple food with tropical/subtropical origination, is susceptible to cold temperature, one of the major constrains on its yield and distribution. Asian cultivated rice consists of two subspecies with diverged chilling tolerance to adapt to different environments. The mechanism underlying this divergence remains obscure, with a few involved factors, including membrane protein COLD1. Here, we revealed vitamin E-vitamin K1 sub-network as regulation core for chilling tolerance divergence through global analyses. Rice genome regions responsible for tolerance divergence were identified with chromosome segment substitution lines (CSSLs). Integrated transcriptomic and metabolomic analysis of chilling-tolerant CSSL uncovered vitamin E-vitamin K1 sub-network in chloroplast as regulation hub, with tocopherol (vitamin E) mediating chloroplast-to-nucleus signaling. COLD1 was confirmed as upstream regulator by transgenic analysis. Our work uncovers a key pathway ranging from membrane protein to metabolic pathways in chloroplast, then to further response in nucleus, through which rice modulates chilling tolerance for thermal adaptation.