Domestication-selected COG4-OsbZIP23 module regulates chilling tolerance in rice

Identifying excellent natural variations is the foundation for breeding. Several major genes of quantitative trait loci for chilling tolerance at the seedling stage (qCTS) have been identified. However, less is known about the dual elite modules for the tolerance. Here, we report the major gene of qCTS1-2, Chilling-tolerance in Geng/japonica rice 4 (COG4), encoding the transcription factor ENAC1, coupled with OsbZIP23 to positively regulate chilling tolerance. The haplotype analysis and geographical distribution show that most of the chilling-tolerant japonica varieties carry Var9(CT) at −317 in COG4 (COG4jap). The COG4jap promoter is preferentially bound by cold-induced OsbZIP23 to cause a higher expression of COG4jap compared to COG4ind, which promotes multiple pathways for the tolerance. Both COG4jap and OsbZIP23jap are artificially selected and retained in japonica varieties during domestication. These results not only reveal the regulatory mechanism of OsbZIP23jap-COG4jap module but also provide valuable variations for molecular design breeding. [Display omitted] •The COG4-OsbZIP23 module positively regulates chilling tolerance in rice•COG4 target genes are involved in multiple pathways for defending against cold stress•Both COG4jap and OsbZIP23jap are selected during japonica domestication The japonica rice exhibits stronger chilling tolerance than indica rice. Sun et al. identify COG4 gene associated with chilling tolerance quantitative trait loci using map-based cloning. The variant in the COG4 promoter affects OsbZIP23 binding. The favorable alleles of COG4 and OsbZIP23 are selected during domestication for enhancing chilling tolerance in japonica rice.