QTL mapping by GWAS and functional analysis of OsbZIP72 for cold tolerance at rice seedling stage

Rice is a major crop susceptible to chilling stress. The identification of quantitative trait loci and genes for cold tolerance is crucial for the rice breeding. Of 30 quantitative-trait loci affecting seedling cold tolerance identified in a genome-wide association study of 540 rice accessions, OsbZIP72 was assigned as the causative gene for one, qCTS9.1. A single-nucleotide polymorphism in its promoter accounted for variation in expression between indica and japonica subspecies. The favorable haplotype of OsbZIP72 originated in wild rice and contributed to the expansion of japonica rice to colder habitats. OsbZIP72 positively regulates genes coding reactive oxygen species (ROS)-scavenging proteins and maintains intracellular ROS homeostasis. These findings not only enhanced our understanding of environmental adaptation but also provide novel genetic resources and potential targets for molecular design breeding for cold tolerance in rice.