The E3 Ubiquitin-Protein Ligase ZmBOIR3 Is a Key Regulator of Low-Temperature Tolerance in Maize Seedlings

Low-temperature stress seriously affects the growth and development of maize seedlings, endangering their quality and yield. In this study, the low-temperature tolerance at the seedling stage of 299 maize inbred lines was evaluated by using the membership function method. A genome-wide association study identified 12 SNPs associated with low-temperature tolerance. By integrating GWAS, RNA-seq, and metabolomics data, we identified a gene ZmBOIR 3 encoding an E3 ubiquitin-protein ligase. Its involvement in low-temperature tolerance during seedling development was further supported by the RT-qPCR analysis. ZmBOIR 3 may regulate the accumulation of secondary metabolites, influencing the plant hormone and membrane-associated signaling. Functional evidence from the ethylmethanesulfonate (EMS) mutant zmboir 3 showed markedly reduced tolerance to low-temperature stress. ZmBOIR 3 acts in synergy with ZmMYB 147 and may be involved in the regulation of low-temperature tolerance in maize seedlings. These support its role in promoting seedling adaptation and deepen the current understanding of cold response pathways in maize.