Genetic Variation of a Heat Shock Transcription Factor Modulates Cold Tolerance in Maize

Understanding how maize (Zea mays L.) responds to cold stress is crucial for facilitating breeding programs of cold-tolerant varieties. Despite the extensive utilization of the genome-wide association study (GWAS) approach in exploring favorable natural alleles associated with maize cold tolerance, there are few reports that have successfully identified the candidate genes contributing to maize cold tolerance. In this study, by employing a diverse panel of maize inbred lines collected from different germplasm sources, we conducted a GWAS on the variation of the relative injured area of maize true leaves during cold stress—a trait most closely correlated with maize cold tolerance—and identified HSF21, encoding a B-class heat shock transcription factor, which positively regulates cold tolerance at both seedling and germination stages. The natural variations within the promoter of the cold-tolerant HSF21Hap1 allele led to increased HSF21 expression under cold stress by inhibiting the binding of bZIP68 transcription factor, a negative regulator of cold tolerance. Through integrated transcriptome deep sequencing, DNA affinity purification sequencing, and targeted lipidomic analysis, we unveiled the function of HSF21 in regulating lipid metabolism homeostasis for modulating cold tolerance in maize. Additionally, HSF21 confers maize cold tolerance without incurring yield penalties. This study thereby establishes HSF21 as a key regulator that enhances cold tolerance in maize, thus providing valuable genetic resources for the breeding of cold-tolerant maize varieties.