Investigating the Heat Shock Transcription Factor (HSF) Gene Family in Coix (Coix lacryma-jobi L.): A Comprehensive Genome-Wide Analysis of Evolution, Expression Profiling, and Responses to Developmental and Abiotic Stresses

INTRODUCTION: Heat shock transcription factors (HSFs) are pivotal regulators in plant responses to a variety of abiotic stresses, including heat, drought, salinity, and cold. They function primarily by modulating the expression of heat shock proteins (HSPs) and other stress-responsive genes, thereby maintaining protein homeostasis under adverse environmental conditions. Although HSF gene families have been systematically characterized in several major crops and model plants, comprehensive information regarding HSF genes in Coix lacryma-jobi L., a widely cultivated medicine-food homologous crop in East and Southeast Asia, remains absent from the current literature. RATIONALE: Given the increasing frequency of extreme climatic events that threaten crop productivity, it is imperative to explore the genetic resources that may confer enhanced stress tolerance in underutilized yet nutritionally and medicinally valuable crops such as coix. The recent release of a high-quality reference genome for coix provides an unprecedented opportunity to systematically identify and analyze the HSF gene family in this species. Elucidating the evolutionary relationships, structural features, and expression patterns of ClHSF genes under developmental and abiotic stress conditions will contribute to a better understanding of their functional roles and inform future molecular breeding efforts aimed at improving coix resilience. RESULTS: In this study, a total of 20 ClHSF genes were identified at the whole-genome level and were found to be unevenly distributed across nine chromosomes. Phylogenetic analysis classified these genes into three subfamilies—HSFA, HSFB, and HSFC—consistent with the clustering patterns observed in Arabidopsis, rice, and maize. All identified ClHSF proteins contained the conserved HSF DNA-binding domain, and gene structure and conserved motif analyses further supported their evolutionary relationships. Collinearity analysis revealed that both tandem and segmental duplication events have contributed to the expansion of the ClHSF gene family, with a notably high degree of synteny observed between coix and sorghum. Promoter cis-acting element analysis identified multiple hormone- and stress-responsive elements, including ABRE, MBS, and LTR, suggesting that ClHSF genes are regulated through complex signaling networks. RNA-seq and qRT-PCR analyses demonstrated that ClHSF genes exhibited tissue-specific expression patterns and were differentially responsive to heat, cold, salt, and drought treatments. Notably, several genes, including ClHSF13, ClHSF14, and ClHSF17, showed significant and specific upregulation or downregulation under multiple stress conditions, highlighting their potential as key regulators in the stress adaptation machinery of coix. CONCLUSION: This study provides the first systematic characterization of the HSF gene family in coix, revealing its evolutionary history, structural diversity, and dynamic expression in response to developmental cues and abiotic stresses. The identification of stress-responsive ClHSF members offers valuable candidate genes for future functional studies and genetic improvement programs. Collectively, these findings establish a foundational framework for understanding the molecular mechanisms through which ClHSF genes contribute to stress tolerance and adaptive growth in coix.