Whole-genome analysis reveals the tandem duplication of Cannabis sativa L. GATA and their stress-responsive expression during seed germination

Abstract Background GATA transcription factors (TFs) are zinc finger proteins that regulate diverse developmental and stress-responsive processes in plants. Despite the growing economic importance of Cannabis sativa L. (hemp) as a source of fiber, seed oil, and bioactive compounds, the GATA TF gene family has not been systematically characterized in this species. This study aimed to perform a comprehensive genome-wide identification and characterization of GATA TF genes in C. sativa L. and to investigate their expression responses during early seed germination under abiotic stress conditions. Results A total of 17 GATA TF genes ( CsGATAs ) were identified in the C. sativa L. genome and phylogenetically classified into three clusters: Cluster I (12 members), Cluster II (one member), and Cluster III (four members). Evidence of localized gene family expansion was observed, with tandem duplication events identified in CsGATA2 , CsGATA5 , CsGATA6 , CsGATA10 , CsGATA11 , and CsGATA14 , distributed across Clusters I and III. Gene structure analysis revealed significant variation, with exon numbers ranging from 2 to 10. Promoter analysis of the 2000 base pairs (bp) upstream regions showed enrichment of stress and hormone-responsive cis -acting elements, with abscisic acid (ABA) responsive elements present in 12 of the 17 promoters. Transcriptomic profiling during early germination under cold stress (4 °C), salt stress (200 mM NaCl), and combined cold and salt stress revealed distinct expression patterns. CsGATA3 was consistently downregulated across all three stress conditions (log 2 FC of -1.14 under salt stress, -1.08 under cold stress, and -1.23 under combined stress). In contrast, CsGATA9 and CsGATA14 responded specifically to combined stress, with CsGATA9 downregulated (log 2 FC of -1.62) and CsGATA14 upregulated (log 2 FC of + 1.62). qRT-PCR analysis of five differentially expressed CsGATA genes confirmed the RNA-seq expression trends, showing strong concordance between the two platforms (Pearson r = 0.83, p < 0.001). Conclusions This study provides the first genome-wide characterization of the GATA TF family in C. sativa L. and reveals gene family expansion driven by tandem duplication. The identification of stress-responsive members, particularly CsGATA3 as a broadly downregulated gene across all stress conditions and CsGATA14 as specifically induced under combined stress, highlights candidate transcriptional modulators of abiotic stress adaptation during hemp seed germination. These findings lay a foundation for functional studies and molecular breeding strategies aimed at improving stress tolerance in hemp.