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

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 (log2FC 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 (log2FC of -1.62) and CsGATA14 upregulated (log2FC 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.