Abstract
BACKGROUND: Seed germination is a critical developmental process in plants, regulated by numerous genetic factors. The delay of germination 1 (DOG) gene family plays a pivotal role in controlling seed dormancy and germination in various species. However, as a heterohexaploid (AABBDD), the genome structure of wheat (Triticum aestivum L.) is complex, and the evolutionary process, functional differentiation and association mechanism of the DOG gene family with pre-harvest sprouting (PHS) have not been clarified, which urgently needs to be systematically analyzed. RESULTS: In this study, we conducted a comprehensive genome-wide analysis of the DOG gene family in wheat, identifying 53 DOG family members (designated TaDOG1 ~ TaDOG53). Phylogenetic analysis grouped wheat, Arabidopsis, rice, and maize DOG proteins into three clades, with wheat genes showing closer relationships to monocots (rice/maize) than to Arabidopsis. Structural diversity, including motif composition and exon-intron organization, suggested functional specialization: Group Ⅰ genes (8 ~ 12 exons) harbored more regulatory motifs, while Group Ⅲ (1 ~ 2 exons) had minimal structures. Promoter analysis revealed abundant ABA (22.52%) and MeJA responsive (36.56%) cis-elements, consistent with hormone-treated expression dynamics: Synteny analysis indicated segmental duplications drove wheat DOG expansion, with 124 intra-genomic events and strong synteny with rice/maize. RT-PCR showed distinct temporal patterns under ABA/MeJA, with early (1 ~ 4 h) and delayed (12 h) responders mediating phased signaling. RNA-seq shows TaDOG genes have diverse expressions in 8 wheat tissues, clustered into 4 groups with distinct expression and roles, with grain-specific genes (TaDOG3) highlighting potential roles in seed dormancy. It was found that there is a negative correlation between TaDOG3 expression and PHS rate, and TaDOG3 can be used as a marker gene to detect the degree of spike germination. CONCLUSION: This study systematically analyzed the evolutionary history and functional differentiation of the wheat TaDOG gene family, confirming that the TaDOG genes play a multi-level role in seed dormancy regulation through differentiated hormone response patterns and tissue expression characteristics. Among them, TaDOG3, as a potential molecular marker of PHS resistance, provides a theoretical basis and practical target for wheat anti-spike germination breeding. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12864-025-12071-1.