Genome-Wide Characterization of the Chalcone Synthase Gene Family in 84K Poplar Reveals Roles in Tissue-Specific Development and Abiotic Stress Responses

Chalcone synthase (CHS), a key enzyme in flavonoid biosynthesis, plays essential roles in plant growth, development, and responses to biotic and abiotic stresses. Despite extensive studies in herbaceous species, CHS genes in forest trees remain poorly characterized, and the CHS gene family in 84K poplar (Populus alba × P. glandulosa) has not yet been systematically investigated. In this study, a total of 15 CHS genes were identified from the 84K poplar reference genome using the HMMER approach and classified into five subgroups. Members within the same subgroup exhibited highly conserved motif compositions and domain structures. Cis-regulatory element analysis indicated that PagCHS genes are potentially involved in responses to multiple environmental stresses. Expression profiling revealed that most PagCHS genes were highly expressed in terminal buds, whereas a subset showed preferential expression in roots, consistent with flavonoid accumulation in actively dividing meristematic tissues. Furthermore, PagCHS03A and PagCHS11B were induced by light, while PagCHS07A, PagCHS08A, and PagCHS09B were significantly upregulated under cold stress. Several genes, including PagCHS04A, PagCHS07A, PagCHS12B, and PagCHS15B, also exhibited differential responses to drought stress. Notably, PagCHS07A responded to both cold and drought stresses, suggesting a potential role in coordinated stress adaptation. Overall, this study provides a comprehensive framework for understanding the functional roles of the PagCHS gene family in abiotic stress responses and offers valuable candidate genes for future functional characterization.