The temporal transcriptional regulation enhances genomic prediction accuracy for poplar radial growth

The growth rhythm of perennial plants is precisely regulated by stage-specific transcriptional programs. This study investigates the genetic mechanisms underlying seasonal radial growth in poplar and improves genomic selection by leveraging these regulatory signals. Longitudinal transcriptome profiles of 100 individuals across five critical developmental stages are integrated with whole-genome and dynamic growth phenotypes to identify core regulatory genes and functional networks. Transcriptome-wide association studies reveal limited overlap of stem diameter-associated genes across developmental stages, with stage-enriched biological processes supporting dynamic transcriptional regulation during poplar radial growth. Co-expression network analysis further demonstrates that energy metabolism centered on the tricarboxylic acid cycle serves as a key biological process driving rapid radial growth. Through multi-omics integration, core candidate genes that coordinately regulate essential pathways are identified, including cell division, polar expansion, energy allocation, and auxin transport. Notably, targeted transcriptome-integrated models incorporating these functionally important genes significantly improve the predictive accuracy of genomic selection for stem diameter compared to conventional whole-genome or transcriptome-based approaches. This study reveals the temporal molecular regulatory mechanisms underlying poplar radial growth and proposes an effective strategy for enhancing genomic prediction accuracy by integrating trait-associated transcriptional signals, offering a promising framework for precision breeding in perennial trees.