Abstract: Populus species, important economic species combining rapid growth with broad ecological adaptability, play a critical role in sustainable forestry and bioenergy production. In this study, we performed whole-genome resequencing of 707 individuals from a full-sib family to develop comprehensive single nucleotide polymorphism (SNP) markers and constructed a high-density genetic linkage map of 19 linkage groups. The total genetic length of the map reached 3623.65 cM with an average marker interval of 0.34 cM. By integrating multidimensional phenotypic data, 89 quantitative trait loci (QTL) associated with growth, wood physical and chemical properties, disease resistance, and leaf morphology traits were identified, with logarithm of odds (LOD) scores ranging from 3.13 to 21.72 and phenotypic variance explained between 1.7 and 11.6%. Notably, pleiotropic analysis revealed significant colocalization hotspots on chromosomes LG1, LG5, LG6, LG8, and LG14, with epistatic interaction network analysis confirming genetic basis of coordinated regulation across multiple traits. Functional annotation of 207 candidate genes showed that R2R3-MYB and bHLH transcription factors and pyruvate kinase-encoding genes were significantly enriched, suggesting crucial roles in lignin biosynthesis and carbon metabolic pathways. Allelic effect analysis indicated that the frequency of favorable alleles associated with target traits ranged from 0.20 to 0.55. Incorporation of QTL-derived favorable alleles as random effects into Bayesian-based genomic selection models led to an increase in prediction accuracy ranging from 1 to 21%, with Bayesian ridge regression as the best predictive model. This study provides valuable genomic resources and genetic insights for deciphering complex trait architecture and advancing molecular breeding in poplar.

Key words: Genomic selection, Genetic map, Quantitative trait loci, Growth, Disease resistance