Whole-genome resequencing reveals the genetic diversity and adaptive evolution of northern Chinese populations of Quercus mongolica

Quercus mongolica is a timber species of significant economic importance and a critical raw material source for various industries. Using whole-genome resequencing of 80 individuals from eight geographic regions in northern China, a genome-wide variation map of Q. mongolica was constructed, containing 90.79 million single nucleotide polymorphisms (SNPs). Population structure, genetic diversity, and genetic differentiation were investigated. Population genetic analyses revealed that Q. mongolica populations can be divided into two major genetic lineages: North China (NC) and Northeast China (NEC). This study describes the phenotypic and genetic variation between the two lineages, with the NC group retaining greater diversity, while the NEC group had greater uniformity. Demographic history inference indicated that Q. mongolica underwent early Pleistocene expansion followed by a bottleneck during the glacial period. The NEC population showed stronger post-glacial recovery, potentially associated with the buffering effect of the Changbai Mountain refugium. Gene flow analysis supports a “NC origin with northward expansion” model and also detected a back-migration event from the NEC to the NC group. Selective sweep and genome-wide association studies identified eight candidate genes associated with key economic traits, primarily involved in cell wall synthesis, response to abiotic stimuli, and hormone signal transduction. These findings provide a theoretical foundation and genetic resources for understanding the evolutionary history and genetic mechanisms underlying important traits in Q. mongolica .