Deciphering genome-wide population differentiation of the soybean pod borer (Leguminivora glycinivorella) using whole-genome re-sequencing data

The soybean pod borer, Leguminivora glycinivorella (Matsumura), is widely distributed across most regions of China and its adjacent areas, often causing severe losses to soybean yield and quality. To date, the molecular adaptive mechanisms enabling this pest to tolerate heterogeneous adverse habitats remain poorly characterized. To address this issue, this study performed whole-genome resequencing on 35 L. glycinivorella samples collected from four representative regions of China, namely Northwest, North, South, and Central China. Population genetic analyses, including phylogenetics, principal component analysis (PCA), and ADMIXTURE, revealed four distinct genetic clusters corresponding to the sampling regions: Northwestern (GSLZ), Southern (GXDA), Northern (HLJH), and Central (HNXX). Among these clusters, HLJH and HNXX exhibited closer genetic admixture, whereas GXDA showed significant genetic differentiation from the other populations. Selective sweep analyses based on the F ST -π ratio and ROD statistics comparing the GXDA and HLJH populations identified 22 overlapping candidate genes underlying latitudinal population genomic differentiation. These genes (e.g., Idh , Torsin ) are involved in key biological processes, including individual development, energy metabolism, and stress response. Additionally, selective signal analyses ( F ST -π ratio, ROD) between GSLZ and HNXX populations identified 43 overlapping candidate genes linked to population differentiation across altitudinal gradients, such as RagA-B and Mmp1 , which are related to hypoxia response and UV resistance. Our results systematically resolve the genome-wide population genetic architecture of L. glycinivorella and, critically, uncover candidate molecular loci driving genomic divergence across latitudinal and altitudinal environmental clines. This work lays a foundation for pest risk assessment and the development of sustainable soybean protection strategies.