Journal Article

Population structure and genome-wide adaptive differentiation of wild Chinese mitten crab (Eriocheir sinensis) across river basins in China

Wang, Anqi, Zhang, Ting, Bai, Yulin, Wang, Wenqian, Hu, Changsui, Liang, Yidong, Ding, Huiming, Gao, Jianxiang, Ma, Junlei, Xu, Dongpo

2026

Overview

Chinese mitten crab ( Eriocheir Sinensis ) is a commercially important species in Chinese aquaculture, yet the genetic structure of wild populations remains poorly understood. A total of 240 wild E. sinensis samples were collected from Liaohe (LH), Yalujiang (YLJ), Huanghe (HH), Yangtze (including Anqing section (YZA), Taixing section (YZT)), Oujiang (OJ), Minjiang (MJ), and Beilunhe (BLH) River basins to investigate the genetic structure of native populations. Through genotyping-by-sequencing (GBS) and stringent quality filtering, a total of 3,120,408 high-quality single- nucleotide polymorphism (SNP) loci were identified. Principal component analysis (PCA) showed that the BLH and MJ populations formed distinct clusters, whereas OJ, YZA, YZT, HH, LH, and YLJ populations were loosely clustered. Phylogenetic tree and population genetic structure analyses revealed that the BLH River population in southern China was the only significantly differentiated group within the native range of the Chinese mitten crab, while northern populations (HH, LH, and YLJ) exhibited stronger admixture, indicating higher levels of gene flow. Additionally, gene flow occurred more frequently among geographically proximate populations, while weaker gene flow persisted between geographically distant groups. Further selective sweep analyses comparing representative southern and northern populations (BLH and LH) identified key genes under strong geographic selection, primarily involved in transcriptional regulation, metabolism and transport, stress response and damage repair, and signal transduction. Overall, this study provides comprehensive insights into the genetic resources of wild E. sinensis across Chinese river basins, laying a foundation for conservation and germplasm resource development. Highlights λ Genome-wide SNP markers were developed to systematically characterize genetic diversity and population structure of wild Eriocheir sinensis across seven major river basins. λ The Beilunhe River population was identified as the only significantly differentiated genetic unit. λ No significant genetic differentiation was found among the northern E. sinensis populations from the Yalujiang, Huanghe and Liaohe Rivers.

• Publisher: BioMed Central,Springer Nature B.V,BMC
• Subject: Adaptation / Adaptation, Physiological - genetics / Admixtures / Animal Genetics and Genomics / Animals / Aquaculture / Biomedical and Life Sciences / Brachyura - classification / Brachyura - genetics / China / Crustaceans / Differentiation / Eriocheir sinensis / Evolution & development / Gene flow / Gene regulation / Genes / Genetic analysis / Genetic diversity / Genetic resources / Genetic structure / Genetics, Population / Genomes / Genotyping-by-sequencing / Germplasm / Life Sciences / Microarrays / Microbial Genetics and Genomics / Mitochondrial DNA / Nucleotides / Phylogeny / Plant Genetics and Genomics / Polymorphism / Polymorphism, Single Nucleotide / Population / Population genetics / Population structure / Populations / Principal Component Analysis / Principal components analysis / Proteomics / Quality control / Resource development / River basins / Rivers / Signal transduction / Single-nucleotide polymorphism