ArticleBMC genomics2023
Whole-genome resequencing reveals genetic differences and the genetic basis of parapodium number in Russian and Chinese Apostichopus japonicus.
Article in BMC genomics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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6 citing papers in PubMed, 10 citations in OpenAlex.
- Notch Signaling Is Associated with LED Light-Regulated Papilla Regeneration in the Sea Cucumber (International journal of molecular sciences · 2026Article
- GWAS and Selective Sweep Analysis Reveal the Genetic Basis of Papilla Number in the Sea Cucumber (Animals : an open access journal from MDPI · 2025Article
- Expression regulation network in papillae of sea cucumbers: Whole-transcriptome and DNA methylation datasets.Scientific data · 2025Article
- Identification of Key Genes Correlated with Economic Trait Superiorities and Their SNP Screening Through Transcriptome Comparisons, WGCNA and Pearson Correlation Coefficient in the Sea Cucumber Apostichopus Japonicus.Marine biotechnology (New York, N.Y.) · 2024Article
- Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping inInternational journal of molecular sciences · 2024Article
- Sea cucumbers: an emerging system in evo-devo.EvoDevo · 2024Review
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Authors and funding
12 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundApostichopus japonicus is an economically important species in the global aquaculture industry. Russian A. japonicus, mainly harvested in the Vladivostok region, exhibits significant phenotypic differentiation, including in many economically important traits, compared with Chinese A. japonicus owing to differences in their habitat. However, both the genetic basis for the phenotypic divergence and the population genetic structure of Russian and Chinese A. japonicus are unknown.
resultIn this study, 210 individuals from seven Russian and Chinese A. japonicus populations were sampled for whole-genome resequencing. The genetic structure analysis differentiated the Russian and Chinese A. japonicus into two groups. Population genetic analyses indicated that the Russian population showed a high degree of allelic linkage and had undergone stronger positive selection compared with the Chinese populations. Gene ontology terms enriched among candidate genes with group selection analysis were mainly involved in immunity, such as inflammatory response, antimicrobial peptides, humoral immunity, and apoptosis. Genome-wide association analysis yielded eight single-nucleotide polymorphism loci significantly associated with parapodium number, and these loci are located in regions with a high degree of genomic differentiation between the Chinese and Russia populations. These SNPs were associated with five genes. Gene expression validation revealed that three of these genes were significantly differentially expressed in individuals differing in parapodium number. AJAP08772 and AJAP08773 may directly affect parapodium production by promoting endothelial cell proliferation and metabolism, whereas AJAP07248 indirectly affects parapodium production by participating in immune responses.
conclusionsThis study, we performed population genetic structure and GWAS analysis on Chinese and Russian A. japonicus, and found three candidate genes related to the number of parapodium. The results provide an in-depth understanding of the differences in the genetic structure of A. japonicus populations in China and Russia, and provide important information for subsequent genetic analysis and breeding of this species.
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