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Genetic Diversity and Runs of Homozygosity in Three Masu Salmon (<i>Oncorhynchus masou</i>) Populations Based on Whole-Genome Resequencing Data.

Overview

Authors: Song Bai1, Chenfan Geng1, Wei Wang1, Xiaoyu Yan1, Tian Dong1, Hailiang Song1, Hongxia Hu1
ORCID iDs: Hailiang Song
  1. Fisheries Science Institute, Beijing Academy of Agriculture and Forestry Sciences & Beijing Key Laboratory of Fisheries Biotechnology, Beijing 100068, China; (S.B.); (C.G.); (W.W.); (X.Y.); (T.D.)
Institutions: Beijing Academy of Agriculture and Forestry Sciences (China)
Journal: Biomolecules, volume 16, issue 8, article 1187
Dates: received 30 June 2026; accepted 12 August 2026; published online 14 August 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.3390/biom16081187 · PMID 42650853 · PMCID PMC13510946 · OpenAlex W7203501690
Open access: gold, a free copy (OpenAlex)
Status: data only
Categories: genetics / omics (modality), other (organism), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning
Keywords: Oncorhynchus masou, whole-genome resequencing, genetic diversity, runs of homozygosity, genomic inbreeding
MeSH: Genetic Variation*, Homozygote*, Oncorhynchus*, Animals, Genetics, Population, Genome, Linkage Disequilibrium, Polymorphism, Single Nucleotide, Whole Genome Sequencing (* major topic)
Topic: Genetic diversity and population structure (Genetics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: Beijing International Science & Technology Cooperation Base (GHPT2026-06); the Scientific and Technological Innovation Capacity Building Project of Beijing Academy of Agricultural and Forestry Sciences: Collection, Evaluation, and Innovation of Germplasm Resources of Important Cultured Fish in Beijing (KJCX20261411); The Beijing Key Laboratory of Fisheries Biotechnology (PT2025-20); Research and Application of Fish Breeding Technologies Based on Genome Editing and Genomic Selection (KJCX20230216)
Citations: not cited yet (Europe PMC); 65 references in the paper

Abstract

Masu salmon (Oncorhynchus masou) is an ecologically and economically important cold-water salmonid in East Asia that exhibits diverse life-history forms. To compare population-level genomic variation and patterns of homozygosity among fish from different sources, we analyzed whole-genome resequencing data from 465 individuals representing one field-collected Tumen River population (TM) and two landlocked cultured populations from Chicheng (CC) and Yanji (YJ). After quality control, 6,220,980 high-quality SNPs were retained. Population-specific filtering identified 5,589,828, 3,545,209, and 4,975,751 polymorphic SNPs in CC, TM, and YJ, respectively; although SNP numbers differed, approximately 91% of variants in each population were located in intronic or intergenic regions. Principal component analysis, ADMIXTURE, and distance-based neighbor-joining analysis clearly distinguished the three populations, with CC and YJ showing the closest genetic relationship. Pairwise FST was lowest between CC and YJ and highest between TM and YJ. CC exhibited the highest linkage disequilibrium, whereas TM showed the fastest LD decay and the lowest nucleotide diversity and heterozygosity. Runs of homozygosity (ROH) burden was highest in TM, intermediate in CC, and lowest in YJ. TM had the highest number of ROHs, cumulative ROH length, and FROH, and ROHs longer than 5 Mb were detected only in this population. CC had an intermediate ROH burden dominated by short segments, whereas YJ had the lowest ROH-based genomic inbreeding. The high and heterogeneous ROH burden in TM indicates elevated genome-wide homozygosity among the sampled fish but does not, by itself, demonstrate recent inbreeding throughout the population. Candidate ROH islands and their annotated genes showed limited overlap among populations. Candidate genes in TM were primarily associated with ion regulation, neural processes, and energy metabolism, whereas those in CC and YJ shared broad functional categories involving development, muscle organization, nutrient transport, and neural regulation but differed in most specific genes. These regions and genes should be regarded as exploratory, hypothesis-generating candidates rather than evidence of selection or causality. Overall, this study reveals distinct population genomic characteristics and ROH patterns among masu salmon populations of different origins and provides a basis for future germplasm conservation and genetic management.

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

The paper links to its data, not to its authors' code: see the Data section.

Tracing map

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Data

Datasets cited

Data Availability Statement

The quality-controlled VCF dataset containing 6,220,980 SNPs from 465 individuals is available from Zenodo at DOI: https://doi.org/10.5281/zenodo.21736114.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 7 authors, 5 keywords, 9 MeSH terms, 4 funders, 64 references.

Cite

This paper

Bai, S., Geng, C., Wang, W., Yan, X., Dong, T., Song, H., & Hu, H. (2026). Genetic Diversity and Runs of Homozygosity in Three Masu Salmon (<i>Oncorhynchus masou</i>) Populations Based on Whole-Genome Resequencing Data. Biomolecules, 16(8), 1187. https://doi.org/10.3390/biom16081187

BibTeX

@article{bai2026genetic,
author = {Bai, Song and Geng, Chenfan and Wang, Wei and Yan, Xiaoyu and Dong, Tian and Song, Hailiang and Hu, Hongxia},
title = {{Genetic Diversity and Runs of Homozygosity in Three Masu Salmon (\<i\>Oncorhynchus masou\</i\>) Populations Based on Whole-Genome Resequencing Data}},
journal = {Biomolecules},
year = {2026},
month = aug,
volume = {16},
number = {8},
pages = {1187},
publisher = {Multidisciplinary Digital Publishing Institute (MDPI)},
issn = {2218-273X},
doi = {10.3390/biom16081187},
url = {https://doi.org/10.3390/biom16081187},
pmid = {42650853},
pmcid = {PMC13510946}
}

RIS

TY - JOUR
AU - Bai, Song
AU - Geng, Chenfan
AU - Wang, Wei
AU - Yan, Xiaoyu
AU - Dong, Tian
AU - Song, Hailiang
AU - Hu, Hongxia
TI - Genetic Diversity and Runs of Homozygosity in Three Masu Salmon (<i>Oncorhynchus masou</i>) Populations Based on Whole-Genome Resequencing Data
T2 - Biomolecules
J2 - Biomolecules
PY - 2026
DA - 2026/08/14
VL - 16
IS - 8
SP - 1187
SN - 2218-273X
PB - Multidisciplinary Digital Publishing Institute (MDPI)
DO - 10.3390/biom16081187
UR - https://doi.org/10.3390/biom16081187
LA - en
ER -

CSL-JSON

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