Genetic diversity and population structure of Metapenaeus ensis in the South China Sea determined via genotyping-by-sequencing
4 affiliations
- 1Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs/South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
- 2College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- 3Key Laboratory of Efficient Utilization and Processing of Marine Fishery Resources of Hainan Province, Sanya Tropical Fisheries Research Institute, Sanya, China
- 4Hainan Seed Industry Laboratory, Sanya, Hainan, China
Abstract
Metapenaeus ensis is a commercially important penaeid shrimp widely distributed across the Indo-West Pacific. However, the population genetic characteristics of its wild stocks along the Chinese coast remain poorly understood. This study employed genotyping-by-sequencing (GBS) to assess genetic diversity, population structure, and historical gene flow in six wild M. ensis populations collected along the Chinese coast, including Beibu Gulf (BB), Lingao (LG), Raoping (RP), Shanwei (SW), Sanya (SY), and Zhuhai (ZH). A total of 285,266 high-quality biallelic SNPs were obtained. All populations exhibited low genetic diversity, with observed heterozygosity (Ho) ranging from 0.0963 to 0.0983 and expected heterozygosity (He) from 0.1202 to 0.1238, along with signals of heterozygote deficiency. Pairwise Fst values ranged from -0.00012 (ZH and SW) to 0.02049 (ZH and BB), indicating weak overall genetic differentiation, although the ZH and BB populations showed relatively greater divergence. ADMIXTURE analysis identified two major ancestral components at K = 2, whereas PCA and neighbor-joining phylogeny revealed extensive individual overlap and limited topological resolution. The SY population may display admixed ancestry and represent a potential genetic admixture hub. TreeMix analysis identified the four-migration model and inferred multiple ancestral admixture events between two major clades (BB-LG and SY-RP-SW-ZH). Overall, the observed pattern of low genetic diversity and weak population differentiation suggests that these wild stocks may be managed as a coordinated fishery unit. Furthermore, these genomic resources provide valuable SNP markers to support germplasm conservation and sustainable fishery management of M. ensis in China.
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BibTeX
@article{su2026genetic,
title = {{Genetic diversity and population structure of Metapenaeus ensis in the South China Sea determined via genotyping-by-sequencing}},
author = {Ningning Su and Ningning Su and Falin Zhou and Falin Zhou and Dianchang Zhang and Qibin Yang and Qibin Yang and Ziyi Jiang and Song Jiang and Lishi Yang and Kun Cao and Yukai Yang and Yangyang Ding and Yundong Li and Yundong Li and Yundong Li},
journal = {Frontiers in Marine Science},
year = {2026},
month = nov,
doi = {10.3389/fmars.2026.1999653},
url = {https://doi.org/10.3389/fmars.2026.1999653},
note = {CC BY},
}
RIS
TY - JOUR
TI - Genetic diversity and population structure of Metapenaeus ensis in the South China Sea determined via genotyping-by-sequencing
AU - Ningning Su
AU - Ningning Su
AU - Falin Zhou
AU - Falin Zhou
AU - Dianchang Zhang
AU - Qibin Yang
AU - Qibin Yang
AU - Ziyi Jiang
AU - Song Jiang
AU - Lishi Yang
AU - Kun Cao
AU - Yukai Yang
AU - Yangyang Ding
AU - Yundong Li
AU - Yundong Li
AU - Yundong Li
PY - 2026
DA - 2026/11/04
JO - Frontiers in Marine Science
DO - 10.3389/fmars.2026.1999653
UR - https://doi.org/10.3389/fmars.2026.1999653
AB - Metapenaeus ensis is a commercially important penaeid shrimp widely distributed across the Indo-West Pacific. However, the population genetic characteristics of its wild stocks along the Chinese coast remain poorly understood. This study employed genotyping-by-sequencing (GBS) to assess genetic diversity, population structure, and historical gene flow in six wild M. ensis populations collected along the Chinese coast, including Beibu Gulf (BB), Lingao (LG), Raoping (RP), Shanwei (SW), Sanya (SY), and Zhuhai (ZH). A total of 285,266 high-quality biallelic SNPs were obtained. All populations exhibited low genetic diversity, with observed heterozygosity (Ho) ranging from 0.0963 to 0.0983 and expected heterozygosity (He) from 0.1202 to 0.1238, along with signals of heterozygote deficiency. Pairwise Fst values ranged from -0.00012 (ZH and SW) to 0.02049 (ZH and BB), indicating weak overall genetic differentiation, although the ZH and BB populations showed relatively greater divergence. ADMIXTURE analysis identified two major ancestral components at K = 2, whereas PCA and neighbor-joining phylogeny revealed extensive individual overlap and limited topological resolution. The SY population may display admixed ancestry and represent a potential genetic admixture hub. TreeMix analysis identified the four-migration model and inferred multiple ancestral admixture events between two major clades (BB-LG and SY-RP-SW-ZH). Overall, the observed pattern of low genetic diversity and weak population differentiation suggests that these wild stocks may be managed as a coordinated fishery unit. Furthermore, these genomic resources provide valuable SNP markers to support germplasm conservation and sustainable fishery management of M. ensis in China.
SN - 2296-7745
ER -