Genetic diversity and differentiation of cultured and wild yesso scallop (Mizuhopecten yessoensis) from China revealed by whole genome resequencing
One of the main bivalve species used in aquaculture in China is the yesso scallop (Mizuhopecten yessoensis). Nevertheless, little is known about the genetic diversity and stock structure of M. yessoensis during long-term culture processes. This study aims to investigate the genetic diversity and dif...
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Elsevier
2025-09-01
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| Series: | Aquaculture Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S235251342500287X |
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| author | Xinyi He Shuo Wang Weiming Teng Hualin Li Xi Xie Shikai Liu Dacheng Li Zuoan Yu Xiangfeng Liu Zunchun Zhou Yaqing Chang Haijiao Liu Qi Li Haitao Ma Qingzhi Wang |
| author_facet | Xinyi He Shuo Wang Weiming Teng Hualin Li Xi Xie Shikai Liu Dacheng Li Zuoan Yu Xiangfeng Liu Zunchun Zhou Yaqing Chang Haijiao Liu Qi Li Haitao Ma Qingzhi Wang |
| author_sort | Xinyi He |
| collection | DOAJ |
| description | One of the main bivalve species used in aquaculture in China is the yesso scallop (Mizuhopecten yessoensis). Nevertheless, little is known about the genetic diversity and stock structure of M. yessoensis during long-term culture processes. This study aims to investigate the genetic diversity and differentiation of cultured stocks in relation to the wild counterparts in the cultivation area and assess the genetic status during long-term aquaculture of M. yessoensis in Dalian. In this study, the whole genome resequencing was used to characterize the genetic diversity of six M. yessoensis stocks in Dalian over the past decade. A total of 15,064,530 SNPs with high quality was detected. The results revealed that the low genetic diversity and heterozygosity, as well as weak genetic differentiation (Fst < 0.05) occurred between paired stocks. AMOVA indicated that most of the genetic variation was found within stocks, and there was no significant differentiation between the cultured and wild groups, or among the stocks within each group, possibly due to frequent gene flow. The small effective population size (Ne) suggested that M. yessoensis might have been affected by limited brood stocks, resulting in genetic drift and exhibiting signs of inbreeding depression. These findings provided valuable insights into the current genomic resources for M. yessoensis and held practical implications for scallop aquaculture. |
| format | Article |
| id | doaj-art-f26678e37da545fa80bcfbe86cc0f0b3 |
| institution | DOAJ |
| issn | 2352-5134 |
| language | English |
| publishDate | 2025-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Aquaculture Reports |
| spelling | doaj-art-f26678e37da545fa80bcfbe86cc0f0b32025-08-20T02:57:08ZengElsevierAquaculture Reports2352-51342025-09-014310290110.1016/j.aqrep.2025.102901Genetic diversity and differentiation of cultured and wild yesso scallop (Mizuhopecten yessoensis) from China revealed by whole genome resequencingXinyi He0Shuo Wang1Weiming Teng2Hualin Li3Xi Xie4Shikai Liu5Dacheng Li6Zuoan Yu7Xiangfeng Liu8Zunchun Zhou9Yaqing Chang10Haijiao Liu11Qi Li12Haitao Ma13Qingzhi Wang14Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China; College of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, ChinaDalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China; Dalian Jinshiwan Laboratory, Dalian 116034, ChinaDalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China; Dalian Jinshiwan Laboratory, Dalian 116034, ChinaDalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China; Dalian Jinshiwan Laboratory, Dalian 116034, ChinaDalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China; Dalian Jinshiwan Laboratory, Dalian 116034, ChinaKey Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, ChinaDalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, ChinaDalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, ChinaDalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, ChinaDalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, ChinaCollege of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, ChinaDalian Changhai-Yide Aquatic Products Co., LTD, Dalian 116001, ChinaKey Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao 266003, ChinaSouth China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; Corresponding author.Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China; College of Fisheries and Life Sciences, Dalian Ocean University, Dalian 116023, China; Dalian Jinshiwan Laboratory, Dalian 116034, China; Corresponding author at: Dalian Key Laboratory of Genetic Resources for Marine Shellfish, Key Laboratory of Protection and Utilization of Aquatic Germplasm Resource, Ministry of Agriculture and Rural Affairs, Liaoning Ocean and Fisheries Science Research Institute, Dalian 116023, China.One of the main bivalve species used in aquaculture in China is the yesso scallop (Mizuhopecten yessoensis). Nevertheless, little is known about the genetic diversity and stock structure of M. yessoensis during long-term culture processes. This study aims to investigate the genetic diversity and differentiation of cultured stocks in relation to the wild counterparts in the cultivation area and assess the genetic status during long-term aquaculture of M. yessoensis in Dalian. In this study, the whole genome resequencing was used to characterize the genetic diversity of six M. yessoensis stocks in Dalian over the past decade. A total of 15,064,530 SNPs with high quality was detected. The results revealed that the low genetic diversity and heterozygosity, as well as weak genetic differentiation (Fst < 0.05) occurred between paired stocks. AMOVA indicated that most of the genetic variation was found within stocks, and there was no significant differentiation between the cultured and wild groups, or among the stocks within each group, possibly due to frequent gene flow. The small effective population size (Ne) suggested that M. yessoensis might have been affected by limited brood stocks, resulting in genetic drift and exhibiting signs of inbreeding depression. These findings provided valuable insights into the current genomic resources for M. yessoensis and held practical implications for scallop aquaculture.http://www.sciencedirect.com/science/article/pii/S235251342500287XMizuhopecten yessoensisWhole genome resequencingGenetic diversityPopulation structure |
| spellingShingle | Xinyi He Shuo Wang Weiming Teng Hualin Li Xi Xie Shikai Liu Dacheng Li Zuoan Yu Xiangfeng Liu Zunchun Zhou Yaqing Chang Haijiao Liu Qi Li Haitao Ma Qingzhi Wang Genetic diversity and differentiation of cultured and wild yesso scallop (Mizuhopecten yessoensis) from China revealed by whole genome resequencing Aquaculture Reports Mizuhopecten yessoensis Whole genome resequencing Genetic diversity Population structure |
| title | Genetic diversity and differentiation of cultured and wild yesso scallop (Mizuhopecten yessoensis) from China revealed by whole genome resequencing |
| title_full | Genetic diversity and differentiation of cultured and wild yesso scallop (Mizuhopecten yessoensis) from China revealed by whole genome resequencing |
| title_fullStr | Genetic diversity and differentiation of cultured and wild yesso scallop (Mizuhopecten yessoensis) from China revealed by whole genome resequencing |
| title_full_unstemmed | Genetic diversity and differentiation of cultured and wild yesso scallop (Mizuhopecten yessoensis) from China revealed by whole genome resequencing |
| title_short | Genetic diversity and differentiation of cultured and wild yesso scallop (Mizuhopecten yessoensis) from China revealed by whole genome resequencing |
| title_sort | genetic diversity and differentiation of cultured and wild yesso scallop mizuhopecten yessoensis from china revealed by whole genome resequencing |
| topic | Mizuhopecten yessoensis Whole genome resequencing Genetic diversity Population structure |
| url | http://www.sciencedirect.com/science/article/pii/S235251342500287X |
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