Population Genetics of Manila Clam (<i>Ruditapes philippinarum</i>) in China Inferred from Microsatellite Markers
The Manila clam (<i>Ruditapes philippinarum</i>) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-04-01
|
| Series: | Biology |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-7737/12/4/557 |
| _version_ | 1797606383783247872 |
|---|---|
| author | Sichen Zheng Tianshi Zhang Kang Tu Li Li Zhihong Liu Biao Wu Liqing Zhou Xiujun Sun |
| author_facet | Sichen Zheng Tianshi Zhang Kang Tu Li Li Zhihong Liu Biao Wu Liqing Zhou Xiujun Sun |
| author_sort | Sichen Zheng |
| collection | DOAJ |
| description | The Manila clam (<i>Ruditapes philippinarum</i>) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (N<sub>e</sub>). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (H<sub>o</sub>) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (H<sub>e</sub>) was calculated to be varying from 0.587 to 0.700. F<sub>st</sub> values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all F<sub>st</sub> values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams. |
| first_indexed | 2024-03-11T05:14:25Z |
| format | Article |
| id | doaj.art-cd3e2c649cd6467aaa208f2559b20ba3 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-11T05:14:25Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-cd3e2c649cd6467aaa208f2559b20ba32023-11-17T18:23:55ZengMDPI AGBiology2079-77372023-04-0112455710.3390/biology12040557Population Genetics of Manila Clam (<i>Ruditapes philippinarum</i>) in China Inferred from Microsatellite MarkersSichen Zheng0Tianshi Zhang1Kang Tu2Li Li3Zhihong Liu4Biao Wu5Liqing Zhou6Xiujun Sun7National Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaNational Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaPutian Institute of Aquaculture Science of Fujian Province, Putian 351100, ChinaNational Oceanographic Center, Marine Science Research Institute of Shandong Province, Qingdao 266104, ChinaNational Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaNational Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaNational Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaNational Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, ChinaThe Manila clam (<i>Ruditapes philippinarum</i>) is one of the most commercially important bivalves along the coast of China. With the continuous expansion of clam farming scale, it may lead to some serious problems, including loss of genetic variation, inbreeding depression, and reduced effective population size (N<sub>e</sub>). In the present study, eleven microsatellite markers were used to investigate the genetic diversity and differentiation among 13 clam populations along the coast of China. As a result, 150 alleles were detected according to the genotyping results of eleven microsatellite loci. The observed heterozygosity (H<sub>o</sub>) was estimated to be ranging from 0.437 to 0.678, while the expected heterozygosity (H<sub>e</sub>) was calculated to be varying from 0.587 to 0.700. F<sub>st</sub> values between populations ranged from 0.0046-0.1983. In particular, the Laizhou population had the highest genetic variability, which was significantly different from the others (all F<sub>st</sub> values > 0.1). For all the clam populations, there was no significant linear regression between genetic and geographic distance, indicating that these populations do not follow a pattern of isolation by distance (IBD). Genetic structure was estimated according to NJ, principal coordinates (PCoA), and structure-based clustering. Estimates of effective population size range from dozens to thousands among different populations, based on linkage-disequilibrium and molecular coancestry methods. The results reveal the genetic diversity of clams and verify the hypothesis that clam population differentiation may be influenced by the mode of southern breeding and northern culture, providing guiding information for natural resource conservation and genetic breeding of clams.https://www.mdpi.com/2079-7737/12/4/557<i>Ruditapes philippinarum</i>SSRgenetic diversitygenetic differentiationeffective population size |
| spellingShingle | Sichen Zheng Tianshi Zhang Kang Tu Li Li Zhihong Liu Biao Wu Liqing Zhou Xiujun Sun Population Genetics of Manila Clam (<i>Ruditapes philippinarum</i>) in China Inferred from Microsatellite Markers Biology <i>Ruditapes philippinarum</i> SSR genetic diversity genetic differentiation effective population size |
| title | Population Genetics of Manila Clam (<i>Ruditapes philippinarum</i>) in China Inferred from Microsatellite Markers |
| title_full | Population Genetics of Manila Clam (<i>Ruditapes philippinarum</i>) in China Inferred from Microsatellite Markers |
| title_fullStr | Population Genetics of Manila Clam (<i>Ruditapes philippinarum</i>) in China Inferred from Microsatellite Markers |
| title_full_unstemmed | Population Genetics of Manila Clam (<i>Ruditapes philippinarum</i>) in China Inferred from Microsatellite Markers |
| title_short | Population Genetics of Manila Clam (<i>Ruditapes philippinarum</i>) in China Inferred from Microsatellite Markers |
| title_sort | population genetics of manila clam i ruditapes philippinarum i in china inferred from microsatellite markers |
| topic | <i>Ruditapes philippinarum</i> SSR genetic diversity genetic differentiation effective population size |
| url | https://www.mdpi.com/2079-7737/12/4/557 |
| work_keys_str_mv | AT sichenzheng populationgeneticsofmanilaclamiruditapesphilippinarumiinchinainferredfrommicrosatellitemarkers AT tianshizhang populationgeneticsofmanilaclamiruditapesphilippinarumiinchinainferredfrommicrosatellitemarkers AT kangtu populationgeneticsofmanilaclamiruditapesphilippinarumiinchinainferredfrommicrosatellitemarkers AT lili populationgeneticsofmanilaclamiruditapesphilippinarumiinchinainferredfrommicrosatellitemarkers AT zhihongliu populationgeneticsofmanilaclamiruditapesphilippinarumiinchinainferredfrommicrosatellitemarkers AT biaowu populationgeneticsofmanilaclamiruditapesphilippinarumiinchinainferredfrommicrosatellitemarkers AT liqingzhou populationgeneticsofmanilaclamiruditapesphilippinarumiinchinainferredfrommicrosatellitemarkers AT xiujunsun populationgeneticsofmanilaclamiruditapesphilippinarumiinchinainferredfrommicrosatellitemarkers |