The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers
Background: Microsatellite loci often used as a genetic tool for estimating genetic diversity population variation in a wide variety of different species. The application of microsatellite markers in genetics and breeding includes investigating the genetic differentiation of wild and cultured popula...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2018-07-01
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| Series: | Electronic Journal of Biotechnology |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S0717345818300204 |
| _version_ | 1818922604035047424 |
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| author | Liwen Jiang Hongtao Nie Chen Li Dongdong Li Zhongming Huo Xiwu Yan |
| author_facet | Liwen Jiang Hongtao Nie Chen Li Dongdong Li Zhongming Huo Xiwu Yan |
| author_sort | Liwen Jiang |
| collection | DOAJ |
| description | Background: Microsatellite loci often used as a genetic tool for estimating genetic diversity population variation in a wide variety of different species. The application of microsatellite markers in genetics and breeding includes investigating the genetic differentiation of wild and cultured populations, assessing and determining the genetic relationship of different populations. The aim of this work is to develop several microsatellite markers via high-throughput sequencing and characterize these markers in commercially important bivalve Ruditapes philippinarum. Results: Among the two populations of R. philippinarum studied, 110 alleles were detected. The number of alleles at the cultured population ranged from 3 to 17 (mean NA = 6.897) and wild population ranged from 2 to 15 (mean NA = 6.793). The observed and expected heterozygosities of cultured population ranged from 0.182 to 0.964, and from 0.286 to 0.900, with an average of 0.647 and 0.692, respectively. The observed and expected heterozygosities of wild population ranged from 0.138 to 1.000, and from 0.439 to 0.906, with an average of 0.674 and 0.693, respectively. The polymorphism information content ranged from 0.341 to 0.910 with an average of 0.687. Sixteen and thirteen microsatellite loci deviated significantly from Hardy–Weinberg equilibrium after correction for multiple tests in cultured and wild population, respectively. Conclusions: Twenty-nine novel microsatellite loci were developed using Illumina paired-end shotgun sequencing and characterized in two population of R. philippinarum.How to cite: Jiang L, Nie H, Li C, et al. The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers. Electron J Biotechnol 2018;34. https://doi.org/10.1016/j.ejbt.2018.05.003. Keywords: Aquaculture industry, Clam, Genetic diversity, High polymorphism, Illumina paired-end shotgun sequencing, Microsatellite, Novel microsatellite loci, Population genetics, Ruditapes philippinarum, Simple sequence repeat |
| first_indexed | 2024-12-20T01:56:10Z |
| format | Article |
| id | doaj.art-9e9e510f479641acaf96114b2a71b69d |
| institution | Directory Open Access Journal |
| issn | 0717-3458 |
| language | English |
| last_indexed | 2024-12-20T01:56:10Z |
| publishDate | 2018-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Electronic Journal of Biotechnology |
| spelling | doaj.art-9e9e510f479641acaf96114b2a71b69d2022-12-21T19:57:29ZengElsevierElectronic Journal of Biotechnology0717-34582018-07-01341721The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markersLiwen Jiang0Hongtao Nie1Chen Li2Dongdong Li3Zhongming Huo4Xiwu Yan5College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, ChinaCorresponding authors.; College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, ChinaCollege of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, ChinaCollege of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, ChinaCollege of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, ChinaCorresponding authors.; College of Fisheries and Life Science, Engineering and Technology Research Center of Shellfish Breeding in Liaoning Province, Dalian Ocean University, Dalian, 116023, ChinaBackground: Microsatellite loci often used as a genetic tool for estimating genetic diversity population variation in a wide variety of different species. The application of microsatellite markers in genetics and breeding includes investigating the genetic differentiation of wild and cultured populations, assessing and determining the genetic relationship of different populations. The aim of this work is to develop several microsatellite markers via high-throughput sequencing and characterize these markers in commercially important bivalve Ruditapes philippinarum. Results: Among the two populations of R. philippinarum studied, 110 alleles were detected. The number of alleles at the cultured population ranged from 3 to 17 (mean NA = 6.897) and wild population ranged from 2 to 15 (mean NA = 6.793). The observed and expected heterozygosities of cultured population ranged from 0.182 to 0.964, and from 0.286 to 0.900, with an average of 0.647 and 0.692, respectively. The observed and expected heterozygosities of wild population ranged from 0.138 to 1.000, and from 0.439 to 0.906, with an average of 0.674 and 0.693, respectively. The polymorphism information content ranged from 0.341 to 0.910 with an average of 0.687. Sixteen and thirteen microsatellite loci deviated significantly from Hardy–Weinberg equilibrium after correction for multiple tests in cultured and wild population, respectively. Conclusions: Twenty-nine novel microsatellite loci were developed using Illumina paired-end shotgun sequencing and characterized in two population of R. philippinarum.How to cite: Jiang L, Nie H, Li C, et al. The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers. Electron J Biotechnol 2018;34. https://doi.org/10.1016/j.ejbt.2018.05.003. Keywords: Aquaculture industry, Clam, Genetic diversity, High polymorphism, Illumina paired-end shotgun sequencing, Microsatellite, Novel microsatellite loci, Population genetics, Ruditapes philippinarum, Simple sequence repeathttp://www.sciencedirect.com/science/article/pii/S0717345818300204 |
| spellingShingle | Liwen Jiang Hongtao Nie Chen Li Dongdong Li Zhongming Huo Xiwu Yan The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers Electronic Journal of Biotechnology |
| title | The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers |
| title_full | The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers |
| title_fullStr | The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers |
| title_full_unstemmed | The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers |
| title_short | The genetic diversity of wild and cultivated Manila clam (Ruditapes philippinarum) revealed by 29 novel microsatellite markers |
| title_sort | genetic diversity of wild and cultivated manila clam ruditapes philippinarum revealed by 29 novel microsatellite markers |
| url | http://www.sciencedirect.com/science/article/pii/S0717345818300204 |
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