Development of Microsatellite Markers from Transcriptome of <i>Eriocheir sinensis</i> and Their Application in Multiplex PCR Panels
Background: The development of genetic markers is crucial for aquaculture and population genetics. Polyallelic microsatellite markers are widely used for breeding and family management of <i>Eriocheir sinensis</i> (<i>E. sinensis</i>), contributing to the sustainable developm...
Saved in:
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2024-11-01
|
| Series: | Animals |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2615/14/22/3200 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850267465902194688 |
|---|---|
| author | Qizhen Xiao Meijun Tang Qingqing Li Pengsheng Dong Yongxu Cheng Deng Deng Xugan Wu |
| author_facet | Qizhen Xiao Meijun Tang Qingqing Li Pengsheng Dong Yongxu Cheng Deng Deng Xugan Wu |
| author_sort | Qizhen Xiao |
| collection | DOAJ |
| description | Background: The development of genetic markers is crucial for aquaculture and population genetics. Polyallelic microsatellite markers are widely used for breeding and family management of <i>Eriocheir sinensis</i> (<i>E. sinensis</i>), contributing to the sustainable development of the industry. Methods: Through transcriptome analysis, 100 highly polymorphic SSR markers were identified and developed. From these, four multiplex PCR panels, each containing 16 markers, were constructed and applied to parentage assignment in six <i>E. sinensis</i> families. Results: The number of alleles (<i>N<sub>a</sub></i>) ranged from 7 to 21, the observed heterozygosity (<i>H<sub>o</sub></i>) varied from 0.356 to 0.951, and the expected heterozygosity (<i>H<sub>e</sub></i>) varied from 0.656 to 0.909. The polymorphism information content (<i>PIC</i>) ranged from 0.633 to 0.900. The CERVUS analysis showed that using only the two most informative multiplex PCR panels, assignment success rates exceeded 90.34%, with 100% accuracy in assigning offspring to parents when three or four panels were used. Conclusions: This method significantly enhances the efficiency of microsatellite marker analysis, which provides a convenient and cost-effective method for breeding programs and family management of <i>E. sinensis</i>. |
| format | Article |
| id | doaj-art-8d377e1be677416a89c02587288c257f |
| institution | OA Journals |
| issn | 2076-2615 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj-art-8d377e1be677416a89c02587288c257f2025-08-20T01:53:48ZengMDPI AGAnimals2076-26152024-11-011422320010.3390/ani14223200Development of Microsatellite Markers from Transcriptome of <i>Eriocheir sinensis</i> and Their Application in Multiplex PCR PanelsQizhen Xiao0Meijun Tang1Qingqing Li2Pengsheng Dong3Yongxu Cheng4Deng Deng5Xugan Wu6Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, ChinaKey Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, ChinaKey Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, ChinaKey Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, ChinaKey Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, ChinaShenzhen Alpha Feed Co., Ltd., Shenzhen 518054, ChinaKey Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, ChinaBackground: The development of genetic markers is crucial for aquaculture and population genetics. Polyallelic microsatellite markers are widely used for breeding and family management of <i>Eriocheir sinensis</i> (<i>E. sinensis</i>), contributing to the sustainable development of the industry. Methods: Through transcriptome analysis, 100 highly polymorphic SSR markers were identified and developed. From these, four multiplex PCR panels, each containing 16 markers, were constructed and applied to parentage assignment in six <i>E. sinensis</i> families. Results: The number of alleles (<i>N<sub>a</sub></i>) ranged from 7 to 21, the observed heterozygosity (<i>H<sub>o</sub></i>) varied from 0.356 to 0.951, and the expected heterozygosity (<i>H<sub>e</sub></i>) varied from 0.656 to 0.909. The polymorphism information content (<i>PIC</i>) ranged from 0.633 to 0.900. The CERVUS analysis showed that using only the two most informative multiplex PCR panels, assignment success rates exceeded 90.34%, with 100% accuracy in assigning offspring to parents when three or four panels were used. Conclusions: This method significantly enhances the efficiency of microsatellite marker analysis, which provides a convenient and cost-effective method for breeding programs and family management of <i>E. sinensis</i>.https://www.mdpi.com/2076-2615/14/22/3200SSRChinese mitten crabmultiplex PCRfamily selectiongenetic diversityparentage assignment |
| spellingShingle | Qizhen Xiao Meijun Tang Qingqing Li Pengsheng Dong Yongxu Cheng Deng Deng Xugan Wu Development of Microsatellite Markers from Transcriptome of <i>Eriocheir sinensis</i> and Their Application in Multiplex PCR Panels Animals SSR Chinese mitten crab multiplex PCR family selection genetic diversity parentage assignment |
| title | Development of Microsatellite Markers from Transcriptome of <i>Eriocheir sinensis</i> and Their Application in Multiplex PCR Panels |
| title_full | Development of Microsatellite Markers from Transcriptome of <i>Eriocheir sinensis</i> and Their Application in Multiplex PCR Panels |
| title_fullStr | Development of Microsatellite Markers from Transcriptome of <i>Eriocheir sinensis</i> and Their Application in Multiplex PCR Panels |
| title_full_unstemmed | Development of Microsatellite Markers from Transcriptome of <i>Eriocheir sinensis</i> and Their Application in Multiplex PCR Panels |
| title_short | Development of Microsatellite Markers from Transcriptome of <i>Eriocheir sinensis</i> and Their Application in Multiplex PCR Panels |
| title_sort | development of microsatellite markers from transcriptome of i eriocheir sinensis i and their application in multiplex pcr panels |
| topic | SSR Chinese mitten crab multiplex PCR family selection genetic diversity parentage assignment |
| url | https://www.mdpi.com/2076-2615/14/22/3200 |
| work_keys_str_mv | AT qizhenxiao developmentofmicrosatellitemarkersfromtranscriptomeofieriocheirsinensisiandtheirapplicationinmultiplexpcrpanels AT meijuntang developmentofmicrosatellitemarkersfromtranscriptomeofieriocheirsinensisiandtheirapplicationinmultiplexpcrpanels AT qingqingli developmentofmicrosatellitemarkersfromtranscriptomeofieriocheirsinensisiandtheirapplicationinmultiplexpcrpanels AT pengshengdong developmentofmicrosatellitemarkersfromtranscriptomeofieriocheirsinensisiandtheirapplicationinmultiplexpcrpanels AT yongxucheng developmentofmicrosatellitemarkersfromtranscriptomeofieriocheirsinensisiandtheirapplicationinmultiplexpcrpanels AT dengdeng developmentofmicrosatellitemarkersfromtranscriptomeofieriocheirsinensisiandtheirapplicationinmultiplexpcrpanels AT xuganwu developmentofmicrosatellitemarkersfromtranscriptomeofieriocheirsinensisiandtheirapplicationinmultiplexpcrpanels |