Development of genome-wide insertion/deletion markers and genetic diversity in Sipunculus nudus along the Beibu Gulf of China
Sipunculus nudus, a marine species of substantial medicinal and commercial importance, requires genetic enhancement to boost its production yield. However, progress in genetic research and selective breeding has been constrained by two critical limitations: the scarcity of available molecular marker...
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Frontiers Media S.A.
2025-04-01
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| Series: | Frontiers in Genetics |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2025.1542287/full |
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| author | Yuzhu Ni Chunli Han Yating Liu Manman Li Weijie He Jialin Yang Jie Zou Huijing Peng Pengliang Wang |
| author_facet | Yuzhu Ni Chunli Han Yating Liu Manman Li Weijie He Jialin Yang Jie Zou Huijing Peng Pengliang Wang |
| author_sort | Yuzhu Ni |
| collection | DOAJ |
| description | Sipunculus nudus, a marine species of substantial medicinal and commercial importance, requires genetic enhancement to boost its production yield. However, progress in genetic research and selective breeding has been constrained by two critical limitations: the scarcity of available molecular markers and the absence of systematic genetic diversity assessments across China’s Beibu Gulf. To address these challenges, our genome-wide investigation identified 168,771 InDel variations, from which we developed 25,558 primer pairs. Experimental validation showed 82 out of 85 synthesized primers (96.47%) successfully amplified target regions, with 81 demonstrating polymorphism. Sixteen high polymorphic markers were subsequently employed to analyze 153 samples collected along the Beibu Gulf coastline, revealing 142 distinct alleles. The number of alleles, effective number of alleles, observed heterozygosity, expected heterozygosity, Shannon’s index and polymorphic information content ranged from 4 to 15 (mean of 8.875), 2.110 to 6.009 (mean of 4.110), 0.009 to 0.768 (mean of 0.232), 0.526 to 0.834 (mean of 0.734), 0.919 to 2.085 (mean of 1.576), and 0.440 to 0.816 (mean of 0.692), respectively. Population structure analysis revealed four genetically distinct subpopulations within the Beibu Gulf population. This delineation of population substructure provides critical insights for optimizing selective breeding programs and formulating germplasm conservation strategies in S. nudus. |
| format | Article |
| id | doaj-art-7cedb38e58424b4ca63820a2f704baca |
| institution | DOAJ |
| issn | 1664-8021 |
| language | English |
| publishDate | 2025-04-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Genetics |
| spelling | doaj-art-7cedb38e58424b4ca63820a2f704baca2025-08-20T03:05:22ZengFrontiers Media S.A.Frontiers in Genetics1664-80212025-04-011610.3389/fgene.2025.15422871542287Development of genome-wide insertion/deletion markers and genetic diversity in Sipunculus nudus along the Beibu Gulf of ChinaYuzhu Ni0Chunli Han1Yating Liu2Manman Li3Weijie He4Jialin Yang5Jie Zou6Huijing Peng7Pengliang Wang8Guangxi Key Laboratory of Marine Environment Change and Disaster in Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, ChinaGuangxi Key Laboratory of Marine Environment Change and Disaster in Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, ChinaGuangxi Key Laboratory of Marine Environment Change and Disaster in Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, ChinaGuangxi Key Laboratory of Marine Environment Change and Disaster in Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, ChinaGuangxi Key Laboratory of Marine Environment Change and Disaster in Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, ChinaGuangxi Key Laboratory of Marine Environment Change and Disaster in Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, ChinaGuangxi Institute of Oceanology, Beihai, ChinaGuangxi Institute of Oceanology, Beihai, ChinaGuangxi Key Laboratory of Marine Environment Change and Disaster in Beibu Gulf, Beibu Gulf University, Qinzhou, Guangxi, ChinaSipunculus nudus, a marine species of substantial medicinal and commercial importance, requires genetic enhancement to boost its production yield. However, progress in genetic research and selective breeding has been constrained by two critical limitations: the scarcity of available molecular markers and the absence of systematic genetic diversity assessments across China’s Beibu Gulf. To address these challenges, our genome-wide investigation identified 168,771 InDel variations, from which we developed 25,558 primer pairs. Experimental validation showed 82 out of 85 synthesized primers (96.47%) successfully amplified target regions, with 81 demonstrating polymorphism. Sixteen high polymorphic markers were subsequently employed to analyze 153 samples collected along the Beibu Gulf coastline, revealing 142 distinct alleles. The number of alleles, effective number of alleles, observed heterozygosity, expected heterozygosity, Shannon’s index and polymorphic information content ranged from 4 to 15 (mean of 8.875), 2.110 to 6.009 (mean of 4.110), 0.009 to 0.768 (mean of 0.232), 0.526 to 0.834 (mean of 0.734), 0.919 to 2.085 (mean of 1.576), and 0.440 to 0.816 (mean of 0.692), respectively. Population structure analysis revealed four genetically distinct subpopulations within the Beibu Gulf population. This delineation of population substructure provides critical insights for optimizing selective breeding programs and formulating germplasm conservation strategies in S. nudus.https://www.frontiersin.org/articles/10.3389/fgene.2025.1542287/fullSipunculus nudusgenetic diversitygenomeinsertion and deletion (InDel)molecular markers |
| spellingShingle | Yuzhu Ni Chunli Han Yating Liu Manman Li Weijie He Jialin Yang Jie Zou Huijing Peng Pengliang Wang Development of genome-wide insertion/deletion markers and genetic diversity in Sipunculus nudus along the Beibu Gulf of China Frontiers in Genetics Sipunculus nudus genetic diversity genome insertion and deletion (InDel) molecular markers |
| title | Development of genome-wide insertion/deletion markers and genetic diversity in Sipunculus nudus along the Beibu Gulf of China |
| title_full | Development of genome-wide insertion/deletion markers and genetic diversity in Sipunculus nudus along the Beibu Gulf of China |
| title_fullStr | Development of genome-wide insertion/deletion markers and genetic diversity in Sipunculus nudus along the Beibu Gulf of China |
| title_full_unstemmed | Development of genome-wide insertion/deletion markers and genetic diversity in Sipunculus nudus along the Beibu Gulf of China |
| title_short | Development of genome-wide insertion/deletion markers and genetic diversity in Sipunculus nudus along the Beibu Gulf of China |
| title_sort | development of genome wide insertion deletion markers and genetic diversity in sipunculus nudus along the beibu gulf of china |
| topic | Sipunculus nudus genetic diversity genome insertion and deletion (InDel) molecular markers |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2025.1542287/full |
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