Genetic assessment of Saccharina germplasm using SNP markers: Facilitating core collection establishment and fingerprinting identification
Saccharina japonica, a commercially significant brown alga, has been cultivated for several decades in China. Despite extensive efforts to collect and preserve its germplasms, the absence of genetic data and reliable molecular markers has obstructed their effective utilization, thereby limiting gene...
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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/S2352513425002856 |
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| author | Zihan Gai Shuxiu Chen Shan Sai Liping Liu Yuting Zhai Rui Qian Ruina Wu Juping Zhao Liqin Wang Yan Li Yanling Liu Weiwei Wang Xiaojie Li Linan Zhang |
| author_facet | Zihan Gai Shuxiu Chen Shan Sai Liping Liu Yuting Zhai Rui Qian Ruina Wu Juping Zhao Liqin Wang Yan Li Yanling Liu Weiwei Wang Xiaojie Li Linan Zhang |
| author_sort | Zihan Gai |
| collection | DOAJ |
| description | Saccharina japonica, a commercially significant brown alga, has been cultivated for several decades in China. Despite extensive efforts to collect and preserve its germplasms, the absence of genetic data and reliable molecular markers has obstructed their effective utilization, thereby limiting genetic improvement of S. japonica. In this study, we performed genetic analysis on an initial collection, consisting of 226 representative Saccharina germplasm accessions, using approximately 4.60 million SNP markers. The results revealed the presence of two major genetic clusters, with clustering patterns consistent with their genetic backgrounds, indicating the reliability of the source information for the representative accessions. Accordingly, we established a core collection of 91 accessions that encompasses all SNP variations and retains the similar clustering structure as the initial collection. Additionally, we identified a set of 130 core SNP markers, which were successfully used for fingerprinting analysis and individual differentiation of the 91 accessions. Notably, one SNP marker located within a candidate sex-determination region demonstrated potential for identifying the sex of Saccharina japonica gametophyte accessions. This study provides valuable genetic insights and a fundamental framework for improving the efficiency of germplasm conservation and utilization in Saccharina. It also offers a foundation for future applications in cultivar identification, genetic research, and the acceleration of molecular breeding efforts in this economically important species. |
| format | Article |
| id | doaj-art-31e52fe2b734445da832b723d27cee62 |
| institution | Kabale University |
| issn | 2352-5134 |
| language | English |
| publishDate | 2025-09-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Aquaculture Reports |
| spelling | doaj-art-31e52fe2b734445da832b723d27cee622025-08-20T03:40:50ZengElsevierAquaculture Reports2352-51342025-09-014310289910.1016/j.aqrep.2025.102899Genetic assessment of Saccharina germplasm using SNP markers: Facilitating core collection establishment and fingerprinting identificationZihan Gai0Shuxiu Chen1Shan Sai2Liping Liu3Yuting Zhai4Rui Qian5Ruina Wu6Juping Zhao7Liqin Wang8Yan Li9Yanling Liu10Weiwei Wang11Xiaojie Li12Linan Zhang13School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Provincial Key Laboratory of Marine Seed Industry of Shandong, Yantai, Shandong 264003, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Shandong Technology Innovation Center of Algae and Sea Cucumber, Yantai, Shandong 264003, ChinaSchool of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, ChinaSchool of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Shandong Technology Innovation Center of Algae and Sea Cucumber, Yantai, Shandong 264003, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Provincial Key Laboratory of Marine Seed Industry of Shandong, Yantai, Shandong 264003, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Shandong Technology Innovation Center of Algae and Sea Cucumber, Yantai, Shandong 264003, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Shandong Technology Innovation Center of Algae and Sea Cucumber, Yantai, Shandong 264003, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Shandong Technology Innovation Center of Algae and Sea Cucumber, Yantai, Shandong 264003, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Provincial Key Laboratory of Marine Seed Industry of Shandong, Yantai, Shandong 264003, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Provincial Key Laboratory of Marine Seed Industry of Shandong, Yantai, Shandong 264003, ChinaShandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China; Shandong Technology Innovation Center of Algae and Sea Cucumber, Yantai, Shandong 264003, China; Corresponding author at: Shandong Oriental Ocean Sci-Tech Co., Ltd., Yantai, Shandong 264003, China.School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao 266109, China; Correspondence to: Qingdao Agricultural University, Qingdao 266109, China.Saccharina japonica, a commercially significant brown alga, has been cultivated for several decades in China. Despite extensive efforts to collect and preserve its germplasms, the absence of genetic data and reliable molecular markers has obstructed their effective utilization, thereby limiting genetic improvement of S. japonica. In this study, we performed genetic analysis on an initial collection, consisting of 226 representative Saccharina germplasm accessions, using approximately 4.60 million SNP markers. The results revealed the presence of two major genetic clusters, with clustering patterns consistent with their genetic backgrounds, indicating the reliability of the source information for the representative accessions. Accordingly, we established a core collection of 91 accessions that encompasses all SNP variations and retains the similar clustering structure as the initial collection. Additionally, we identified a set of 130 core SNP markers, which were successfully used for fingerprinting analysis and individual differentiation of the 91 accessions. Notably, one SNP marker located within a candidate sex-determination region demonstrated potential for identifying the sex of Saccharina japonica gametophyte accessions. This study provides valuable genetic insights and a fundamental framework for improving the efficiency of germplasm conservation and utilization in Saccharina. It also offers a foundation for future applications in cultivar identification, genetic research, and the acceleration of molecular breeding efforts in this economically important species.http://www.sciencedirect.com/science/article/pii/S2352513425002856SaccharinaSNPsGermplasm collectionCore germplasmDNA fingerprinting |
| spellingShingle | Zihan Gai Shuxiu Chen Shan Sai Liping Liu Yuting Zhai Rui Qian Ruina Wu Juping Zhao Liqin Wang Yan Li Yanling Liu Weiwei Wang Xiaojie Li Linan Zhang Genetic assessment of Saccharina germplasm using SNP markers: Facilitating core collection establishment and fingerprinting identification Aquaculture Reports Saccharina SNPs Germplasm collection Core germplasm DNA fingerprinting |
| title | Genetic assessment of Saccharina germplasm using SNP markers: Facilitating core collection establishment and fingerprinting identification |
| title_full | Genetic assessment of Saccharina germplasm using SNP markers: Facilitating core collection establishment and fingerprinting identification |
| title_fullStr | Genetic assessment of Saccharina germplasm using SNP markers: Facilitating core collection establishment and fingerprinting identification |
| title_full_unstemmed | Genetic assessment of Saccharina germplasm using SNP markers: Facilitating core collection establishment and fingerprinting identification |
| title_short | Genetic assessment of Saccharina germplasm using SNP markers: Facilitating core collection establishment and fingerprinting identification |
| title_sort | genetic assessment of saccharina germplasm using snp markers facilitating core collection establishment and fingerprinting identification |
| topic | Saccharina SNPs Germplasm collection Core germplasm DNA fingerprinting |
| url | http://www.sciencedirect.com/science/article/pii/S2352513425002856 |
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