Development and validation of a Pacific Abalone (Haliotis discus hannai) custom 60K SNP array
The Pacific abalone (Haliotis discus hannai) is a commercially important abalone species native to South Korea, which is immensely popular as a seafood delicacy. Selective breeding programs have been implemented to ensure the production of high-quality abalone, resulting in genetic improvement withi...
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| Format: | Article |
| Language: | English |
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Elsevier
2025-07-01
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| Series: | Aquaculture Reports |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2352513425001565 |
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| author | Jeong Woen Shin Sangwon Yoon Seung Hwan Lee Jung-Youn Park Jong-Won Park Hyun-Chul Kim Woo-Jin Kim Young-Ok Kim Dongwon Seo Eun Soo Noh |
| author_facet | Jeong Woen Shin Sangwon Yoon Seung Hwan Lee Jung-Youn Park Jong-Won Park Hyun-Chul Kim Woo-Jin Kim Young-Ok Kim Dongwon Seo Eun Soo Noh |
| author_sort | Jeong Woen Shin |
| collection | DOAJ |
| description | The Pacific abalone (Haliotis discus hannai) is a commercially important abalone species native to South Korea, which is immensely popular as a seafood delicacy. Selective breeding programs have been implemented to ensure the production of high-quality abalone, resulting in genetic improvement within domestic populations. With recent advances in statistical and scientific methodologies, there has been a shift toward genome-based selective breeding methods and away from traditional phenotype- or pedigree-based approaches. To improve the accuracy of genome-based selection, it is necessary to obtain genomic data from as many individuals as possible. Single nucleotide polymorphism (SNP) markers are commonly used genetic markers, which can be analyzed using SNP arrays. Genetic variation can be detected efficiently using SNP arrays, which are semiconductor chips carrying information on tens of thousands of genetic variants. We have developed and validated an abalone SNP array carrying 65,740 variants (60 K abalone SNP array). Utilizing whole-genome sequence data from 29 abalones, the SNP array was designed by extracting and filtering variants based on a number of criteria, including minor allele frequency > 0.2, genotype missing ratio > 0.9, Hardy-Weinberg Equilibrium P < 0.0001, SNP even spacing, and final score > 0.9. Validation experiments demonstrated good performance of the designed SNP array with a call rate of 90.47 %, polymorphic SNPs of 76.03 %, and linkage disequilibrium correlation with whole-genome sequence data of 0.991. This 60 K SNP array is suitable for use in constructing genomic databases and will be beneficial for genome-based selective abalone breeding programs. |
| format | Article |
| id | doaj-art-2a8398e5da5b46a8913ebdc259fa1b67 |
| institution | DOAJ |
| issn | 2352-5134 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Aquaculture Reports |
| spelling | doaj-art-2a8398e5da5b46a8913ebdc259fa1b672025-08-20T03:09:51ZengElsevierAquaculture Reports2352-51342025-07-014210277010.1016/j.aqrep.2025.102770Development and validation of a Pacific Abalone (Haliotis discus hannai) custom 60K SNP arrayJeong Woen Shin0Sangwon Yoon1Seung Hwan Lee2Jung-Youn Park3Jong-Won Park4Hyun-Chul Kim5Woo-Jin Kim6Young-Ok Kim7Dongwon Seo8Eun Soo Noh9Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of KoreaDepartment of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; Bigdata Center, TNT Research Co., Ltd., Wonjangdong-gil 102, Deokjin-gu, Jeonju-si, Jeollabuk-do 54810, Republic of KoreaDivision of Animal & Dairy Science, Chungnam National University, Daejeon 34134, Republic of KoreaBigdata Center, TNT Research Co., Ltd., Wonjangdong-gil 102, Deokjin-gu, Jeonju-si, Jeollabuk-do 54810, Republic of KoreaGenetics and Breeding Research Center, National Institute of Fisheries Science, Geoje 53334, Republic of KoreaGenetics and Breeding Research Center, National Institute of Fisheries Science, Geoje 53334, Republic of KoreaBiotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of KoreaBiotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of KoreaBigdata Center, TNT Research Co., Ltd., Wonjangdong-gil 102, Deokjin-gu, Jeonju-si, Jeollabuk-do 54810, Republic of Korea; Corresponding authors.Biotechnology Research Division, National Institute of Fisheries Science, Busan 46083, Republic of Korea; Corresponding authors.The Pacific abalone (Haliotis discus hannai) is a commercially important abalone species native to South Korea, which is immensely popular as a seafood delicacy. Selective breeding programs have been implemented to ensure the production of high-quality abalone, resulting in genetic improvement within domestic populations. With recent advances in statistical and scientific methodologies, there has been a shift toward genome-based selective breeding methods and away from traditional phenotype- or pedigree-based approaches. To improve the accuracy of genome-based selection, it is necessary to obtain genomic data from as many individuals as possible. Single nucleotide polymorphism (SNP) markers are commonly used genetic markers, which can be analyzed using SNP arrays. Genetic variation can be detected efficiently using SNP arrays, which are semiconductor chips carrying information on tens of thousands of genetic variants. We have developed and validated an abalone SNP array carrying 65,740 variants (60 K abalone SNP array). Utilizing whole-genome sequence data from 29 abalones, the SNP array was designed by extracting and filtering variants based on a number of criteria, including minor allele frequency > 0.2, genotype missing ratio > 0.9, Hardy-Weinberg Equilibrium P < 0.0001, SNP even spacing, and final score > 0.9. Validation experiments demonstrated good performance of the designed SNP array with a call rate of 90.47 %, polymorphic SNPs of 76.03 %, and linkage disequilibrium correlation with whole-genome sequence data of 0.991. This 60 K SNP array is suitable for use in constructing genomic databases and will be beneficial for genome-based selective abalone breeding programs.http://www.sciencedirect.com/science/article/pii/S2352513425001565Pacific abaloneGenome-based selective breeding methodsSNP60K SNP arrayCall rate |
| spellingShingle | Jeong Woen Shin Sangwon Yoon Seung Hwan Lee Jung-Youn Park Jong-Won Park Hyun-Chul Kim Woo-Jin Kim Young-Ok Kim Dongwon Seo Eun Soo Noh Development and validation of a Pacific Abalone (Haliotis discus hannai) custom 60K SNP array Aquaculture Reports Pacific abalone Genome-based selective breeding methods SNP 60K SNP array Call rate |
| title | Development and validation of a Pacific Abalone (Haliotis discus hannai) custom 60K SNP array |
| title_full | Development and validation of a Pacific Abalone (Haliotis discus hannai) custom 60K SNP array |
| title_fullStr | Development and validation of a Pacific Abalone (Haliotis discus hannai) custom 60K SNP array |
| title_full_unstemmed | Development and validation of a Pacific Abalone (Haliotis discus hannai) custom 60K SNP array |
| title_short | Development and validation of a Pacific Abalone (Haliotis discus hannai) custom 60K SNP array |
| title_sort | development and validation of a pacific abalone haliotis discus hannai custom 60k snp array |
| topic | Pacific abalone Genome-based selective breeding methods SNP 60K SNP array Call rate |
| url | http://www.sciencedirect.com/science/article/pii/S2352513425001565 |
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