Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content in Larimichthys crocea
Whole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. Genotyping-By-Sequencing (G...
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PeerJ Inc.
2016-12-01
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| author | Shijun Xiao Panpan Wang Linsong Dong Yaguang Zhang Zhaofang Han Qiurong Wang Zhiyong Wang |
| author_facet | Shijun Xiao Panpan Wang Linsong Dong Yaguang Zhang Zhaofang Han Qiurong Wang Zhiyong Wang |
| author_sort | Shijun Xiao |
| collection | DOAJ |
| description | Whole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. Genotyping-By-Sequencing (GBS) provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used an EcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by Sequenom MassARRAY assay. The association studies with the muscle eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content discovered 39 significant SNP markers, contributing as high up to ∼63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such as APOB, CRAT and OSBPL10. Notably, PPT2 Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified that EcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA and DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms. |
| first_indexed | 2024-03-09T07:53:14Z |
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| language | English |
| last_indexed | 2024-03-09T07:53:14Z |
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| spelling | doaj.art-0909267496204dabb9704a0661c6f0af2023-12-03T01:20:51ZengPeerJ Inc.PeerJ2167-83592016-12-014e266410.7717/peerj.2664Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content in Larimichthys croceaShijun Xiao0Panpan Wang1Linsong Dong2Yaguang Zhang3Zhaofang Han4Qiurong Wang5Zhiyong Wang6Fisheries College, Jimei University, Xiamen, Fujian, ChinaFisheries College, Jimei University, Xiamen, Fujian, ChinaFisheries College, Jimei University, Xiamen, Fujian, ChinaFisheries College, Jimei University, Xiamen, Fujian, ChinaFisheries College, Jimei University, Xiamen, Fujian, ChinaFisheries College, Jimei University, Xiamen, Fujian, ChinaFisheries College, Jimei University, Xiamen, Fujian, ChinaWhole-genome single-nucleotide polymorphism (SNP) markers are valuable genetic resources for the association and conservation studies. Genome-wide SNP development in many teleost species are still challenging because of the genome complexity and the cost of re-sequencing. Genotyping-By-Sequencing (GBS) provided an efficient reduced representative method to squeeze cost for SNP detection; however, most of recent GBS applications were reported on plant organisms. In this work, we used an EcoRI-NlaIII based GBS protocol to teleost large yellow croaker, an important commercial fish in China and East-Asia, and reported the first whole-genome SNP development for the species. 69,845 high quality SNP markers that evenly distributed along genome were detected in at least 80% of 500 individuals. Nearly 95% randomly selected genotypes were successfully validated by Sequenom MassARRAY assay. The association studies with the muscle eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content discovered 39 significant SNP markers, contributing as high up to ∼63% genetic variance that explained by all markers. Functional genes that involved in fat digestion and absorption pathway were identified, such as APOB, CRAT and OSBPL10. Notably, PPT2 Gene, previously identified in the association study of the plasma n-3 and n-6 polyunsaturated fatty acid level in human, was re-discovered in large yellow croaker. Our study verified that EcoRI-NlaIII based GBS could produce quality SNP markers in a cost-efficient manner in teleost genome. The developed SNP markers and the EPA and DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.https://peerj.com/articles/2664.pdfGenotyping-By-Sequencing (GBS)Single nucleotide polymorphism (SNP)TeleostMarker developmentLarge yellow croaker |
| spellingShingle | Shijun Xiao Panpan Wang Linsong Dong Yaguang Zhang Zhaofang Han Qiurong Wang Zhiyong Wang Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content in Larimichthys crocea PeerJ Genotyping-By-Sequencing (GBS) Single nucleotide polymorphism (SNP) Teleost Marker development Large yellow croaker |
| title | Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content in Larimichthys crocea |
| title_full | Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content in Larimichthys crocea |
| title_fullStr | Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content in Larimichthys crocea |
| title_full_unstemmed | Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content in Larimichthys crocea |
| title_short | Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content in Larimichthys crocea |
| title_sort | whole genome single nucleotide polymorphism snp marker discovery and association analysis with the eicosapentaenoic acid epa and docosahexaenoic acid dha content in larimichthys crocea |
| topic | Genotyping-By-Sequencing (GBS) Single nucleotide polymorphism (SNP) Teleost Marker development Large yellow croaker |
| url | https://peerj.com/articles/2664.pdf |
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