Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content by Genotyping-By-Sequencing (GBS) in teleost Larimichthys crocea
- Published
- Accepted
- Subject Areas
- Aquaculture, Fisheries and Fish Science, Biodiversity, Genomics
- Keywords
- Genotyping-By-Sequencing (GBS), single nucleotide polymorphism (SNP), teleost, marker development, large yellow croaker
- Copyright
- © 2016 Xiao et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2016. Whole-genome single-nucleotide polymorphism (SNP) marker discovery and association analysis with the eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) content by Genotyping-By-Sequencing (GBS) in teleost Larimichthys crocea. PeerJ Preprints 4:e2116v1 https://doi.org/10.7287/peerj.preprints.2116v1
Abstract
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. 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 SequenomMassARRAYassay. The association studies with the muscle EPA and 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/DHA associated SNP loci provided invaluable resources for the population structure, conservation genetics and genomic selection of large yellow croaker and other fish organisms.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Supplementary Table 1 for SNP primers used
Primers used for SNP validation in Sequenom MassARRAY assay