Abstract
Single nucleotide polymorphisms (SNPs) are the most preferred DNA markers for genetic studies. We employed bioinformatics tools to screen genome-wide gene-associated SNPs from more than 487 million raw sequencing reads of RNA-seq data available for Asian seabass (Lates calcarifer). 48,048 putative SNPs in genes were identified. We improved a SNP genotyping method and used it for genotyping a subset of potential SNPs. Over 82 % of the putative SNPs were validated in tested populations. The improved SNP genotyping method was cost-effective and easy to conduct. The genome-wide SNPs discovered in genes supply an important resource for genetic studies of Asian seabass and comparative genomic studies. The improved genotyping method is suitable for small to middle-scale genotyping of SNPs.
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We thank our colleague Ms. May Lee and Mr. Baoqing Ye for English editing.
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12686_2015_444_MOESM5_ESM.xls
38 SNP loci sequences from Asian seabass with length of flanking regions between 30 and 60 bases on each side of the variable site. SNPs used for population genetic study are indicated at the first row (XLS 35 kb)
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Wang, L., Huang, S.Q., Xia, J.H. et al. Genome-wide discovery of gene-related SNPs in Barramundi Lates calcarifer . Conservation Genet Resour 7, 605–608 (2015). https://doi.org/10.1007/s12686-015-0444-4
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DOI: https://doi.org/10.1007/s12686-015-0444-4