Research Article

Development and validation of single nucleotide polymorphism markers in Odontobutis potamophila from transcriptomic sequencing

Published: March 20, 2015
Genet. Mol. Res. 14 (1) : 2080-2085 DOI: https://doi.org/10.4238/2015.March.20.18

Abstract

Transcriptome sequencing technology has been applied in the development and discovery of single nucleotide polymorphism (SNP) markers in fish. In this study, a panel of 120 expressed sequence tag (EST)-derived SNPs was selected by several selection filters from the resultant EST library of Odontobutis potamophila using Illumina Sequencing. In total, 37 SNPs from 120 putative SNPs were considered as the true SNPs using Sanger sequencing. For each SNP locus of 30 individuals of one wild population of O. potamophila that was successfully calculated, the number of alleles per locus was 2 with an observed heterozygosity of 0.0000-0.9000 and an expected heterozygosity of 0.1000-0.5263. A total of 33 loci conformed to Hardy-Weinberg equilibrium (HWE), and 4 loci deviated from HWE after Bonferroni correction. These 33 SNP markers will benefit the studies of population genetic structure, population evolution analysis, and construction of a high-density linkage map of O. potamophila.

Transcriptome sequencing technology has been applied in the development and discovery of single nucleotide polymorphism (SNP) markers in fish. In this study, a panel of 120 expressed sequence tag (EST)-derived SNPs was selected by several selection filters from the resultant EST library of Odontobutis potamophila using Illumina Sequencing. In total, 37 SNPs from 120 putative SNPs were considered as the true SNPs using Sanger sequencing. For each SNP locus of 30 individuals of one wild population of O. potamophila that was successfully calculated, the number of alleles per locus was 2 with an observed heterozygosity of 0.0000-0.9000 and an expected heterozygosity of 0.1000-0.5263. A total of 33 loci conformed to Hardy-Weinberg equilibrium (HWE), and 4 loci deviated from HWE after Bonferroni correction. These 33 SNP markers will benefit the studies of population genetic structure, population evolution analysis, and construction of a high-density linkage map of O. potamophila.