title: SNP discovery from transcriptome of the swimbladder of Takifugu rubripes.
abstract: Single nucleotide polymorphisms (SNPs) have become the marker of choice for genome-wide association studies in many species. High-throughput sequencing of RNA was developed primarily to analyze global gene expression, while it is an efficient way to discover SNPs from the expressed genes. In this study, we conducted transcriptome sequencing of the swimbladder of Takifugu rubripes using Illumina HiSeq2000 platform to identify gene-associated SNPs in the swimbladder. A total of 30,312,181 unique-mapped-reads were obtained from 44,736,850 raw reads. A total of 62,270 putative SNPs were discovered, which were located in 11,306 expressed genes and 2,246 scaffolds. The average minor allele frequency (MAF) of the SNPs was 0.26. GO and KEGG pathway analysis were conducted to analyze the genes containing SNPs. Validation of selected SNPs revealed that 54% of SNPs (26/48) were true SNPs. The results suggest that RNA-Seq is an efficient and cost-effective approach to discover gene-associated SNPs. In this study, a large number of SNPs were identified and these data will be useful resources for population genetic study, evolution analysis, resource assessment, genetic linkage analysis and genome-wide association studies.
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Cui
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
authors.forename: Hongdi
authors.initials: H
authors.lastname: Wang
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Shikai
authors.initials: S
authors.lastname: Liu
authors.affiliation: School of Environmental and Chemical Engineering, Dalian Jiaotong University, Dalian, China.
authors.forename: Lifu
authors.initials: L
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
authors.forename: Xuemei
authors.initials: X
authors.lastname: Qiu
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
authors.forename: Zhiqiang
authors.initials: Z
authors.lastname: Jiang
authors.affiliation: Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University, Dalian, China.
authors.forename: Xiuli
authors.initials: X
authors.lastname: Wang
authors.affiliation: The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, Alabama, United States of America.
authors.forename: Zhanjiang
authors.initials: Z
authors.lastname: Liu
mesh_terms: D000483:Alleles; D000818:Animals; D019295:Computational Biology / Q000379:methods; D005787:Gene Frequency; D005819:Genetic Markers; D055106:Genome-Wide Association Study; D005838:Genotype; D006801:Humans; D008168:Lung; D058977:Molecular Sequence Annotation; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D023741:Takifugu / Q000235:genetics*; D059467:Transcriptome; D051153:Wnt Proteins / Q000235:genetics
chemical_list: D005819:Genetic Markers; D051153:Wnt Proteins