Location: Cool and Cold Water Aquaculture ResearchTitle: A resource of single-nucleotide polymorphisms for rainbow trout generated by restriction-site associated DNA sequencing of doubled haploids) Author
Submitted to: Molecular Ecology Resources
Publication Type: Peer reviewed journal
Publication Acceptance Date: 11/15/2013
Publication Date: 5/1/2014
Publication URL: http://handle.nal.usda.gov/10113/59070
Citation: Palti, Y., Gao, G., Miller, M., Vallejo, R.L., Wheeler, P.A., Quillet, E., Yao, J., Thorgaard, G.H., Salem, M., Rexroad III, C.E. 2014. A resource of single-nucleotide polymorphisms for rainbow trout generated by restriction-site associated DNA sequencing of doubled haploids. Molecular Ecology Resources. 14(3):588-596. DOI:10.1111/1755-0998.12204. Interpretive Summary: Rainbow trout is one of the most important aquaculture species in the United States and around the world, and continued development of research tools and resources are necessary to enhance the genetic improvement of this species. Recent biotechnological advancements have increased productivity in dairy cattle and poultry through the utilization of molecular genetics in selective breeding. To this end, an assay called high-density single nucleotide polymorphism (SNP) chip is used to assess relationships between the DNA make-up of the animal and desired production traits, which enables accurate prediction of the genetic merit and breeding potential of the animal. Here we report on the development of a large database of SNP markers towards the development of a high-density SNP chip assay for genetic analyses in rainbow trout. This resource will facilitate the identification of genes affecting important aquaculture production traits and enhance strategies targeting the genetic improvement of this species for production efficiency.
Technical Abstract: Salmonid genomes are considered to be in a pseudo-tetraploid state as a result of an evolutionarily recent genome duplication event. This situation complicates single nucleotide polymorphism (SNP) discovery in rainbow trout as many putative SNPs are actually paralogous sequence variants (PSVs) and not simple allelic variants. To minimize false discovery of PSVs we used a panel of 19 homozygous doubled haploid (DH) lines that represent a wide geographic range of rainbow trout populations. In the first phase of the study, we analyzed SbfI restriction-site associated DNA (RAD) sequence data from all the 19 lines and selected 11 lines for an extended SNP discovery. In the second phase, we conducted extended SNP discovery using PstI RAD sequence data from the selected 11 lines. The dataset is composed of 145,168 high-quality putative SNPs that were genotyped in at least 9 of the 11 lines, of which 71,446 (49%) had minor allele frequencies (MAF) of at least 18% (i.e. at least 2 of the 11 lines). Approximately 14% of the RAD SNPs in this dataset are from expressed or coding rainbow trout sequences. In the support files for this resource we provided annotation to the positions of the SNPs in the working draft of the rainbow trout reference genome, provided the genotypes of each sample in the discovery panel and identified SNPs that are likely to be in coding sequences. Our comparison of the current dataset with previous SNP discovery datasets revealed that 99% of our SNPs are novel.