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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #216730

Title: Single Nucleotide Polymorphism Discovery in Rainbow Trout

item Rexroad, Caird

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/12/2008
Publication Date: 1/12/2008
Citation: Castano, C., Yao, J., Rexroad III, C.E. 2008. Single Nucleotide Polymorphism Discovery in Rainbow Trout. Meeting Abstract.

Interpretive Summary:

Technical Abstract: Single Nucleotide Polymorphisms (SNPs) are often functionally relevant markers which are highly abundant and evenly distributed throughout the genome. Therefore, they have been used for fine mapping of genes and for candidate gene association studies to identify alleles potentially affecting important traits. To add SNPs to the growing number of genome tools available for genome analyses in rainbow trout, we evaluated multiple bioinformatic pipelines for their ability to detect SNPs from expressed sequence tag data. The occurrence of the evolutionarily recent genome duplication common to most salmonids resulted in the assemblies of a large number of paralogous sequences, resulting in a majority of false positives. For comparison, a custom SNP discovery process using 3’ expressed sequence tag data from NCBI was developed using stringent assembly parameters to overcome issues associated with the genome duplication. Candidate SNPs were evaluated first on a panel of diploid and doubled haploid individuals. Successful candidates were then genotyped on a panel of 96 unrelated broodstock from the NCCCWA selective breeding program. To date we have tested a combined 90 putative SNPs from 3 bioinformatic pipelines.