ARS | Publication request: Single nucleotide polymorphism discovery in rainbow trout using reduced representation libraries

Submitted to: Meeting Abstract
Publication Type: Abstract
Publication Acceptance Date: November 3, 2008
Publication Date: January 10, 2009
Citation: Castano, C., Smith, T.P., Wiedmann, R.T., Yao, J., Rexroad III, C.E. 2009. Single nucleotide polymorphism discovery in rainbow trout using reduced representation libraries. Meeting Abstract.

Technical Abstract: Single Nucleotide Polymorphisms (SNPs) are highly abundant, widespread and evenly distributed markers, which can be easily genotyped using high-throughput assays. These characteristics explain their increasing popularity in genome analyses such as quantitative trait loci mapping, linkage disequilibrium studies and genomic selection. A wide variety of strategies targeting SNP discovery have utilized sequence data from specific candidate genes, expressed sequence tags, and whole genome assemblies. Our previous efforts aimed at high-throughput SNP discovery for rainbow trout using expressed sequence tags were unsuccessful due to a large number of sequencing errors and difficulties parsing allelic variation from the high frequency of duplicated genes common in salmonids. In an effort to discover a large number of SNPs from genomic data, we turned to sequencing of reduced representation libraries which were constructed from genomic DNA of 96 unrelated individuals from NCCCWA broodstock. To date, 30,068 putative SNPs have been identified. A subset of these SNPs has been characterized on a broodstock panel and on doubled haploid individuals, which has allowed for the determination of allelic variation vs. gene duplication.