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United States Department of Agriculture

Agricultural Research Service

Research Project: UTILIZATION OF GENOMICS FOR IMPROVING PRODUCTION TRAITS IN COOL AND COLD WATER AQUACULTURE

Location: Cool and Cold Water Aquaculture Research

Title: Use of RADs and doubled haploids to identify SNPs in rainbow trout

Authors
item Rexroad, Caird
item Salem, Mohamed -
item Miller, Michael -
item Yao, Jianbo -
item Gao, Guangtu
item Liu, Sixin
item Thorgaard, Gary -
item Palti, Yniv

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: March 23, 2012
Publication Date: June 17, 2012
Citation: Rexroad III, C.E., Salem, M., Miller, M., Yao, J., Gao, G., Liu, S., Thorgaard, G., Palti, Y. 2012. Use of RADs and doubled haploids to identify SNPs in rainbow trout [abstract]. p. 246.

Technical Abstract: Contemporary genomic analyses require large suites of polymorphic markers that are amenable to high-throughput genotyping protocols. Salmonid genomes are considered to be in a semi-tetraploid state as a result of an evolutionarily recent genome duplication, therefore complicating application of traditional molecular genetic approaches. As a result, DNA or RNA sequence assemblies often produce contigs that contain paralogs that arose from a genome duplication event. This situation complicates single nucleotide polymorphism (SNP) discovery as putative SNPs are actually paralogous sequence variants (PSVs). In an effort to reduce the number of PSVs identified in SNP discovery we employed doubled haploids (DH) in a series of strategies that use next generation sequencing technologies to identify PSVs and remove them from datasets of putative SNPs, therefore increasing SNP discovery efficiency. The first strategy centered on construction of reduced representation libraries from pooled genomic DNA of 96 broodstock or a single DH fish to identify 5700 putative SNPs. A second similar strategy was employed in multiple analyses to identify SNPs in coding sequences. An in-depth DH transcriptome was sequenced and used as a reference for RNA-Seq to identify true SNP markers associated with production traits using a global allele-specific expression approach. A subset of 361 SNPs showing allele-specifc expression for growth were identified from 6140 putative SNPs, 149 of which were informative in a resource population. Recently, we have employed restriction-site associated DNA (RAD) technology to genotype samples that represent a great degree of genetic diversity from the major commercial U.S. breeders, the USDA-ARS and INRA experimental populations and samples of California golden rainbow trout. The samples include multiple DH fish and pedigrees that will aid in distinguishing true SNPs from PSVs. Our intent is to choose the most informative loci across populations that represent the entire genome in the construction of a high-density genotyping array.

Last Modified: 12/20/2014
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