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Research Project: Integrated Research Approaches for Improving Production Efficiency in Salmonids

Location: Cool and Cold Water Aquaculture Research

Title: A new single nucleotide polymorphism database for North American Atlantic salmon generated through whole genome re-sequencing

item Gao, Guangtu
item Pietrak, Michael
item Burr, Gary
item Rexroad, Caird
item Peterson, Brian
item Palti, Yniv

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/27/2020
Publication Date: 2/21/2020
Citation: Gao, G., Pietrak, M.R., Burr, G.S., Rexroad III, C.E., Peterson, B.C., Palti, Y. 2020. A new single nucleotide polymorphism database for North American Atlantic salmon generated through whole genome re-sequencing. Frontiers in Genetics. 11:85.

Interpretive Summary: Atlantic salmon is the most economically-important cold-water aquaculture species worldwide. Atlantic salmon farming in eastern US and Canada is restricted to genetic stocks of North American (NA) origin due to ecological and conservation concerns. The NA Atlantic salmon is a different sub-species with substantial genomic and genetic differences from the European sub-species. Recent biotechnological advancements have enhanced our ability to improve selective breeding in Atlantic salmon and other aquaculture species through the utilization of molecular genetics and genomics. 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 genome sequencing and development of a large database of SNP markers to imporve current resources for genetic analyses in NA Atlantic salmon and to enable development of new high density SNP chip assays. This resource will facilitate the identification of genes affecting important aquaculture production traits, wild fisheries management and basic biological research, and will enhance strategies targeting the genetic improvement of this fish for better production efficiency.

Technical Abstract: Recently we initiated efforts to generate genomic research resources for the breeding program in the USDA-ARS National Cold Water Marine Aquaculture Center (NCWMAC). We used high coverage whole genome Illumina re-sequencing for SNP discovery in 80 North American (NA) Atlantic salmon individuals from three aquaculture stocks that are propagated in the NCWMAC. Sequences of four doubled haploid (DH) European Atlantic salmon were added to the analysis to detect putative paralogous sequence variants and multi-sequence variants. Overall, we discovered about 6.6 million SNP markers, including over 1.5 million markers having high minor allele frequency (MAF = 0.25). In addition, we identified 5,822 candidate markers that can potentially distinguish between NA and European Atlantic salmon by comparing genotypes of the 80 NA Atlantic salmon with publicly available whole genome sequence information from 31 Atlantic salmon representing a diversity of European populations. The SNP database we generated from this work provides an important resource for a high-density SNP array design, as well as for other SNP genotyping platforms that can be used for genetic and genomic studies of NA Atlantic salmon.