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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #303413
Title: The development and characterization of a 57K SNP Chip for rainbow trout

Author
item Palti, Yniv
item Gao, Guangtu
item MOEN, THOMAS - Aquagen
item Liu, Sixin
item KENT, MATTHEW - Centre For Integrative Genetics (CIGENE)
item SIGBJORN, LIEN - Centre For Integrative Genetics (CIGENE)
item MILLER, MICHAEL - University Of California
item Rexroad, Caird

Submitted to: World Congress of Genetics Applied in Livestock Production
Publication Type: Proceedings
Publication Acceptance Date: 4/10/2014
Publication Date: 8/22/2014
Citation: Palti, Y., Gao, G., Moen, T., Liu, S., Kent, M., Sigbjorn, L., Miller, M., Rexroad Iii, C.E. 2014. The development and characterization of a 57K SNP Chip for rainbow trout [abstract]. World Congress of Genetics Applied in Livestock Production. Paper No. 268.

Interpretive Summary:

Technical Abstract: In this paper we describe the development and characterization of the first high density SNP chip for rainbow trout. The chip included 57,500 putative SNPs, of which 49,500 (86%) were validated as high quality and polymorphic in our validation panel of 960 rainbow trout samples. This array is comparable to those of other farm animals and is much higher than previous smaller scale SNP validation studies in rainbow trout. The SNPs are distributed throughout the genome with good representation across all 29 chromosomes. The chip is more useful for rainbow trout aquaculture populations with more than 83% polymorphic markers per population, however in wild populations the number of polymorphic markers was greater than 10,000. The SNP chip is publicly available and it has already been used in a proof- of concept study to demonstrate its utility for genome enabled selection in rainbow trout presented in a companion WCGALP 2014 paper by Vallejo et al.