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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #367515

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

Location: Cool and Cold Water Aquaculture Research

Title: Improving the functional annotation of the rainbow trout genome.

item Palti, Yniv
item Gao, Guangtu
item ZHOU, HUAIJUN - University Of California, Davis
item SALEM, MOHAMED - University Of Maryland

Submitted to: International Conference on Integrative Salmonid Biology
Publication Type: Abstract Only
Publication Acceptance Date: 9/23/2019
Publication Date: 11/17/2019
Citation: Palti, Y., Gao, G., Zhou, H., Salem, M. 2019. Improving the functional annotation of the rainbow trout genome. In Proceedings of the International Conference on Integrative Salmonid Biology. Fourth International Conference on Integrative Salmonid Biology, November 17, 2019, Edinburgh, Scotland,UK. P.No.Poster - 18.

Interpretive Summary:

Technical Abstract: With sustained high rates of human population growth and depletion of natural fisheries resources, the US seafood imports are expected to continue to increase sharply. Aquaculture is the world’s fastest-growing agri-food business. Rainbow trout is the most cultivated cold-water fish in the US. The US aquaculture industry needs applications of genomics in breeding programs to define genetic and phenotypic parameters that control complex traits such as disease resistance and feed efficiency. The FAASG international consortium "Functional Analysis of All Salmonid Genomes" has been established to study the functional genomic basis of phenotypic variation in all salmonids including rainbow trout ( A trout reference genome sequence is now available (GenBank Accession GCA_002163495). However, major improvements in genome reference and annotation can improve the accuracy and efficiency of the genomic applications such as GWAS, identification of causative variations, marker assisted selection and genomic selection in rainbow trout. Therefore, the objectives of our current USDA-supported project are: 1) Closing the Swanson reference genome assembly by utilizing the long-read PacBio sequencing platform in combination with the BioNano whole genome optical map. 2) Annotate the reference genome for the coding and non-coding transcript isoforms and alternative splicing, by full-length single-molecule sequencing. 3) Annotate the genome for chromatin histone modifications and chromatin accessibility by integrating data from RNA-seq, DNAse-seq, and ChIP-seq across a wide range of rainbow trout tissues. The improved assembly and annotation of the reference genome will accelerate the genetic selection efforts, particularly through GWAS and genomic selections, for improving important production traits in rainbow trout.