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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #380163
Research Project: Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout

Location: Cool and Cold Water Aquaculture Research

Title: Identification of high confidence structural variants in domesticated rainbow trout using whole-genome sequencing

Author
item Liu, Sixin
item Gao, Guangtu
item LAYER, RYAN - University Of Colorado
item THORGAARD, GARY - Washington State University
item Wiens, Gregory - Greg
item Leeds, Timothy - Tim
item MARTIN, KYLE - Troutlodge, Inc
item Palti, Yniv

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/8/2021
Publication Date: 2/25/2021
Citation: Liu, S., Gao, G., Layer, R.M., Thorgaard, G.H., Wiens, G.D., Leeds, T.D., Martin, K.E., Palti, Y. 2021. Identification of high confidence structural variants in domesticated rainbow trout using whole-genome sequencing. Frontiers in Genetics. 12:639355. https://doi.org/10.3389/fgene.2021.639355.
DOI: https://doi.org/10.3389/fgene.2021.639355

Interpretive Summary: Genomic structural variants (SVs) refer to DNA changes in fragment size or orientation. SVs are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout. Using whole-genome sequences of 96 fish, 13,863 high confidence SVs were identified in this study. Both high SV validation rate and genetic analysis indicate that the SVs reported in this study are robust. Because fish from three breeding populations were used for SV discovery in this study, the SVs reported in this study provide a useful resource to identify SVs associated traits targeted by selective breeding.

Technical Abstract: Genomic structural variants (SVs) are a major source of genetic and phenotypic variation but have not been investigated systematically in rainbow trout. This study’s objectives were 1) to identify and validate high confidence SVs in rainbow trout using whole-genome sequencing; and 2) to examine the contribution of transposable elements (TEs) to SVs in rainbow trout. A total of 96 rainbow trout, including 11 homozygous lines and 85 outbred fish from three breeding populations, were whole-genome sequenced with an average genome coverage of 17.2x. Putative SVs were identified using the program Smoove which integrates LUMPY and other associated tools into one package. After rigorous filtering, 13,863 high confidence SVs were identified. Pacific Biosciences long reads of the homozygous fish Arlee validated 98% (3,948 of 4,030) of the high confidence SVs present in this fish. Based on principal component analysis, the 85 outbred fish clustered into three groups consistent with their populations of origin, further indicating that the high confidence SVs identified in this study are robust. The repetitive DNA content of the high confidence SV sequences was 86.5%, which is much higher than the 57.1% repetitive DNA content of the reference genome of rainbow trout, and is also higher than the repetitive DNA content of Atlantic salmon SVs reported previously. TEs make up the majority of the repetitive sequences. Thus, TEs contribute substantially to SVs in rainbow trout. Hundreds of the high confidence SVs were annotated as exon loss variants or gene fusion variants, and may have phenotypic effects. The high confidence SVs reported in this study provide a foundation for further rainbow trout SV studies.