Genotyping of rainbow trout using low-pass whole- genome sequencing for genomic selection
https://doi.org/10.36038/2307-3497-2025-202-85-94
EDN: OSUUNE
Abstract
Goal: To verify a low-pass sequencing method (lpWGS) with subsequent genotype imputation in rainbow trout.
Materials and Methods: DNA extraction was performed by a customized protocol in plate format (4 × 96 samples), sample preparation and sequencing were performed using the MGI AgriHigh Low-pass WGS Package, reference database creation, and imputation were performed using the VNIRO Bioinformatics Group computing cluster.
Novelty: low-pass sequencing was conducted on rainbow trout for genomic selection purposes for the first time in Russia.
Result: Analysis of 260 rainbow trout individuals using this method demonstrated high genotyping reliability; on average, approximately 90 % of the 12 million loci in the genomic marker panel were reliably identified for each fish. High genetic differentiation was demonstrated among the four studied rainbow trout breeding lines.
Practical significance: The verified low-pass sequencing genotyping method can be used as a cheaper and more informative alternative to traditional DNA microarrays. This method enables both GWAS analysis and breeding value estimation for forming a trout breeding nucleus at the genomic selection Center.
About the Authors
Nikolai S. Mugue
Russian Federal Research Institute of Fisheries and Oceanography («VNIRO»); N. K. Koltzov Institute of Developmental Biology RAS («IDB RAS»)
Russian Federation
Russian Federation
19, Okruzhnoy proezd, Moscow, 105187
Fedor S. Sharko
Russian Federal Research Institute of Fisheries and Oceanography («VNIRO»); National Research Center I. V. Kurchatov Institute (NRC «Kurchatov Institute»)
Russian Federation
Russian Federation
19, Okruzhnoy proezd, Moscow, 105187
1, Akademik Kurchatov Square, Moscow, 123182
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Review
For citations:
Mugue N.S., Sharko F.S. Genotyping of rainbow trout using low-pass whole- genome sequencing for genomic selection. Trudy VNIRO. 2025;202(4):85-94. (In Russ.) https://doi.org/10.36038/2307-3497-2025-202-85-94. EDN: OSUUNE
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