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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #428136
Research Project: Improving the Efficiency of Salmonid Aquaculture

Location: Cool and Cold Water Aquaculture Research

Title: Development and application of an updated haplotype reference panel for association analysis of spontaneous sex reversal in XX rainbow trout

Author
item Liu, Sixin
item Weber, Gregory
item MARTIN, KYLE - Troutlodge, Inc
item Long, Roseanna
item Birkett, Jill
item Palti, Yniv

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/25/2025
Publication Date: 12/10/2025
Citation: Liu, S., Weber, G.M., Martin, K.E., Long, R., Birkett, J.E., Palti, Y. 2025. Development and application of an updated haplotype reference panel for association analysis of spontaneous sex reversal in XX rainbow trout. Frontiers in Genetics. 16: Article 1692544. https://doi.org/10.3389/fgene.2025.1692544.
DOI: https://doi.org/10.3389/fgene.2025.1692544

Interpretive Summary: High-throughput genotyping methods are essential for modern genetics and breeding of rainbow trout. With the rapid cost reduction of DNA sequencing, low-coverage whole genome sequencing has emerged as a cost-effective approach for high-throughput genotyping. In this study, we obtained high-coverage sequences from 129 additional fish from several populations. After combining with the sequences generated in our previous study, we developed an updated reference panel to predict genotypes from low-coverage whole-genome sequencing data. The updated panel outperformed the previous panel in terms of genotype accuracy and genotype quality. We also used this updated reference panel for association analysis and identified DNA markers associated with spontaneous sex reversal from female to male rainbow trout. Thus, we developed a useful tool for rainbow trout breeding and the markers reported in this study can be used to select against spontaneous males and develop all-female populations, which are preferred for rainbow trout production.

Technical Abstract: With the rapid cost reduction of next-generation sequencing, low-coverage whole-genome sequencing (lcWGS) followed by genotype imputation is becoming a cost-effective alternative to SNP (single nucleotide polymorphism) array genotyping. Previously, we constructed a reference panel consisting of 410 samples representing five breeding populations of rainbow trout (Oncorhynchus mykiss). However, the reference panel had a limited representation of the major commercial populations in the U.S. The objectives of this study were two-fold: 1) to update the haplotype reference panel of rainbow trout by adding more reference populations and more samples from the previous reference populations; and 2) to identify SNPs associated with spontaneous sex reversal to males in XX rainbow trout (sXX sex reversal). To update the reference panel, high-coverage whole-genome sequences were obtained from 129 additional fish from several populations. To identify SNPs associated with sXX sex reversal, samples from two mapping families were genotyped with both the Axiom 57K SNP array and lcWGS. The updated reference panel outperformed the previous panel with an increase in imputation accuracy and a reduction in low-confidence genotypes. Based on the array genotypes, 55 significant SNPs associated with sXX sex reversal were identified and 53 out of the 55 SNPs were located on chromosome OmyA26. Based on the imputed genotypes, 743 SNPs on chromosome OmyA26 and 7 SNPs on chromosome OmyA19 were associated with sXX sex reversal. Two of the significant SNPs on chromosome OmyA26 were identified by both genotyping methods. In conclusion, the updated haplotype reference panel improved the accuracy of genotype imputation from lcWGS, and enabled us to identify additional SNPs associated with sXX sex reversal in rainbow trout.