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ARS Home » Northeast Area » Leetown, West Virginia » Cool and Cold Water Aquaculture Research » Research » Publications at this Location » Publication #410854

Research Project: Integrated Research Approaches for Improving Production Efficiency in Rainbow Trout

Location: Cool and Cold Water Aquaculture Research

Title: Haplotype association analyses to inform future fine-mapping of IHNV resistant QTLs

item SETZKE, CHRISTOPHER - University Of Washington
item Palti, Yniv
item Vallejo, Roger
item PURCELL, MAUREEN - Us Geological Survey (USGS)
item GAO, GUANGTU - Collaborator
item Liu, Sixin
item MARTIN, KYLE - Troutlodge, Inc
item NAISH, KERRY - University Of Washington

Submitted to: International Conference on Integrative Salmonid Biology
Publication Type: Abstract Only
Publication Acceptance Date: 1/2/2024
Publication Date: 3/11/2024
Citation: Setzke, C., Palti, Y., Vallejo, R.L., Purcell, M., Gao, G., Liu, S., Martin, K., Naish, K. 2024. Haplotype association analyses to inform future fine-mapping of IHNV resistant QTLs. International Conference on Integrative Salmonid Biology. 0311:0314.

Interpretive Summary:

Technical Abstract: Genome-wide association studies (GWAS) can identify quantitative trait loci (QTLs) associated with complex traits. However, trait-associated SNPs rarely detect the casual variants, especially when GWAS is performed using lower-density marker panels. Recombination events between markers and variants can diminish the utility of marker-assisted selection in aquaculture, or in tracking fitness traits in wild populations. Therefore, higher resolution mapping is frequently employed to identify markers more closely linked to causal variants or candidate SNPs for further investigation. In large mapping populations, it is often more efficient and cost-effective to sequence individuals that are segregating at a QTL, rather than attempt to perform high resolution genotyping on all individuals used in the initial GWAS. Here we describe an analytical approach to achieve this objective in two commercial lines of rainbow trout. QTLs for infectious hematopoietic necrosis virus (IHNV) resistance were previously detected using 57K SNP array genotype data from 100 (N=1,867) and 103 (N=1,772) full-sib families from the two lines respectively. Here, QTLs that were shared between commercial lines or explained a considerable proportion of the additive genetic variance within lines were prioritized for further statistical analysis. Chromosomes were phased and 3-SNP haplotypes spanning >0.5Mb within these QTL regions were constructed. Haplotype inheritance error was measured, and association analyses were performed to identify specific haplotypes associated with resistance and susceptibility to IHNV. The Pearson correlation coefficient was then calculated between the number of resistance haplotypes in the two parents and IHNV survival rate in their offspring in order to estimate the combined phenotypic effects of haplotypes at several QTL. Offspring of parents segregating at resistant and susceptible haplotypes were then selected for future high-density sequencing. This approach can help inform future fine-mapping studies from lower-density SNP arrays and improve marker-assisted selection in commercial aquaculture.