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ARS Home » Northeast Area » Orono, Maine » National Cold Water Marine Aquaculture Center » Research » Publications at this Location » Publication #408822
Research Project: Genetic Improvement of North American Atlantic Salmon and the Eastern Oyster for Aquaculture Production

Location: National Cold Water Marine Aquaculture Center

Title: Microhaplotypes generate higher breeding value accuracy compared to SNPs for imputation-based breeding strategies

Author
item Delomas, Thomas
item HOLLENBECK, CHRISTOPHER - Texas A&M University
item MATT, JOSEPH - Texas A&M University
item THOMPSON, NEIL - US Department Of Agriculture (USDA)

Submitted to: Aquaculture
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/5/2024
Publication Date: 3/7/2024
Citation: Delomas, T.A., Hollenbeck, C.M., Matt, J.L., Thompson, N.F. 2024. Microhaplotypes generate higher breeding value accuracy compared to SNPs for imputation-based breeding strategies. Aquaculture. 586:740779. https://doi.org/10.1016/j.aquaculture.2024.740779.
DOI: https://doi.org/10.1016/j.aquaculture.2024.740779

Interpretive Summary: Genetically improved strains of fish and shellfish produced through selective breeding can improve productivity of the aquaculture industry. Genomic selection is a technique that can increase the efficiency of selective breeding, but it requires genotyping many animals. The expense of genotyping prohibits many breeding programs from adopting genomic selection. We developed and tested a strategy for lowering the cost of genotyping in a breeding program by targeting regions of the genome termed microhaplotypes and using a statistical technique called imputation. This strategy allows genomic selection to be implemented at a reduced cost, thereby making it possible for more breeding programs to apply genomic selection.

Technical Abstract: The cost of genotyping remains a persistent barrier to the adoption of genomic selection for many breeding programs. This is particularly prominent in the aquaculture industry because the high number and diversity of cultured species impedes the reduction of genotyping costs through a shared genetic panel (e.g., a high-density SNP array). One solution is to reserve high-density genotyping for key individuals and apply a low-density SNP panel along with pedigree based imputation to the remaining individuals. We examined the possibility of further lowering the cost of this strategy by targeting microhaplotypes instead of SNPs in the low-density panel, which could allow smaller panels to be used. We simulated Pacific oyster, eastern oyster, and Atlantic salmon breeding programs for three generations and compared imputation and GEBV accuracy using low-density panels targeting SNPs or microhaplotypes. Panels targeting microhaplotypes yielded higher imputation and GEBV accuracy than that of equally sized panels targeting SNPs. In the Pacific and eastern oyster simulations, close to the maximum imputation and GEBV accuracy was reached when the low-density panel contained 150 - 250 microhaplotypes or 350 - 450 SNPs. In the Atlantic salmon simulations, this level of accuracy was reached with low-density panels of 350 - 450 microhaplotypes or 650 - 750 SNPs. Using low-density panels targeting microhaplotypes instead of SNPs can reduce the cost of genotyping and thereby make genomic selection feasible for a wider range of programs.