Accuracy of genotype imputation of a low-density SNP array for the Amazon fish Colossoma macropomum.

ABSTRACT: In South America, Tambaqui (Colossoma macropomum) stands as the primary target for aquaculture, yet breeding programs for this Amazon native species are in their early stages. While high-density single nucleotide polymorphism (SNP) arrays are pivotal for aquaculture breeding, their costs can be prohibitive for non- or semi-industrial species. To overcome this, a cost-effective approach involves developing low-density SNP arrays followed by genotype imputation to higher densities. In this study, a 1K SNP array for tambaqui was created and validated, offering a balance between SNP quantity and genome representativity. The imputation accuracy from various SNP densities to a medium-density array was evaluated, with the 1K density demonstrating the best trade-off (accuracy of 0.93). This subset

SUBMITTER: Agudelo JFG 

PROVIDER: S-EPMC11445733 | biostudies-literature | 2024

REPOSITORIES: biostudies-literature