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Title: Optimal design of low density marker panels for genotype imputation
Contributor(s): Aliloo, H  (author)orcid ; Mrode, R (author); Okeyo, A M (author); Ojango, J (author); Dessie, T (author); Rege, J E O (author); Goddard, M E (author); Gibson, J P  (author)orcid 
Publication Date: 2018
Open Access: Yes
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Abstract: Cost-effective genotyping of livestock species can be done through a process which involves genotyping part of the population using a high density (HD) panel and the remainder with a lower density panel and then use imputation to infer the missing genotypes that are not included on the low density panel. Therefore, it is desirable to have a method of selecting markers for an assay that maximises imputation accuracy. Here we present a marker selection method that relies on the pairwise (co)variances between single nucleotide polymorphisms (SNPs) and the minor allele frequency (MAF) of SNPs. The performance of the developed method was tested in a 5 fold cross-validation process using genotypes of crossbred dairy cattle in East Africa, a population in which it is unclear whether existing low density SNP assays designed for purebred populations will maintain high imputation accuracies. Various densities of SNPs were selected using the (co)variance method and alternative SNP selection methods and then imputed up to the HD panel. The (co)variance method provided the highest imputation accuracies at all marker densities, with accuracies being up to 19% higher than the random selection of SNPs. The presented method is straightforward in its application and can ensure high accuracies in genotype imputation of crossbred dairy population in East Africa.
Publication Type: Conference Publication
Conference Details: WCGALP 2018: 11th World Congress on Genetics Applied to Livestock Production, Auckland, New Zealand, 11th - 16th February, 2018
Source of Publication: Proceedings of the World Congress on Genetics Applied to Livestock Production, v.11, p. 1-5
Publisher: Massey University
Place of Publication: Palmerston North, New Zealand
Fields of Research (FoR) 2008: 060412 Quantitative Genetics (incl. Disease and Trait Mapping Genetics)
070201 Animal Breeding
060408 Genomics
Fields of Research (FoR) 2020: 310506 Gene mapping
300305 Animal reproduction and breeding
310509 Genomics
Socio-Economic Objective (SEO) 2008: 839999 Animal Production and Animal Primary Products not elsewhere classified
Socio-Economic Objective (SEO) 2020: 109999 Other animal production and animal primary products not elsewhere classified
Peer Reviewed: Yes
HERDC Category Description: E1 Refereed Scholarly Conference Publication
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Appears in Collections:Conference Publication
School of Environmental and Rural Science

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