title: LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms.
abstract: Obtaining genome-wide genotype data from a set of individuals is the first step in many genomic studies, including genome-wide association and genomic selection. All genotyping methods suffer from some level of missing data, and genotype imputation can be used to fill in the missing data and improve the power of downstream analyses. Model organisms like human and cattle benefit from high-quality reference genomes and panels of reference genotypes that aid in imputation accuracy. In nonmodel organisms, however, genetic and physical maps often are either of poor quality or are completely absent, and there are no panels of reference genotypes available. There is therefore a need for imputation methods designed specifically for nonmodel organisms in which genomic resources are poorly developed and marker order is unreliable or unknown. Here we introduce LinkImpute, a software package based on a k-nearest neighbor genotype imputation method, LD-kNNi, which is designed for unordered markers. No physical or genetic maps are required, and it is designed to work on unphased genotype data from heterozygous species. It exploits the fact that markers useful for imputation often are not physically close to the missing genotype but rather distributed throughout the genome. Using genotyping-by-sequencing data from diverse and heterozygous accessions of apples, grapes, and maize, we compare LD-kNNi with several genotype imputation methods and show that LD-kNNi is fast, comparable in accuracy to the best-existing methods, and exhibits the least bias in allele frequency estimates.
authors.affiliation: Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada daniel.money@dal.ca.
authors.forename: Daniel
authors.initials: D
authors.lastname: Money
authors.affiliation: Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada.
authors.forename: Kyle
authors.initials: K
authors.lastname: Gardner
authors.affiliation: Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada.
authors.forename: Zoë
authors.initials: Z
authors.lastname: Migicovsky
authors.affiliation: USDA-ARS Plant Genetic Resources Unit, Geneva, New York 14456.
authors.forename: Heidi
authors.initials: H
authors.lastname: Schwaninger
authors.affiliation: USDA-ARS Plant Genetic Resources Unit, Geneva, New York 14456.
authors.forename: Gan-Yuan
authors.initials: GY
authors.lastname: Zhong
authors.affiliation: Department of Plant and Animal Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, B2N 5E3, Canada.
authors.forename: Sean
authors.initials: S
authors.lastname: Myles
mesh_terms: D018745:Genome, Plant; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D027845:Malus / Q000235:genetics; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D012984:Software
keywords: SNP; apple; genotyping by sequencing; imputation