Imputation to whole-genome sequence using multiple pig populations and its use in genome-wide association studies.

ABSTRACT:

Background

Use of whole-genome sequence data (WGS) is expected to improve identification of quantitative trait loci (QTL). However, this requires imputation to WGS, often with a limited number of sequenced animals for the target population. The objective of this study was to investigate imputation to WGS in two pig lines using a multi-line reference population and, subsequently, to investigate the effect of using these imputed WGS (iWGS) for GWAS.

Methods

Phenotypes and genotypes were available on 12,184 Large White pigs (LW-line) and 4943 Dutch Landrace pigs (DL-line). Imputed 660 K and 80 K genotypes for the LW-line and DL-line, respectively, were imputed to iWGS using Beagle v.4.1. Since only 32 LW-line and 12 DL-line boars were sequenced, 142 animals from eight commercia

SUBMITTER: van den Berg S 

PROVIDER: S-EPMC6346588 | biostudies-literature | 2019 Jan

REPOSITORIES: biostudies-literature