Using 1K SNP panel for genomic selection in 3 French pig breeds: Accuracy of Imputation and estimation of genomic breeding values using 1K SNP panel, designed for several breeds in French pig populations

Céline Carillier-Jacquin (Université de Toulouse, INRA, INPTet ENVT)  et al., World Congress on Genetics Applied to Livestock Production, Auckland, Nouvelle-Zélande, 11–16 février 2018, p. 294-298

The current cost of medium density SNP chips is a limit to the development of genomic selection in pig populations (Badke et al., 2014; Wellmann et al., 2013). To reduce the cost of genotyping, a low density (LD) SNP chip was designed in 2016 and has been used in routine.
This LD panel of around 1100 SNP was optimized for imputation accuracy in the French Landrace (Land) pig population using equally spaced SNP with minor allele frequency (MAF) larger than 0.2. In the present study, we proposed to adapt the panel to two other major French pig breeds i.e. Large White (LW) and Pietrain (PI) lines. Imputation accuracy as well as the impact on genomic estimated breeding value (GEBV) were estimated in the three breeds using this new SNP chip design.