Imputation from CaprineSNP50 BeadChip to sequence : a case-study in French Alpine and Saanen data from the VarGoats project

Goats were domesticated 10,500 years ago with the aim of supplying milk, meat and fibers. Since then, breeds have specialized and adapted to their local environment developing specific genetic profiles. The VarGoats project is an international resequencing program which aims at covering at best the genetic diversity of the Capra species. To date the sequence data available include 16 wild types and 578 Capra hircus of 65 different breeds. Variant calling led to the identification of a total of 105,772,894 variants on the 29 autosomal chromosomes. For French Alpine and Saanen individuals the concordance with 50k genotypes was checked. Mean concordance rate was 97.74% and ranged from 90.16% to 99.96%. Quality checks were applied to sequence variants using various indicators: QUAL, GQ, DP, MAF and position. Imputation was tested on the 5,926,620 filtered variants using FImpute software. Pedigree was provided and different reference populations were compared in a leave-one-out scenario. Mean concordance rate ranged from 90.6 to 92.5% and from 89.7 to 91.7% in Alpine and Saanen breeds respectively. Correlation between true and imputed sequence ranged from 0.78 to 0.83 and from 0.76 to 0.81 in Alpine and Saanen respectively. Imputation will be applied to a population of 3,618 French Alpine and Saanen goats genotyped with the CaprineSNP50 BeadChip. The next step will be to compare association studies using 50K data or SNPs imputed from the sequence data. This research provides insights on how to implement a solid quality check, and imputation that will ensure the quality of subsequent analyses.