Efficiency of imputing missing genotypes by INDUSCHIP v2 in HF Crossbred cattle

Abstract

INDUSCHIPan Illumina platform based custom made genotyping chip was designed with 45K polymorphic markers for Indian cattle breeds and 8K base SNPs of Illumina BovineLD chip to genotype indigenous and crossbred cattle in India. Current study was undertaken to assess the genotype imputation efficiency of INDUSCHIP v2 microarray in HF crossbred cattle and compare its efficiency of imputation with that of GGP-35K microarray. HD genotyping data of total 869 cattle from 14 indicine breeds, 2 crossbred (HF and Jersey crossbred) and 2 exotic breeds (HF, Jersey) were used for this study. Post quality control, only 846 animals and 449955 SNPs remained for imputation study. Only 23.65% of 35339 SNPs in GGP-35K chip are found to be common with INDUSCHIP v2 SNP panel. Imputation was carried out with the help of Beagle 5.0 software using subset of both INDUSCHIP v2 and GGP-35K SNP panels. The study revealed higher average concordance rate (CR) and squared correlation (DR 2 ) for INDUSCHIP v2 as compared to GGP-35K in crossbred HF population.