Effect of composition and size of the reference population in genotype imputation efficiency of INDUSCHIP in HF Crossbred cattle

Abstract

The objective of this study was to investigate the effect of composition and size of the reference population in imputation efficiency of INDUSCHIP v2 in Indian HF crossbred cattle. Data set consisted of a total of 869 cattle from 14 Indicine breeds, 2 crossbreds (HF and Jersey crossbreds) and 2 exotic breeds (HF, Jersey) genotyped with Illumina BovineHD (Illumina, San Diego, CA) panel. Post QC, 846 animals and 449955 SNPs remained for imputation study. 3 test groups each with randomly selected 25 HFCB animals with subset genotype of INDUSCHIP v2 were created, whereas with HD genotyping data of remaining animals, 3 different categories of reference groups were created namely reference 1 (HF, Jersey, all 14 Indicine breeds, HF and Jersey crossbreds), reference 2 (HF, HF crossbred, Sahiwal, Gir and Kankrej) and reference 3 (pure HF, Sahiwal, Gir and Kankrej). Imputation efficiency of INDUSCHIP v2 was expressed in terms of concordance rate and Dosage R2 (DR2). Reference groups 1 and 2 were found to be better than Reference group 3. Further, the size of the reference population had an impact on imputation efficiency. The concordance rate and DR2 decreased with decline about population size. However, a reference population with 280 animals was found to be sufficient to obtain a concordance rate of around 95% or more and DR2 around 0.93. More number of HF, HF crossbred, Sahiwal, Gir and Kankrej animals need to be HD genotyped and incorporated in the reference population to improve the imputation efficiency of INDUSCHIP v2.

Genomic selection in Gir cattle using female reference population

“…Genotypes: Of the 9,108 recorded animals, 2,571 animals were genotyped using INDUSCHIP developed by National Dairy Development Board (Saha et al 2020) having around 53 K SNPs covering the whole genome. Other 804 animals that were from the same herds or villages were genotyped using INDUSCHIP.…”

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

“…In addition to the above, 2000 ancestry informative SNPs for above mentioned six breeds, ISAG recommended parentage SNPs and some known opensource genetic markers were also included (Nayee et al 2017). Subsequently, INDUSCHIP v1 was upgraded to INDUSCHIP v2 (52363 SNPs) incorporating additional 6663 highly polymorphic SNPs (Saha et al 2020).…”