Genomic Evaluation Using 50K and Imputed HD Genotypes in Guzera (Bos indicus) Breed

Abstract Text: Lower and medium (Illumina 3K, 7K, 50K) density SNP markers have been shown to be less informative and explains a small proportion of the total additive genetic variance for most traits, in Bos indicus dairy and beef cattle breeds. The objective of this study was to estimate the proportion of additive genetic variance explained by actual Illumina 50K and imputed 777K (HD) genotypes in Guzera (Bos indicus) breed for milk (MY), fat (FY) and protein (PY) yield. We also studied the accuracy of genomic prediction. Imputation of 936 cows was done with FImpute using 75 sires. The proportion of the total additive genetic variance explained by markers increased from 0.62 (actual 50K SNPs) to 0.91 for the imputed HD. Imputed HD markers increased prediction accuracy by 13%, 2% and 10% for MY, FY and PY respectively, compared to the actual 50K.

Keywords: Additive variance, Accuracy, Imputation, FImpute, Bos indicus