Small SNP panels for breed proportion estimation in Indian crossbred dairy cattle

Abstract

<p>Reliably identifying breed proportions in crossbred cattle in smallholder farms is a crucial step to improve mating decisions and optimizing management in these systems. High-density genotype information is able to estimate higher-order breed proportions accurately, but, are too expensive for mass application in smallholder systems. We used high-density genotype information (777 k SNPs) of 623 crossbred cattle from India that had Holstein-Friesian (HFX) and/or Jersey and indigenous breeds in their ancestry to select a smaller number of SNPs for breed proportion estimation. The accuracy of estimates obtained from panels with 100-500 SNP was compared to estimates based on all SNPs. Panels were selected for highest absolute allele frequency difference between exotic dairy versus indigenous <i>Bos indicus</i>, or between HFX versus Jersey breeds. A step-wise pruning approach was developed showing that and increased physical distances between markers of 8.5 Mb improved breed proportion estimation compared to a standard 1 Mb distance. A panel of 500 SNPs optimized to estimate HFX versus Jersey versus indicine ancestry was able to estimate indicine breed proportions with r² = .991, HFX proportions with r² = .979 and Jersey proportions with r² = .949. The number of markers was a deciding factor in estimation accuracy, together with the distribution of markers across the genome.</p>