Real-time qPCR is a powerful assay to estimate the 171 R/Q alleles at the PrP locus directly in a flock's raw milk: a comparison with the targeted next-generation sequencing.

•Scrapie is a fatal neurodegenerative brain disease affecting sheep and goat.•An original qPCR to quantify the 171 Q/R alleles in bulk milk is proposed.•The aim is to survey the 171 Q/R allele frequencies in flocks undergoing selection.•The assay was validated “in field” on tank raw milk from individual flocks.•Comparison between real-time PCR and next-generation sequencing was carried out.