Accurate determination of phenotypic information from historic thoroughbred horses by single base extension

Abstract

Historic DNA data have the potential to identify phenotypic information otherwise invisible in the historical, archaeological and palaeontological record. In order to determine whether a single nucleotide polymorphism typing protocol based on single based extension (SNaPshot™) could produce reliable phenotypic data from historic samples, we genotyped three coat colour markers for a sample of historic Thoroughbred horses for which both phenotypic and correct genotypic information were known from pedigree information in the General Stud Book. Experimental results were consistent with the pedigrees in all cases. Thus we demonstrate that historic DNA techniques can produce reliable phenotypic information from museum specimens.

Figure 1. Allele ratios varying between three replicates of the same sample (Ormonde) due to stochastic effects.

There is evidence of allelic dropout in the second replicate. The differences in location of the peaks between the repetitions are due to variation between genotyping runs.

Figure 2. Comparison between allele frequencies of MC1R determined by cloning (a) and those determined by SNaPshot™ (b).

Although the SNaPshot™ reaction (bottom) has isolated both peaks, cloning and sequencing (top) has reduced the T-allele to a frequency more parsimoniously attributable to a homozygous C animal where T alleles have originated from C→T transitions resulting from post-mortem deamination of cytosine.