A simple and powerful method for linkage analysis by amplification of DNA from single sperm cells

Haplotypes of three bovine casein loci were analyzed as a way of determining genetic linkage. A total of 330 individual sperm cells from a triply heterozygous bull were selected by means of a new method involving fixing the sperm cells into low-melting-point agarose gels. The method is simple and very accurate with an efficiency close to 100% for picking sperm cells and producing amplifiable DNA templates, circumventing the complicated statistical analysis mandated by automated cell sorting. The DNA was amplified in a two-step polymerase chain reaction (PCR) to achieve the necessary high specificity of amplification. In the first reaction, primers flanking the polymorphic site at each locus were used. The PCR product from the first reaction was then reamplified in a second PCR using primers that create allele-specific restriction sites (ACRS) in the PCR products for two of the three loci, allowing the alleles to be determined by gel electrophoresis. No recombinants were found among the 330 single sperm cells analyzed, giving a lod score higher than 30 and proving a very strong linkage between bovine casein genes.