Comparative evaluation of whole genome amplification methods in water buffalo frozen semen

Abstract

Whole genome amplification (WGA) provides a large amount of genomic DNA for various genetic analyses from depleting stock or scarce sources of DNA. In the present study, the performance of two routinely used WGA methods i.e., Multiple displacement amplification (MDA) and OmniPlex amplification was compared against the unamplified semen DNA of 9 water buffalo bulls by PCR, RFLP, sequencing and microsatellite genotyping. Using wgaDNA, no difference was seen in RFLP or sequencing results by either method. However, 2.2% erroneous microsatellite genotype calls were observed in OmniPlex amplification compared to 0.6% by MDA technique. Though, the two whole genome amplification methods provide large amount of template DNA required for applications such as genome mapping, a careful selection of methodologies would be required in view of inconsistency in genotyping results.