Nine porcine microsatellite loci tested for size homoplasy in genetically diverse breeds

Abstract

Kind and probability of homoplasy across allelic microsatellite fragments can be investigated using DNA of genetically diverse pig breeds. In this study, nine microsatellite loci (SW1897, SW2427, SW489, SW957, TNFB, IFNG, SW2410, SW2019 and S0215) were analysed using DNA samples of pigs from Vietnam (Indigenous breeds Co, Meo, Muong Khuong, Tap Na) and Germany (European Wild Boar, Pietrain). In a total of 39 sequences, 20 differences within isomorphic alleles were observed in comparison with the respective reference sequences. They affected five of the nine tested microsatellite loci. The majority (18) of SNPs occurred in the 5'-flanking regions of the microsatellite repeats, 10 were found in the 3'-flanking regions and only one SNP occurred within the repeat of the Wild Boar sequence of SW2427. The compound microsatellites IFNG and S0215 were unaffected by size homoplasy (SH) within our material. We conclude that the fragment length analysis of microsatellites is a reliable tool for intraspecific phylogenetic studies because SH rates within a species were low.

Individual-breed Assignment Analysis in Swine Populations by Using Microsatellite Markers

“…Besides the intrinsic characteristics of microsatellites such as polymorphisms and assignment power, and size homoplasy (Peischl et al, 2005), exterior factors also should be taken consideration for individual-breed assignments. The PCR results' stability, stutter bands, and the occurrence of null alleles during the procedure of microsatellite genotyping should be examined with great caution.…”