Nine porcine microsatellite loci tested for size homoplasy in genetically diverse breeds.
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.
Peischl
T
T
Department of Animal Breeding and Biotechnology, University of Hohenheim, D-70593 Stuttgart, Germany.
Kuss
A W
AW
Melchinger-Wild
E
E
Geldermann
H
H
D000818:Animals; D001483:Base Sequence; D014644:Genetic Variation; D018895:Microsatellite Repeats / Q000235:genetics*; D008957:Models, Genetic; D008969:Molecular Sequence Data; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D034421:Sus scrofa / Q000235:genetics*; D014744:Vietnam