Genotyping Free-ranging Rodents with Heterologous Pcr Primer Pairs for Hypervariable Nuclear Micro Satellite Loci

The application of commercially available microsatellite primers, developed for genomic analysis of the laboratory rat (Rattus norvegicus) and laboratory mouse (Mus musculus), to the genotyping of wild rodents provides a rapid and inexpensive alternative to cloning, sequencing and synthesizing species-specific primers de novo. The effort required to identify a useful panel of heterologous (interspecifically derived) primers for loci in genetically unknown rodents is illustrated with a study of three wild rodents in Thailand. Eight out of 13 (62%) of the rat primer pairs tested amplified polymorphic sequences in a representative of a closely related genus, Maxomys surifer, and all 8 of these primer pairs amplified polymorphic sequences in the wild congener, R. rattus. Of the mouse primer pairs 33% (10/30) amplified polymorphic sequences in a distantly related tree mouse, Chiropodomys gliroides. Preliminary surveys of wild M. surifer and C. gliroides in Thai forests revealed high levels of polymorphism at these microsatellite loci and up to 20 alleles segregating per loeus. These loci are variable enough to be used to establish pedigree relationships and population structure, and monitor gene flow and genetic erosion. Multiloeus genotyping based on noninvasive DNA sampling and PCR employing both homologous and heterologous microsatellite primers promises to revolutionize genetic analyses of freeranging rodents.