Abstract
ObjectiveThis study was designed to facilitate genetic studies that would allow information on population structure and genetic diversity of natural or captive stocks of paca (Cuniculus paca), a species of ecological and socioeconomic importance, by testing cross-amplification of 20 heterologous microsatellite primer pairs developed for guinea pigs (Cavia porcellus) and capybara (Hydrochoerus hydrochaeris).ResultsThose primers that showed the best amplification profile in blood samples were subsequently applied to scats and saliva samples, to evaluate their efficiency. Of the 13 microsatellite pairs that amplified in blood, one-third (32%) were successfully amplified in saliva and scat samples. This initial work demonstrates successful cross-amplification in paca providing a solid and promising foundation for future genetic studies with this species. The ability to quantify genetic diversity using noninvasive samples from free-ranging paca is essential to developing applied management strategies for this large neotropical rodent that is not only a prey favored by wide-ranging carnivores [e.g., jaguar (Panthera onca), puma (Puma concolor)], but is also a species targeted by illegal hunting and wildlife trade.
Highlights
The paca (Cuniculus paca, Linnaeus, 1766), a grounddwelling, herbivorous rodent, is a unique genus in the family Cuniculidae
While initial testing of cross-amplification would be done with invasive samples, the long-term goal is to have the selected primers work with noninvasive samples or forensic Deoxyribonucleic acid (DNA) from free-ranging populations, including in the biological corridor proposed for northerncentral zone of Misiones, Argentina [27]
Thirteen (65.0%) of heterologous primers pairs amplified DNA extracted from blood (100% of samples), saliva (46.2% of samples), and scat (20.5% of samples), while seven (35.0%) of heterologous primers pairs could not be consistently scored and interpreted (Table 1)
Summary
Thirteen (65.0%) of heterologous primers pairs amplified DNA extracted from blood (100% of samples), saliva (46.2% of samples), and scat (20.5% of samples), while seven (35.0%) of heterologous primers pairs could not be consistently scored and interpreted (Table 1). Seven (53.9%) of the microsatellite primers pairs that successfully cross-amplified in paca were from the twelve developed for guinea pigs (CUY5, CUY7, CUY9, CUY17, CUY22, CAVY2, and CAVY12; Table 1). Thirteen (65.0%) of the tested loci in paca produced amplicon size ranges similar to those in the two species (guinea pig and capybara) for which the primers were originally developed (Table 3). Three primers (CAVY2, CAVY12, and CAPY9) had amplicons that fell within the published ranges for guinea pig and capybara. Eight primers (CUY7, CUY9, CUY17, CAPY4, CAPY6, CAPY10, CAPY12 and CAPY24) had amplicons that showed light shifts (± 1 to 49 bp) from the expected size ranges. Two primers (CUY5 and CUY22) had amplicons that showed larger shifts (± 43–130 bp) from the published size ranges. All 13 (100%) of these amplified loci were polymorphic (range: 2–6 loci), showing different sized loci (Table 3)
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