Blastocerus dichotomus is the largest deer in South America. We have used 25 microsatellite markers detected and genotyped by Next Generation Sequencing to estimate the genetic variability of B. dichotomus in Argentina, where most of its populations are threatened. Primer design was based on the sequence of a shallow partial genome (15,967,456 reads; 16.66% genome coverage, mean depth 1.64) of a single individual. From the thousands of microsatellite loci found, even under high stringency selection, we chose and tested a set of 80 markers on 30 DNA samples extracted from tissue and feces from three Argentinean populations. Heterozygosity levels were low across all loci in all populations (H=0.31 to 0.40). Amplicon sequencing is a fast, easy, and affordable technique that can be very useful for the characterization of microsatellite marker sets for the conservation genetics of non-model organisms. This work is also one of the first ones to use amplicon sequencing in non-invasive samples and represents an important development for the study of threatened species.

Ozotoceros bezoarticus is categorized as Threatened in Argentina. In this study, we report 15 microsatellite loci-in the Argentinian populations, 12 are polymorphic and 3 monomorphic-isolated from a dinucleotide enriched genomic library. Among 59 individuals sampled from the four remaining populations in Argentina, the mean number of alleles was 7.58, the expected heterozygosity ranged from 0.33 to 0.88 and the observed heterozygosity from 0.08 to 0.83. Three loci showed deviation from Hardy-Weinberg equilibrium. Some of the loci showed linkage disequilibrium, although there was no coincident pattern for this parameter in all populations. The primers reported here constitute the first specific set for the species, and their use will be invaluable to generate the necessary information on genetic diversity in order to help conservation plans.