Data from: From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon

The use of genetic information is crucial in conservation programs for the
establishment of breeding plans and for the evaluation of restocking
success. Short tandem repeats (STRs) have been the most widely used
molecular markers in such programs, but next-generation sequencing
approaches have prompted the transition to genome-wide markers such as
single-nucleotide polymorphisms (SNPs). Until now, most sturgeon species
have been monitored using STRs. The low diversity found in the critically
endangered European sturgeon (Acipenser sturio), however, makes its future
genetic monitoring challenging and the current resolution needs to be
increased. Here, we describe the discovery of a highly informative set of
79 SNPs using Double Digest Restriction Associated DNA (ddRAD) sequencing
and its validation by genotyping using the MassArray system. Comparing
with STRs, the SNP panel proved to be highly efficient and reproducible,
allowing for more accurate parentage and kinship assignments’ on 195
juveniles of known pedigree and 40 wild-born adults. We explore the
effectiveness of both markers to estimated relatedness and inbreeding,
using simulated and empirical datasets. Interestingly, we found
significant correlations between STRs and SNPs at individual
heterozygosity and inbreeding that give support to a reasonable
representation of whole genome diversity for both markers. These results
are useful for the conservation program of A. sturio in building a
comprehensive studbook, which will optimize conservation strategies. This
approach also proves suitable for other case studies in which highly
discriminatory genetic markers are needed to assess parentage and kinship.