Reference‐free SNP discovery for the E urasian beaver from restriction site–associated DNA paired‐end data

Abstract

In this study, we used restriction site–associated DNA ( RAD ) sequencing to discover SNP markers suitable for population genetic and parentage analysis with the aim of using them for monitoring the reintroduction of the E urasian beaver ( C astor fibre ) to S cotland. In the absence of a reference genome for beaver, we built contigs and discovered SNP s within them using paired‐end RAD data, so as to have sufficient flanking region around the SNP s to conduct marker design. To do this, we used a simple pipeline which catalogued the Read 1 data in stacks and then used the assembler cortex _ var to conduct de novo assembly and genotyping of multiple samples using the Read 2 data. The analysis of around 1.1 billion short reads of sequence data was reduced to a set of 2579 high‐quality candidate SNP markers that were polymorphic in N orwegian and B avarian beaver. Both laboratory validation of a subset of eight of the SNP s (1.3% error) and internal validation by confirming patterns of M endelian inheritance in a family group (0.9% error) confirmed the success of this approach.

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