RAD-Seq of yellow perch for diversity assessment

We applied restriction site-associated DNA sequencing (RAD-Seq) to yellow perch geographic demes to develop large numbers of polymorphic genetic markers, including single nucleotide polymorphisms and simple sequence repeats, and to evaluate nucleotide diversity. A total of 258,056 contigs were assembled with the length of 605 ± 71 (mean ± SD) bp, which were longer than those just using HiSeq data. Nucleotide diversity (π) was 0.00304 with 95% confidence intervals from 0.00303 to 0.00304. Based on the assembled sequences, a total of 59,766 perfect single sequence repeats were detected, with AC/GT being the most common repeat motif and GC being the rarest. Based on this breeding population, 41,736 high-quality single nucleotide polymorphisms and 10,412 polymorphic single sequence repeats were obtained. Validation of amplification by randomly selecting 40 polymorphic single sequence repeats showed a high success rate (85%).