AUTHOR=Guo Liang , Yao Hong , Shepherd Brian , Sepulveda-Villet Osvaldo J. , Zhang Dian-Chang , Wang Han-Ping 

TITLE=Development of a Genomic Resource and Identification of Nucleotide Diversity of Yellow Perch by RAD Sequencing

JOURNAL=Frontiers in Genetics

VOLUME=Volume 10 - 2019

YEAR=2019

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2019.00992

DOI=10.3389/fgene.2019.00992

ISSN=1664-8021

ABSTRACT=Yellow perch (Perca favescens) is an important native North American fish in ecology and aquaculture. However, molecular markers are minimal for this species, especially those with genome-wide distribution. Single sequence repeat markers are always developed based on sequences from a single individual, which is time consuming with a low success rate. In this study, combining data from HiSeq and MiSeq platforms, 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%). Our approach for polymorphic single sequence repeats development enables new usage of data from RAD-seq techniques. These developed markers could be used in finfish broodstock management, genetic improvement and resource conservation, and would contribute to sustainable development of fisheries and the aquaculture industries.