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.
Highlights
Yellow perch, Perca favescens, is a freshwater fish, natively distributed in temperate and subarctic areas of North America, and its abundance and native distribution center are in the lower Great Lakes region (Craig, 1987; Sepulveda-Villet et al, 2009)
Its long-term population distribution has been shaped by global climate change, mainly by Pleistocene glaciations and geophysical modifications (Sepulveda Villet and Stepien, 2012), with short-term population dynamics influenced by factors such as adaptive competition and capture fisheries (Coots, 1956; Malison, 2003; Marsden and Robillard, 2004; Houde et al, 2014; Bodamer Scarbro, 2014)
During the Pleistocene glaciations, populations persisted in the three primary North American glacial refugia: Missourian, Mississippian, and Atlantic
Summary
Perca favescens, is a freshwater fish, natively distributed in temperate and subarctic areas of North America, and its abundance and native distribution center are in the lower Great Lakes region (Craig, 1987; Sepulveda-Villet et al, 2009). Current yellow perch populations are attributed to at least two primary glacial refugia and divided into six major geographic regions: Northwest Lake Plains, Great Lakes watershed, Lake Champlain, US North Atlantic coastal, South Atlantic coastal, and Gulf coastal (Sepulveda Villet and Stepien, 2012). This species is in high demand for human consumption in the Great Lakes Region and a high-priority species for aquaculture production (Malison, 2003). For paired-end RAD reads assemblies, usually the forward reads are first clustered, whether the data are from an individual (Wang et al, 2016) or population (Hohenlohe et al, 2013), and the reverse reads within the same cluster are assembled according to the paired-end relationships
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