Development of a genomic resource and identification of nucleotide diversity of yellow perch by RAD sequencing

Authors: GUO, LIANG - The Ohio State University; YAO, HONG - The Ohio State University; Shepherd, Brian; SEPULVEDA-VILLET, O - University Of Wisconsin; ZHANG, DIAN-CHANG - Chinese Academy Of Sciences; WANG, HAN-PING - The Ohio State University

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/18/2019
Publication Date: 10/14/2019
Citation: Guo, L., Yao, H., Shepherd, B.S., Sepulveda-Villet, O.J., Zhang, D., Wang, H. 2019. Development of a genomic resource and identification of nucleotide diversity of yellow perch by RAD sequencing. Frontiers in Genetics. https://doi.org/10.3389/fgene.2019.00992.
DOI: https://doi.org/10.3389/fgene.2019.00992

Interpretive Summary: Yellow perch, Perca favescens, is a freshwater fish, natively distributed in temperate and subarctic areas of North America and its distribution center is in the lower Great Lakes region. This species is in high demand for human consumption and, consequently, numbers in the wild have been substantially reduced due to overfishing and other factors. Despite continuing pressure on wild populations, basic population level studies are needed for conservation genetics and for genetic improvement programs for the aquaculture industry. Historically, a number of studies have used various genetic markers to characterize population-level (e.g., broodstock) genetics, but use of these traditional tools have come with limitations. The availability of a larger number, and type, of genetic markers, amenable to genome-wide studies, would enable more cost-effective and higher resolution genetics studies to support modern aquaculture practices. In this work, we have developed libraries consisting of two types of genomic markers called microsatellite markers (also simple sequence repeats, SSRs) and single nucleotide polymorphisms (SNPs). SSRs are areas of DNA that display repetitive 2-5-base areas of sequence, whereas SNPs are single point mutations in areas of DNA, which can vary highly between individuals, families and populations. Both types of markers were identified in a restriction site-associated DNA sequence (RAD-seq) database developed from various yellow perch broodstock populations. We report the identification of new SSRs and SNPs from this RAD sequence library. Identified SSRs were shown to be polymorphic, which means that they can be used to genotype individuals and enable identification of populations, sub-populations and parentage. Availability of new SSRs and SNPs makers will enable scientists to increase the pace of genetic gain for traits of interest in yellow perch aquaculture.

Technical Abstract: Yellow perch (Perca favescens) is an important native North American fish species for aquaculture. However, availability of molecular markers needed for genetics studies is minimal, especially markers with genome-wide distribution. Single sequence repeat (SSR) markers are always developed using sequences from a single individual, which is time consuming and has a low success rate. In this study, we combined sequencing data from HiSeq and MiSeq platforms, to that of restriction site-associated DNA sequencing (RAD-Seq) data developed from various yellow perch geographic strains. The aim was to develop a large number of polymorphic SNP and SSR genetic markers and to evaluate nucleotide diversity of these markers. 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 (p) was 0.00304 with 95% confidence intervals from 0.00303 to 0.00304. Based on the assembled sequences, a total of 59,766 perfect SSRs were detected, with AC/GT being the most common repeat motif and GC being the rarest. Based on this sample population, 41,736 high-quality single nucleotide polymorphisms and 10,412 polymorphic SSRs were obtained. Validation of amplification by randomly selecting 40 polymorphic SSRs showed a high success rate (85%) for polymorphic markers. This approach for development of polymorphic SSRs demonstrates that sequences from RAD-seq data sets can be a new source for SSR development. The developed markers could be used in the management of wild fisheries, and in the genetic improvement of yellow perch broodstocks for commercial aquaculture.