Genetic Dissection of a Precocious Phenotype in Male Tiger Pufferfish (Takifugu rubripes) using Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di)

Sota Yoshikawa,Masaomi Hamasaki,Sho Hosoya,Kazushi Kadomura,Toshiyuki Yamada,Hisashi Chuda,Kiyoshi Kikuchi

doi:10.1007/s10126-020-10013-4

Abstract

The novel non-targeted PCR-based genotyping system, namely Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di), is characterized by the simplicity in library construction and robustness against DNA degradation and is expected to facilitate advancements in genetics, in both basic and applied sciences. In this study, we tested the utility of GRAS-Di for genetic analysis in a cultured population of the tiger pufferfish Takifugu rubripes. The genetic analyses included family structure analysis, genetic map construction, and quantitative trait locus (QTL) analysis for the male precocious phenotype using a population consisting of four full-sib families derived from a genetically precocious line. An average of 4.7 million raw reads were obtained from 198 fish. Trimmed reads were mapped onto a Fugu reference genome for genotyping, and 21,938 putative single-nucleotide polymorphisms (SNPs) were obtained. These 22 K SNPs accurately resolved the sibship and parent–offspring pairs. A fine-scale linkage map (total size: 1,949 cM; average interval: 1.75 cM) was constructed from 1,423 effective SNPs, for which the allele inheritance patterns were known. QTL analysis detected a significant locus for testes weight on Chr_14 and three suggestive loci on Chr_1, Chr_8, and Chr_19. The significant QTL was shared by body length and body weight. The effect of each QTL was small (phenotypic variation explained, PVE: 3.1–5.9%), suggesting that the precociousness seen in the cultured pufferfish is polygenic. Taken together, these results indicate that GRAS-Di is a practical genotyping tool for aquaculture species and applicable for molecular breeding programs, such as marker-assisted selection and genomic selection.

Highlights

Recent advances in genomic tools have been proven to be very useful for ecological and evolutionary studies and for the agricultural sciences
The aim of this study is three-fold: (1) to test the utility of single-nucleotide polymorphisms (SNPs) obtained by GRAS-Di for a family structure analysis using a cultured population of the tiger pufferfish, (2) to evaluate the applicability of these SNPs for genetic map construction, and (3) to investigate the feasibility of the linkage map to dissect the genetic architecture of the precocious traits by means of quantitative trait locus (QTL) analysis
We investigated the utility of GRAS-Di for genetic studies, i.e., family structure analysis, genetic linkage map construction, and QTL analysis, using a cultured population of the tiger pufferfish

Summary

Introduction

Recent advances in genomic tools have been proven to be very useful for ecological and evolutionary studies and for the agricultural sciences. Developments in various high-throughput cost-effective genotypingby-sequencing (GBS) systems, such as RADseq (and its derivatives) (Baird et al 2008; Peterson et al 2012; Andrews et al 2016), MIGseq (Suyama and Matsuki 2015), and Ampliseq (Sato et al 2019), facilitate a wide range of genetic analyses, including population structure analysis (Hohenlohe et al 2010; Cavender-Bares et al 2015; Hirase et al 2020), linkage map construction (Elshire et al 2011; Hoshino et al 2016; Escudero et al 2018), and forward genetics (Wilson et al 2014; Zhou et al 2015; Ieda et al 2018; Kim et al 2019), even for non-model organisms These technologies are recognized as powerful tools for aquaculture studies, as they are utilized in the implementation of selective breeding programs and the management of genetic diversity of target populations (Houston et al 2012; Palaiokostas et al 2013; Hosoya et al 2018).

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