Reviews in Fish Biology and Fisheries

, Volume 27, Issue 3, pp 535–559 | Cite as

Advances of genotyping-by-sequencing in fisheries and aquaculture

Reviews
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Abstract

The use of genotyping has enabled the characterization and mapping of genes and the study of stock identification, population genetics, evolution, ecological speciation, and invasion, as well as genomic evaluation, sex control and sex determination, nutrition, biomarkers for disease, and quantitative trait loci mapping for marker-assisted selection in fisheries and aquaculture. High-throughput variant discovery has been made possible in multiple species by the recent advent of next-generation DNA sequencing technologies. New genotyping methods that are high-throughput, accurate, and inexpensive are urgently needed for gaining full access to the abundant genetic variation of organisms. This approach is known as genotyping-by-sequencing (GBS), which holds great promise as a research tool because of its ability to allow simultaneous marker discovery and genotyping at low cost and with a simple molecular biology workflow for fisheries and aquaculture studies. Since it was first developed for rice in 2009, GBS has been applied in over 50 species/studies by the end of 2014. It is also increasingly in use in fisheries and aquaculture and has been applied in nearly 40 species/studies from 2015 to present. This review summarizes the genotyping methodologies, recent advances in next-generation DNA sequencing technologies to achieve GBS, and the promises this approach holds as a genome-wide genotyping application in fisheries and aquaculture. Additionally, we discuss the potential of whole-genome sequencing (WGS) in GBS and present the advances of WGS in fisheries and aquaculture.

Keywords

Fish Genotyping-by-sequencing Next-generation sequencing Single nucleotide polymorphism markers Whole-genome sequencing 

Notes

Acknowledgements

This study was supported by the National Institute of Food and Agriculture (NIFA), U.S. Department of Agriculture, under Agreement No. 2010-38,879-20946. Salaries and research support were provided by state and federal funds appropriated to The Ohio State University, Ohio Agricultural Research and Development Center, and Huazhong Agricultural University. We thank Joy Bauman for her comments on the manuscript.

Supplementary material

11160_2017_9473_MOESM1_ESM.docx (42 kb)
Supplementary material 1 (DOCX 42 kb)

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Copyright information

© Springer International Publishing Switzerland 2017

Authors and Affiliations

  1. 1.Fish Genetics and Breeding LaboratoryThe Ohio State University South CentersPiketonUSA
  2. 2.College of FisheriesHuazhong Agricultural UniversityWuhanPeople’s Republic of China

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