Advances of genotyping-by-sequencing in fisheries and aquaculture.
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.