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      Applications of genotyping by sequencing in aquaculture breeding and genetics

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          Abstract

          Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism ( SNP) arrays for some species have been developed recently, direct genotyping by sequencing ( GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing ( RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.

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          Most cited references 96

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          Prediction of total genetic value using genome-wide dense marker maps.

          Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of approximately 50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size N(e) = 100, the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
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            Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

            Single nucleotide polymorphism (SNP) discovery and genotyping are essential to genetic mapping. There remains a need for a simple, inexpensive platform that allows high-density SNP discovery and genotyping in large populations. Here we describe the sequencing of restriction-site associated DNA (RAD) tags, which identified more than 13,000 SNPs, and mapped three traits in two model organisms, using less than half the capacity of one Illumina sequencing run. We demonstrated that different marker densities can be attained by choice of restriction enzyme. Furthermore, we developed a barcoding system for sample multiplexing and fine mapped the genetic basis of lateral plate armor loss in threespine stickleback by identifying recombinant breakpoints in F2 individuals. Barcoding also facilitated mapping of a second trait, a reduction of pelvic structure, by in silico re-sorting of individuals. To further demonstrate the ease of the RAD sequencing approach we identified polymorphic markers and mapped an induced mutation in Neurospora crassa. Sequencing of RAD markers is an integrated platform for SNP discovery and genotyping. This approach should be widely applicable to genetic mapping in a variety of organisms.
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              Genome-wide genetic marker discovery and genotyping using next-generation sequencing.

              The advent of next-generation sequencing (NGS) has revolutionized genomic and transcriptomic approaches to biology. These new sequencing tools are also valuable for the discovery, validation and assessment of genetic markers in populations. Here we review and discuss best practices for several NGS methods for genome-wide genetic marker development and genotyping that use restriction enzyme digestion of target genomes to reduce the complexity of the target. These new methods -- which include reduced-representation sequencing using reduced-representation libraries (RRLs) or complexity reduction of polymorphic sequences (CRoPS), restriction-site-associated DNA sequencing (RAD-seq) and low coverage genotyping -- are applicable to both model organisms with high-quality reference genome sequences and, excitingly, to non-model species with no existing genomic data.
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                Author and article information

                Contributors
                ross.houston@roslin.ed.ac.uk
                Journal
                Rev Aquac
                Rev Aquac
                10.1111/(ISSN)1753-5131
                RAQ
                Reviews in Aquaculture
                John Wiley and Sons Inc. (Hoboken )
                1753-5123
                1753-5131
                04 February 2017
                August 2018
                : 10
                : 3 ( doiID: 10.1111/raq.2018.10.issue-3 )
                : 670-682
                Affiliations
                [ 1 ] The Roslin Institute and Royal (Dick) School of Veterinary Studies University of Edinburgh Midlothian UK
                [ 2 ] Department of Comparative Biomedicine and Food Science University of Padova Legnaro Padova Italy
                [ 3 ] Department of Zoology Genetics and Physical Anthropology Faculty of Veterinary University of Santiago de Compostela Lugo Spain
                Author notes
                [* ] Correspondence

                Ross Houston, The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, EH25 9RG UK. Email:  ross.houston@ 123456roslin.ed.ac.uk

                Article
                RAQ12193
                10.1111/raq.12193
                6128402
                © 2017 The Authors. Reviews in Aquaculture Published by Wiley Publishing Asia Pty Ltd

                This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                Page count
                Figures: 0, Tables: 3, Pages: 13, Words: 10579
                Product
                Funding
                Funded by: European Union's Seventh Framework Programme
                Award ID: 613611
                Award ID: 311920
                Funded by: Biotechnology and Biological Science Research Council (BBSRC)
                Award ID: BB/N024044/1
                Award ID: BB/M028321/1
                Award ID: BB/J004235/1
                Award ID: BB/J004324/1
                Categories
                Review
                Review Articles
                Custom metadata
                2.0
                raq12193
                August 2018
                Converter:WILEY_ML3GV2_TO_NLMPMC version:version=5.4.4 mode:remove_FC converted:20.08.2018

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