Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Aquatic Living Resources Aquat. Living Resour. 2018, 31, 2 © EDP Sciences 2017 https://doi.org/10.1051/alr/2017043 Available online at: www.alr-journal.org REVIEW ARTICLE Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations Roman Wenne* Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland Received 16 March 2017 / Accepted 4 November 2017 Handling Editor: Costas Tsigenopoulos Abstract – An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed. Keywords: Aquaculture and mariculture / identification of escapees / SNP / QTL / resistance to pathogens / genomic selection / gene editing 1 Introduction Exploitation of living marine and freshwater resources is an important source of food for human population worldwide. Global aquatic production has been increasing substantially for over 60 years and reached 167.2 million tonnes in 2014, of which 55.86% was capture fisheries production (FAO, 2016). However, aquaculture has hugely increased over the last 25 years and shows a higher potential for future development in comparison with capture fisheries. Further increases in production will be achieved by extending aquaculture areas geographically (finding new areas suitable for aquaculture industry), employing new species for culture, and using new technologies. A technology developed in recent years and useful for increasing aquaculture *Corresponding author: production and improving the protection of biodiversity is the application of genomics (McAndrew and Napier, 2010; Abdelrahman et al., 2017; Macqueen et al., 2017). New Generation Sequencing (NGS) has enabled the assembly of genomes of an increasing a number of species, and the characterization of number of genes in some cultured species has been followed by the characterization of their gene pools. This has, in turn, lead to functional studies of genes relevant to the goals of aquaculture. Genotyping by sequencing (GBS) techniques have laid the foundation for advances in aquaculture genetics and breeding (Robledo et al., 2017). Genome complexity reduction has facilitated the discovery of a large number of molecular markers, especially single nucleotide polymorphism (SNP). A range of techniques have been used for SNP discovery. The smaller scale methods include SSCP and heteroduplex analyses, random shotgun, direct polymerase chain reaction (PCR) product sequencing and expressed R. Wenne: Aquat. Living Resour. 2018, 31, 2 sequence tags (ESTs) (Liu and Cordes, 2004). Large scale SNP discovery enabled with high throughput sequencing platforms NGS and whole genome sequencing in fish has been reviewed more recently (Abdelrahman et al., 2017; Kumar and Kocour, 2017). SNP have been used for the identification of brood stocks, traits and strains in aquaculture. SNP can be applied to finding candidate genes of traits and quantitative trait loci (QTL) useful in aquaculture (Oyarzun et al., 2013; Yáñez et al., 2015). QTL are genomic regions associated with phenotypic variation for a specific trait, which can be significant for aquaculture, such as growth, skin pigmentation, body shape, color of meat, age of maturity (grilsing), thermal tolerance, lipid metabolism and resistance to stress and diseases. Selective breeding of farmed animals for economically important quantitative traits has high potential for increasing aquaculture production. In classic selection schemes best linear unbiased prediction (BLUP) is applied to assess the selection candidates based on the phenotypes of relatives without the use of genetic markers (Boichard et al., 2016). In order to reinforce phenotypic based selection QTL markers were developed with the intended applications in marker assisted selection (MAS). The identified QTL for economically useful traits in aquaculture have been summarized recently (Abdelrahman et al., 2017). Linkage analysis to detect QTL includes family and progeny data (Rabier et al., 2016). Segregation of QTL has been studied within family. MAS can be successful if significant variance explained by a QTL (association) is not overestimated and linkage disequilibrium between marker and QTL persists throughout the population. Alternatively, large number of markers covering whole genome can be used for estimation of breeding value (Meuwissen et al., 2001). Genotyping with high density markers can shorten generation phase. Genome-wide association studies (GWAS) seek to find associations between SNPs and traits in unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genomic selection (GS) involves prediction of breeding values of selection candidates using high density markers irrespective of significance in their association studies. GS relies on the assumption that some QTL are in strong linkage disequilibrium with molecular markers (SNPs). Finding functional implications of particular SNP will enable genetic engineering by the incorporation of single nucleotides or short sequences (Dunham et al., 2014). Such alterations can make alleles in aquaculture more alike to the alleles of specimens with desirabl (...truncated)