Proc. Once an adequate training data set against commercially well-defined breeding objectives has been completed, a robust test-set and validation phase is required to determine the accuracy of the genomic predictions. Evol. Genomic prediction of host resistance to sea lice in farmed Atlantic salmon populations. J. Hered. 78, 157160 (2013). 47:76. doi: 10.1186/s12711-015-0155-z, Fan, B., Du, Z.-Q., Gorbach, D. M., and Rothschild, M. F. (2010). J. Zhejiang. Natl Acad. Lpez, M. E. et al. A fundamental difference is in the stage of domestication, and being able to fully close life cycles between the species, which is a significant limitation for the adoption of advanced breeding systems in P. monodon. Biological innovations are grouped into four . doi: 10.1016/j.aquaculture.2013.02.017, Thorpe, J. E. (1994). They then concluded that using a family size of 100, at least 24,000 loci (100Ne for 30 morgan) are needed to obtain adequate selection accuracy. Google Scholar. Similarly, MVSs have been used for pearl oyster growth data as well as pearl quality traits (e.g., color, size, luster, and completion). Computer vision is an enabling technology and has already allowed many animal and plant production traits to be measured efficiently and accurately across different production industries, including aquaculture (i.e., McCarthy etal., 2010; Mathiassen etal., 2011; Cobb etal., 2013; Nasirahmadi etal., 2017; Saberioon etal., 2017). Potential of promotion of alleles by genome editing to improve quantitative traits in livestock breeding programs. Loss of stomach, loss of appetite? (2014). Furthermore, aquaculture does not have the benefit of standardized global phenotyping programs such as in livestock (e.g., dairy cattle). Sel. Biotechnol. 15, 647658. Bioengineering is one area of biological innovation, propelled by a series of breakthroughs including the mapping of the human genome (completed in 2003) and the decreasing cost and speed of sequencing DNA. Limnol. Bishop, S. C. & Woolliams, J. QTL mapping for disease resistance has also been conducted in the eastern oyster Crassostrea virginica for MSX and Dermo (Yu and Guo, 2006), the European flat oyster Ostrea edulis for Bonamiosis (Lallias etal., 2009), and the Atlantic salmon for salmonid alphavirus (Gonen etal., 2015), ISAv (Moen etal., 2007), and Gyrodactylus salaris parasitic disease (Gilbey etal., 2006; for review, see Yez etal., 2014). Rev. Robot. Moreover, increasing the marker density eightfold (from 1Ne/morgan to 8Ne/morgan) can increase the accuracy of genomic selection from 0.69 to 0.86 (Solberg etal., 2008). Google Scholar. Following traditional phenotypic or genetic selection (i.e., EBVs), the integration of genetic markers into MAS breeding programs was expected to increase the genetic response observed by increasing the efficiency and accuracy of selection (Laghari etal., 2014; Yue, 2014; Abdelrahman etal., 2017). Gutierrez, A. P., Lubieniecki, K. P., Davidson, E. A., Lien, S., Kent, M. P., Fukui, S., et al. Rev. (2006). Precision fish farming: a new framework to improve production in aquaculture. (2017). However, a recent review by Guppy etal. Fish Fish. In the context of genome editing, the unintended impacts on traits other than the target trait due to a specific edit. Electron. 16:1047. doi: 10.1186/s12864-015-2252-3, Dong, L., Xiao, S., Wang, Q., and Wang, Z. Knutsen, T. M. Lumpfish (Cyclopterus lumpus) draft genome assembly. doi: 10.1111/1755-0998.12291, Mathiassen, J. R., Misimi, E., Toldnes, B., Bond, M., and stvik, S. O. Proc. In the case of pearl oyster, the multi-factorial nature of pearl value adds to the complexity of setting up multi-trait genomic selection. Biol. Identification of a single major genetic locus controlling the resistance to lymphocystis disease in Japanese flounder (Paralichthys olivaceus). Res. Robledo, D., Palaiokostas, C., Bargelloni, L., Martnez, P. & Houston, R. Applications of genotyping by sequencing in aquaculture breeding and genetics. Mar. BMC. Cell Biol. Genetic improvement for aquaculture species: A promising approach for Wanninger, A. Nat. Lafferty, K. D. et al. Aquaculture 434, 476485. Fernndez, J., Toro, M. ., Sonesson, A. K. & Villanueva, B. Optimizing the creation of base populations for aquaculture breeding programs using phenotypic and genomic data and its consequences on genetic progress. Major quantitative trait loci affect resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar). Early-feeding exposure to a plant-based diet improves its future acceptance and utilization in rainbow trout. (2010). LinkImpute: fast and accurate genotype imputation for nonmodel organisms. Med. Agric. van Dijk, E. L., Jaszczyszyn, Y., Naquin, D. & Thermes, C. The third revolution in sequencing technology. (2008). With the realization that traditional breeding programs for traits other than growth are difficult to implement, alternative approaches to estimate the genetic merit of breeding individuals of these traits have been explored. doi: 10.1007/s00343-017-6038-0, Witte, J. S. (2010). These later traits are typically harder to select for as they are difficult-to-measure, can often only be measured late in life, involve destructive sampling, or have low heritability (e.g., Yez etal., 2015). As such, GBS is rapidly becoming one of the SNP genotyping methods of choice for aquaculture species (see Robledo etal., 2017), either by directly providing genotype data or by discovering markers for the design of solid-state SNP arrays. Asche, F., Hansen, H., Tveteras, R. & Tveteras, S. The salmon disease crisis in Chile. Defining loci in restriction-based reduced representation genomic data from nonmodel species: sources of bias and diagnostics for optimal clustering. Res. (MAS). Int. Principles of hyperspectral imaging technology. This is a preview of subscription content, access via your institution. A., Kawamoto, K., Buckler, E. S., et al. A comparison of five methods to predict genomic breeding values of dairy bulls from genome-wide SNP markers. However, in reality, this almost certainly will not be the case (particularly with disease), and the impact of G E interactions could be substantial. However, the accuracy of imputed genotypes is critical for efficient use of these low-density panels. doi: 10.1371/journal.pone.0085413, Baranski, M., Moen, T., and Vge, D. I. Dairy Sci. Apart from optimizing the number of training or selection candidates for routine genotyping (i.e., based on genomic selection modeling and farm breeding scheme, e.g., Sonesson and Meuwissen, 2009), reducing the cost or number of genome-wide markers is a viable solution. Although this sounds straightforward enough, practical limitations become immediately apparent in situations where traits under commercial grow-out conditions vary substantially from performance recording environments in often pathogen-free central nucleus breeding facilities (as used in specific pathogen free shrimp breeding programs, for instance). doi: 10.1186/1471-2164-10-368, Moen, T., Sonesson, A. K., Hayes, B., Lien, S., Munck, H., and Meuwissen, T. H. (2007). J. Anim. Linking together of short sequence reads to provide long-range orientation, based on the addition of a unique DNA barcode to each read generated from an individual molecule. Using genomic information, accuracy of prediction strongly depends on linkage disequilibrium (LD) between QTL and marker loci, as well as co-segregation over multiple generations (Sun etal., 2016). Yue, G. H. Recent advances of genome mapping and marker-assisted selection in aquaculture. Parker, L. M., OConnor, W. A., Raftos, D. A., Prtner, H.-O. BMC Genet. Genetic (co)variance of rainbow trout (Oncorhynchus mykiss) body weight and its uniformity across production environments. Genet. 34, 18121819 (2017). (2006) and Holtsmark etal. Crossing phenotypic heritability and candidate gene expression in grafted Black-lipped pearl oyster Pinctada margaritifera, an Animal chimera. (2018a). Jennings, S. et al. USA 111, 1325713263 (2014). However, these QTL only explain a small proportion of the total additive genetic variation, and the validation of these QTL is limited, with only a few being confirmed in multiple independent families or populations. This may allow QTL to be mapped down to quantitative trait nucleotide (QTN) polymorphisms as the causative determinants for such complex traits. Aquac. 110, 720726 (2019). 18, 466488 (2017). Within-family marker-assisted selection for aquaculture species. 35, 672684 (2019). ZooKeys (695), 135152. 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Joshi, R., Skaarud, A., de Vera, M., Alvarez, A. T. & degrd, J. Genomic prediction for commercial traits using univariate and multivariate approaches in Nile tilapia (Oreochromis niloticus). Mol. (2014). Nature 418, 700707 (2002). Progress of DNA marker-assisted breeding in maricultured finfish. Heredity 105, 318327 (2010). Together with reference 219, this study describes a very large effect QTL for disease resistance in aquaculture populations, leading to widespread adoption of marker-assisted selection to help reduce disease incidence. Sel. Genet. Nature 528, 405408 (2015). & Wellenreuther, M. High-density linkage map and QTLs for growth in snapper (Chrysophrys auratus). 17, 159173 (2017). doi: 10.1146/annurev.publhealth.012809.103723, Wringe, B. F., Devlin, R. H., Ferguson, M. M., Moghadam, H. K., Sakhrani, D., and Danzmann, R. G. (2010). Penaeid shrimp genome provides insights into benthic adaptation and frequent molting. Reis, V., Neto, R., Yoshida, G., Lhorente, J. P., and Yez, J. Goswami, M., Mishra, A., Ninawe, A., Trudeau, V. & Lakra, W. Bio-banking: an emerging approach for conservation of fish germplasm. Genet. Construction of a high-density linkage map and fine mapping of QTL for growth in Asian seabass. 12, 137156 (2019). Agric. A novel approach to estimating heterozygosity from low-coverage genome sequence. Evol. Aquaculture 516, 734641 (2020). The utilization of dominance and epistasis can potentially increase the power of genomic selection in cross-bred populations including family line crosses. Skaarud etal. By developing and selecting the correct architecture, ANNs can distinguish parameters of effect from inputs of noisy digital image data to outputs of the key signals of effect, to be used in regression, classification, clustering, reducing dimensionality, or detecting anomalies (Bishop, 2006; Schmidhuber, 2015). Sci. Ecol. Transgene delivery. 42, 103114. Yoshizaki, G. & Yazawa, R. Application of surrogate broodstock technology in aquaculture. Genome-scale CRISPR-Cas9 knockout screening in human cells. Finally, genomic selection can help track signatures of artificial selection and genetic diversity in the process of domestication of farmed species (Lpez etal., 2014; Yez etal., 2015). (2007). Uren Webster, T. M., Consuegra, S., Hitchings, M. & Garcia de Leaniz, C. Interpopulation variation in the Atlantic salmon microbiome reflects environmental and genetic diversity. Norris, A. Ann. First, the predicted genetic response and realized inbreeding are far superior over the management of multiple single-family lines. doi: 10.1111/j.1439-0388.2010.00912.x, Andonov, S., Lourenco, D., Fragomeni, B., Masuda, Y., Pocrnic, I., Tsuruta, S., et al. A., Moghadam, H. K., Danzmann, R. G., and Ferguson, M. M. (2011). J. Anim. Biotechnol. doi: 10.2527/af.2011-0027. Assoc. J. Furthermore, in commercial breeding designs, some females produce most of the commercial progeny, and this puts an emphasis on investigating the importance and prediction of maternal effects through genomic selection, especially in aquatic systems where the number of breeders is low. Genet. Linkage variation at the sex-determining locus within Fraser strain Arctic charr Salvelinus alpinus. Evol. doi: 10.2527/jas.2007-0010, Sonesson, A. K. (2005). Second, the enormous costs in establishing and maintaining single-family mating, spawning, and rearing facilities are not required under a genomic selection program using a large-scale multi-family breeding program. 89, 17311741. Sel. Li, M. et al. Within our own current selective breeding research programs, genomic selection has been evaluated for direct integration into shrimp breeding programs for multiple production traits (e.g., size, disease resistance, color, and survival; Khatkar etal., 2017), as well as pearl oyster breeding programs for both host oyster and donor oyster traits (e.g., shell size and pearl quality traits; Jones etal., 2017a). Genet. Trends Ecol. Genomic selection models double the accuracy of predicted breeding values for bacterial cold water disease resistance compared to a traditional pedigree-based model in rainbow trout aquaculture. 47, 2135 (2016). The FAASG white paper, which followed on from the FAANG equivalent (reference 88), describes an initiative to improve annotation of all salmonid genomes, and similar initiatives are likely to follow for other major aquaculture species. In essence this affords us new and more cost-effective approaches to produce, maintain, and distribute genetic improvement across the breadth of cultured aquatic species .
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