how would genetic engineering help aquaculture be more effective?

Res. Bishop, S. C. & Woolliams, J. Rev. Second, genomic selection programs become increasingly more complex when harvest yields are determined by diverse genomes, as is the case of pearl oyster, with a host recipient seeded with the saibo of a donor. Moen, T., Baranski, M., Sonesson, A. K. & Kjglum, S. Confirmation and fine-mapping of a major QTL for resistance to infectious pancreatic necrosis in Atlantic salmon (Salmo salar): population-level associations between markers and trait. Evol. However, subsequent analysis using higher number of loci (1,0005,000) in combination with greater population size (3060) increased the accuracy of selection and genetic gain over five generations (Sonesson and Meuwissen, 2009). Tsai, H. Y. et al. Expertomica Fishgui: comparison of fish skin colour. Genet. Endocrinol. 47, 55 (2015). Although still in development, sliding window algorithms and convolutional neural network (CNN) with rule association-based clustering yielded high accuracy (exceeding 96%) in object character recognition for the pearl oysters in nets within the full spectrum of commercial situations (Figure 3; Zenger etal., 2017). . Loss of stomach, loss of appetite? Genotype imputation to improve the cost-efficiency of genomic selection in farmed Atlantic salmon. Genetic improvement of production traits in aquaculture has great potential to help meet the rising seafood demands driven by human population growth. Rev. Sci. 5, 23832390. Osmond, Angelisa T.Y. 292, 231242. In contrast, many terrestrial animal protein . Within aquaculture breeding programs, the initial focus has been on growth, which is a moderately heritable trait and relatively easy to select. In practice, QTL mapping is a powerful approach, where large family groups are clearly defined even if marker density is low. 45:32. doi: 10.1186/1297-9686-45-32, Holtsmark, M., Klemetsdal, G., Sonesson, A. K., and Woolliams, J. Llewellyn, M. S., Boutin, S., Hoseinifar, S. H. & Derome, N. Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries. Apart from ensuring the highest quality sequence reads (i.e., QScore30), a commonly used method to discard possible sequencing errors in GBS data sets consists in the elimination of very low minor allele frequency SNPs (i.e., 1/50 allele ratio), particularly when not observed among multiple individuals or populations (Roesti etal., 2012; Lal etal., 2016). Article Harbitz, A. Donor and recipient contribution to phenotypic traits and the expression of biomineralisation genes in the pearl oyster model Pinctada margaritifera. (2014). Ahmed, N., Thompson, S. & Glaser, M. Global aquaculture productivity, environmental sustainability, and climate change adaptability. This is also the case with emerging breeding programs in aquaculture in particular those that do not have a strong historical background in structured genetic improvement programs. doi: 10.1534/g3.117.040717, Uleberg, E., and Meuwissen, T. H. E. (2011). Front. Sci. Within-family marker-assisted selection for aquaculture species. Aquacult. Ann. doi: 10.1111/faf.12020, Zeng, Q., Fu, Q., Li, Y., Waldbieser, G., Bosworth, B., Liu, S., et al. Yoshida, G. M. et al. 3, 175192 (2015). Anderson, J. L., Asche, F., Garlock, T. & Chu, J. Aquaculture: its role in the future of food. Front. 51, 42 (2019). These gene effects are typically detected through QTL linkage mapping and association studies. volume21,pages 389409 (2020)Cite this article. One successful MAS disease resistance case study has been reported on infectious pancreatic necrosis (IPN) resistance in Atlantic salmon, where major QTL explain more than 29% of the observed variance (Moen etal., 2009; Houston etal., 2010). Dev. Agric. 42, 103114. The impact of genetic relationship information on genome-assisted breeding values. The chance factor in the process of distributing half the genetic material from each parent to the offspring, which is the source of within-family genetic variation. B., et al. The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. It is approximate to the number of individuals that contribute gametes to the next generation. Genet. A second case study is on the Lymphocytis disease in the Japanese flounder Paralichthys olivaceus, whereby one QTL, inherited in a dominant Mendelian fashion, accounted for over 50% of the total phenotypic variance associated with survival to the Lymphocytis disease (Fuji etal., 2006; Sakamoto etal., 2006; Ozaki etal., 2012). Establishing a base population for a breeding program in aquaculture, from multiple subpopulations, differentiated by genetic drift: I. Accuracy of genotype imputation and genomic predictions in a two-generation farmed Atlantic salmon population using high-density and low-density SNP panels. https://edin.ac/3bFHXs0. Initial theoretical investigations of genomic selection in aquatic species suggest that a higher accuracy of selection and subsequently higher rates of genetic gain (up to 10% for body weight) can be achieved compared to traditional selection (Campos-Montes etal., 2013; degrd etal., 2014b; Castillo-Jurez etal., 2015). Georges, M., Charlier, C. & Hayes, B. Agric. Genet. J. Virol. More importantly, these technologies are advancing toward being fully non-invasive and automated, whereby animals need not be removed from their environment or sacrificed to obtain accurate phenotypic measurements. Based on the continued interest in this area, it is highly likely that approaches to fully utilize GBS data (particularly in aquaculture species) will continue to be developed, or at least until high-density solid-state SNP genotyping arrays become more accessible and cost-effective. Hwang, B., Lee, J. H. & Bang, D. Single-cell RNA sequencing technologies and bioinformatics pipelines. GSE 48:77. doi: 10.1186/s12711-016-0255-4, Taylor, J. F. (2014). Genetics 158, 12031215 (2001). Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. (2010). Heggberget, T. G. et al. Fortunately, genomic selection platforms allow for field data to be linked to nucleus broodstock through DNA derived genomic relationships and on-farm phenotyping. When applying these outcomes to genomic selection implementation on farm, the data suggest that total genotyping effort and hence cost can be greatly reduced by using a staged selection approach while capturing most if not all the benefits of genomic selection. Mapping the sex determination locus in the Atlantic halibut (Hippoglossus hippoglossus) using RAD sequencing. Nature 533, 200205 (2016). (2014). Front. 110, 720726 (2019). 15, 181195 (2014). Genet. Aquaculture 434, 476485. Biol. doi: 10.1007/s10709-008-9308-0, Goddard, M. E., Hayes, B. J., and Meuwissen, T. H. E. (2011). Genet. 88, 125132. Correspondence to It was further shown that increasing the number of families from 50 to 400 and applying the optimum contribution selection increased total genetic gain, while using 400 full-sib families kept the selection intensity at approximately 0.6 (Skaarud etal., 2014). Accuracy of genomic within-family selection in aquaculture breeding programmes. Rev. The prediction equations are then validated on independent test animals (i.e., related generations to reference population). doi: 10.1002/ece3.2466, Viazzi, S., Van Hoestenberghe, S., Goddeeris, B., and Berckmans, D. (2015). 3, 13781379 (2019). Accuracy of multi-trait genomic selection using different methods. 35, 672684 (2019). doi: 10.1371/journal.pone.0110377, Bilton, T. P., Schofield, M. R., Black, M. A., Chagn, D., Wilcox, P. L., and Dodds, K. G. (2018). Furthermore, genomic selection can reduce rates of inbreeding by up to 81% when compared with traditional selection programs (Vandeputte and Haffray, 2014). 22, 121124. Vallejo, R. L. et al. The development of advanced image analysis software including artificial neural network (ANN) algorithms based on machine learning approaches has been an important step forward in the development of analysis systems for automated MVS phenotyping (e.g., Grys etal., 2017). Dairy Sci. Gratacap, R. L. et al. Jonsson, B. Google Scholar. doi: 10.1016/j.margen.2015.10.010, Lallias, D., Gomez-Raya, L., Haley, C. S., Arzul, I., Heurtebise, S., Beaumont, A. R., et al. Therefore, optimizing the contribution of families can significantly improve the efficiency of the breeding program. PubMed Evol. Garcia, A. L. S. et al. (2011) compared breeding designs with 8 to 200 progeny per family and showed genetic gain increased sharply by increasing family size to 50 with diminishing returns with further increases in family size, especially beyond 100. Diamond, J. Evolution, consequences and future of plant and animal domestication. Robledo, D., Palaiokostas, C., Bargelloni, L., Martnez, P. & Houston, R. Applications of genotyping by sequencing in aquaculture breeding and genetics. (IntechOpen, 2019). Optimum contribution selection using traditional best linear unbiased prediction and genomic breeding values in aquaculture breeding schemes. Genetic engineering in aquaculture. - CAB Direct A relationship matrix including full pedigree and genomic information. 17:81. doi: 10.1038/nrg.2015.28, Ashby, R., Hess, A., Baird, H., Roberts, R., King, N., Symonds, J., et al. Front. 12, 10011016 (2019). Genome wide association and genomic prediction for growth traits in juvenile farmed Atlantic salmon using a high density SNP array. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. Univ. Evol. B 10, 589594. Daetwyler, H. D., Calus, M. P. L., Pong-Wong, R., de los Campos, G. & Hickey, J. M. Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking. 47, 2135 (2016). Genetic manipulations involving gyn ogenesis, androgenesis, triploidy, and sex reversal are already established . Agriculture can help aquaculture become greener | Nature Food & Goddard, M. E. Prediction of total genetic value using genome-wide dense marker maps. Gen. Genom. (2018). Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing. Breed. Sel. Single-nucleotide polymorphisms (SNPs) have become the marker of choice in genetics research due to their high abundance, co-dominant inheritance, relative ease of high-throughput discovery, and low cost of genotyping per locus. (2017). Genet. The inbreeding coefficient in all scenarios increased over 20 generations using both pedigree and genomic information, but genomic selection was more efficient at reducing inbreeding and increasing genetic gain compared to pedigree-based selection. A similar approach has also been applied in a novel genetic linkage mapping method, whereby improved confidence in placement of loci was obtained by incorporating GBS read depth information, improved filtering capability, and using a statistical approach to model and correct errors (Bilton etal., 2018). G3 9, 15971611 (2019). Ecol. GSE 43, 2020. Sci. A perspective of the future value and challenges of genetic engineering Genome-wide SNP validation and mantle tissue transcriptome analysis in the silver-lipped pearl oyster, Pinctada maxima. Front. Genet. Biol. PLoS One 6:e19379. 17, 159173 (2017). Wang, Q. et al. Bioeconomic modelling in aquaculture: an overview of the literature. It is unlikely that simply screening commercial stocks will yield data of sufficient quality to obtain genomic breeding values for disease resistance, since most disease field challenges are uncontrolled, and often resistance to multiple pathogens is of interest. (2017). Genet. Introduction of genetic engineering in aquaculture: Ecological and doi: 10.1186/1471-2164-15-90, Ibarra, A. M., and Famula, T. R. (2008). BMC Bioinf. 47:12. doi: 10.1186/s12711-015-0102-z, Grys, B., Lo, D., Sahin, N., Kraus, O., Morris, Q., Boone, C., et al. ZooKeys (695), 135152. (2017) reported high accuracy (0.890.97) of imputing genotypes from a low-density panel (0.55K) to a high-density panel (78K) using a multi-generation reference population in farmed Tasmanian Atlantic salmon. (2018). Genomic selection requires genomic control of inbreeding. Article (2015). The success of the practical implementation of genomic selection in aquaculture is through well-designed breeding programs negating genotype by environment interactions (Ibarra and Famula, 2008; Rauw and Gomez-Raya, 2015) and common environmental and inbreeding effects (Bentsen and Olesen, 2002; Havenstein etal., 2003; Hely etal., 2013). Appl. Evol. A phasing and imputation method for pedigreed populations that results in a single-stage genomic evaluation. No studies have considered these aspects in the application of genomic selection. G3: Genes, Genomes, Genet. Segregation of infectious pancreatic necrosis resistance QTL in the early life cycle of Atlantic Salmon (Salmo salar). Sun, D.-W. San Diego: Academic Press, 343. (2016). doi: 10.1186/1297-9686-45-39, Liu, D., Zeng, X.-A., and Sun, D.-W. (2013). Rep. 6:19244. doi: 10.1038/srep19244, Druet, T., Schrooten, C., and De Roos, A. Evol. Anim. 91, 44144423. Microbiome of Pacific Whiteleg shrimp reveals differential bacterial community composition between wild, aquacultured and AHPND/EMS outbreak conditions. doi: 10.1186/1297-9686-40-5-541, Ilut, D. C., Nydam, M. L., and Hare, M. P. (2014). Moreover, if all the contributing broodstocks are genotyped with the high-density panel, the accuracy of imputation in the progeny, genotyped with even smaller SNP panel, could be quite high using a pedigree-based imputation approach (Hickey etal., 2012). (2017). Palaiokostas, C. et al. These general principles equally apply to selective breeding programs incorporating genomic selection. In the long term, incorporation of accurate and low-cost industrial-scale genotyping and on-farm phenotyping technologies will become the pipeline to generate data-rich resources matching genotype, by the way of full genome sequence, to extensive trait panels on many hundreds of thousands of animals phenotyped. Construction and annotation of a high density SNP linkage map of the Atlantic salmon (Salmo salar) genome. Mar. Figshare https://doi.org/10.6084/m9.figshare.7301546.v1 (2018). (2014). This is primarily a result of the molecular technique itself, which can introduce spurious and missing data without rigorous QC and data filtering methods. Zenger, K. R. et al. Sci. 32, 665680 (2017). Automatic scaling of fish images. BMC Genom. et al. Cell Biol. A. Kumar, S., Stecher, G., Suleski, M. & Hedges, S. B. TimeTree: a resource for timelines, timetrees, and divergence times. Genetics 193, 347365 (2013). Eng. BMC Genomics 14, 566 (2013). Aquaculture 453, 6772. doi: 10.1007/s00343-017-6038-0, Witte, J. S. (2010). Evol. 63, 159172 (2019). Evol. doi: 10.1016/j.aquaculture.2010.11.023, Skaarud, A., Woolliams, J. Both finfish and shellfish are very suitable types of animals to use in terms of the introduction of novel genes into their genomes (transgenic induction). Lien, S., Gidskehaug, L., Moen, T., Hayes, B., Berg, P., Davidson, W., et al. Yoshida, G. M., Carvalheiro, R., Rodrguez, F. H., Lhorente, J. P., and Yez, J. M. (2018). Genome-Wide Association and genomic selection for resistance to Amoebic Gill Disease in Atlantic Salmon. Bentsen, H. B. et al. Derome, N. Microbial Communities in Aquaculture Ecosystems: Improving Productivity and Sustainability (Springer, 2019). Efficient computation of the genomic relationship matrix and other matrices used in single-step evaluation. Introduction A meta-analysis. Genet. (2006). (2006). Harnessing the power of RADseq for ecological and evolutionary genomics. 48, 47 (2016). As a result, these QTL studies searching for specific loci may be of limited commercial value in the era of genomic selection. Fish. Polyploid fish and shellfish: production, biology and applications to aquaculture for performance improvement and genetic containment. However, in reality, this almost certainly will not be the case (particularly with disease), and the impact of G E interactions could be substantial. Mar. Evolution 55, 10951103 (2001). These techniques are able to quantify and evaluate the chemical (e.g., fat, protein, and moisture) and physical (e.g., freshness, texture, and color) attributes of aquatic animals with relatively high accuracies of prediction (r>0.8; see Liu etal., 2013; Saberioon etal., 2017). Vallejo, R. L. et al. Wang, Q., Yu, Y., Li, F., Zhang, X. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Sex. Utilizing simulation studies, the effect of altering the number of generations within aquaculture selective breeding programs has yet to be studied separately. Accuracy of predicting the genetic risk of disease using a genome-wide approach. 11:e1005628. Rev. Nguyen, N. H., Premachandra, H. K. A., Kilian, A. Feron, R. et al. Keywords Aquaculture 505, 190198 (2019). 12:94. doi: 10.1186/1471-2148-12-94, Saberioon, M., Gholizadeh, A., Cisar, P., Pautsina, A., and Urban, J. In contrast, since association testing exploits linkage disequilibrium, it is more suitable for large outbred populations with small family sizes and requires high marker density (Witte, 2010). Evaluation of genome-enabled selection for bacterial cold water disease resistance using progeny performance data in rainbow trout: insights on genotyping methods and genomic prediction models. Typically, such traits are based on yields of harvested product. Rep. 7:40347. doi: 10.1038/srep40347, Zenger, K. R., Khatkar, M. S., Jerry, D. R., and Raadsma, H. W. (2017). Biotechnol. (2014). doi: 10.1111/j.1365-2109.2010.02669.x. Aquaculture 358359, 6170. For aquaculture species that have been improved, such as Atlantic salmon (Salmo salar), Nile tilapia (Oreochromis niloticus), and the Pacific white shrimp (Litopenaeus vannamei), selection for growth has dramatically increased efficiencies helping establish these species as global commodities. (2014). A., and Meuwissen, T. H. E. (2012b). Any error in the trait recording will reduce effective estimated heritability and hence realized genetic gain. Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities. Natl Acad. Marker-assisted breeding of a lymphocystis disease-resistant Japanese flounder (Paralichthys olivaceus). Implementation and accuracy of genomic selection. Res. Aquac. Genet. 10, 368368. Biol. The genetic architecture of growth and fillet traits in farmed Atlantic salmon (Salmo salar). So much for transgenicswhat about cloning? Handisyde, N., Telfer, T. C. & Ross, L. G. Vulnerability of aquaculture-related livelihoods to changing climate at the global scale. Genet. 128, 409421. Development and validation of a high density SNP genotyping array for Atlantic salmon (Salmo salar). doi: 10.1093/jhered/esy015, Brouard, J.-S., Boyle, B., Ibeagha-Awemu, E. M., and Bissonnette, N. (2017). This study is the first to apply CRISPR genome editing to an aquaculture species, and highlights the possibility of creating double-allele-knockout individuals in the F0 generation. Additionally, the estimation of breeding values (EBVs) for breeding candidates themselves often cannot be estimated for these traits based on individual phenotypes, but rather they are estimated based on phenotypic records and EBV of their siblings (termed sib selection). Application of machine vision systems in aquaculture with emphasis on fish: state-of-the-art and key issues. J. Hered. doi: 10.1016/j.aquaculture.2012.06.017, Gutierrez, A., Lubieniecki, K., Fukui, S., Withler, R., Swift, B., and Davidson, W. (2014b). (2011). Genetics 202, 877881 (2016). (2012). These data are used to estimate genetic marker effects, which are then applied to predict breeding values for genotyped selection candidates. Environmental stress and disease in pearl oysters, focusing on the Akoya pearl oyster (Pinctada fucata Gould 1850). 63, 6271. Nevertheless, the levels of accuracies observed in these initial investigations demonstrate potentially for applying genomic selection in breeding schemes in aquaculture species. doi: 10.1186/1471-2164-10-368, Moen, T., Sonesson, A. K., Hayes, B., Lien, S., Munck, H., and Meuwissen, T. H. (2007). 21, 806812 (2019). Evol. Widespread use of antibiotics in aquaculture has led to the development of antibiotic-resistant bacteria and the accumulation of antibiotics in the environment, resulting in water and soil pollution. Tsairidou, S., Hamilton, A., Robledo, D., Bron, J. E. & Houston, R. D. Optimizing low-cost genotyping and imputation strategies for genomic selection in Atlantic salmon. Comparison of Minolta colorimeter and machine vision system in measuring colour of irradiated Atlantic salmon. Abstract. One major QTL for sexual maturation in the Atlantic salmon was found independently by two studies (Ayllon etal., 2015; Barson etal., 2015). A., and Gjen, H. M. (2011). Aquaculture 258, 241249. Front. Eng. Half a century of genetic interaction between farmed and wild Atlantic salmon: status of knowledge and unanswered questions. PubMed The importance of production focused outputs, versus key determinants that affect production efficiency, particularly disease outbreaks and production inputs (largely feed and labor requirements), will remain a technological challenge in defining appropriate multi-trait breeding objectives and selection programs for both shrimp and oyster. Yoshida, G. M. et al. Long-term effects of stock transfers: synergistic introgression of allochthonous genomes in salmonids. It provides a large part of high-quality protein food for humans, and thus, a sustainable aquaculture industry is of great importance for the worldwide food supply and economy. Genomewide single nucleotide polymorphism discovery in Atlantic salmon (Salmo salar): validation in wild and farmed American and European populations. doi: 10.1534/g3.115.019570, Hely, F. S., Amer, P. R., Walker, S. P., and Symonds, J. E. (2013). Biotechnol. doi: 10.1186/1297-9686-44-27, Sture, ., ye, E. R., Skavhaug, A., and Mathiassen, J. R. (2016). This may allow QTL to be mapped down to quantitative trait nucleotide (QTN) polymorphisms as the causative determinants for such complex traits. Aquaculture 311, 110114. The reduced biological fitness in a given population as a result of inbreeding, typically due to deleterious recessive alleles. Science 339, 823826 (2013). doi: 10.1083/jcb.201610026, Guo, X., Li, Q., Wang, Q., and Kong, L. (2012). Choosing the right optimized mating strategy is one of the key components in any breeding design that could affect the rates of inbreeding and long-term genetic gain (Nirea etal., 2012a; Sonesson and degrd, 2016). 5, 340 (2014). Res. Drugs 15:213. doi: 10.3390/md15070213, Yue, G. H. (2014). Within silver lipped pearl oyster Pinctada maxima breeding programs, host oyster shell size, donor oyster pearl quality traits (i.e., size, weight, color, luster, and complexion), and disease resistance have all been identified as important phenotypes for selection based on their economic value and genetic basis (Kuchel etal., 2011; Jerry etal., 2012; Jones etal., 2014a,b). (2017). A dense SNP-based linkage map for Atlantic salmon (Salmo salar) reveals extended chromosome homeologies and striking differences in sex-specific recombination patterns. 16, 57 (2015). 49, 17 (2017). Sveier, H. & Breck, O. in Cleaner Fish Biology and Aquaculture Applications (5m Publishing, 2018). PDF Genetically Modified Organisms and Aquaculture 11, 570584. BMC Genomics 19, 981 (2018). The susceptibility of Atlantic salmon fry to freshwater infectious pancreatic necrosis is largely explained by a major QTL. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes of biological and economic importance. doi: 10.1111/mec.12870, Li, H., Liu, X., and Zhang, G. (2012). Genet. Badiola, M., Basurko, O. C., Piedrahita, R., Hundley, P. & Mendiola, D. Energy use in recirculating aquaculture systems (RAS): a review. 33, cobi.13295 (2019). BMC Genom. A consensus microsatellite-based linkage map for the hermaphroditic bay scallop (Argopecten irradians) and its application in size-related QTL analysis. Genet. J. Anim. The selection of breeding individuals for genetic improvement of a trait of interest based on the use of genome-wide genetic markers to estimate genomic breeding values. ISSN 1471-0056 (print). Predictive ability of genomic selection models for breeding value estimation on growth traits of Pacific white shrimp Litopenaeus vannamei. Lillehammer, M., Meuwissen, T. H. E., and Sonesson, A. K. (2013). Sci. doi: 10.1016/j.livsci.2017.05.014, Nguyen, N. H., Rastas, P. M. A., Premachandra, H. K. A., and Knibb, W. (2018). 8, 369393 (2016). Predicting growth traits with genomic selection methods in Zhikong scallop (Chlamys farreri). Sel. This review provides insight into (1) the current status of fish vaccine and vaccination in aquaculture, (2) plant biotechnology and edible crops for fish vaccines for oral administration, (3). 16, 51 (2015). Breeding for disease resistance of Penaeid shrimps. Evol. Thus, vaccination is the most effective and environmentally-friendly approach to combat diseases in aquaculture to manage fish health. Bioinformatics 30, 18441849. 28 November 2022, Scientific Reports GWAS analysis of QTL for enteric septicemia of catfish and their involved genes suggest evolutionary conservation of a molecular mechanism of diseaseresistance. PLoS Biol. doi: 10.3168/jds.2009-2061, Lexer, C., West, R., Mangili, S., Heuertz, M., Stlting, K. N., Pearman, P. B., et al. However, despite the rapid growth in aquaculture production, only ~10% is currently based on genetically improved animals (Gjedrem etal., 2012). In our experience, the transition from existing/traditional selection programs into a genomic selection program is challenging since most mating and infrastructure designs in central nucleus breeding facilities do not capture the advantages offered by genomic selection programs. Accuracy of genomic selection for a sib-evaluated trait using identity-by-state and identity-by-descent relationships. In HSI, the spectral reflectance of each pixel is acquired for a range of wavelengths including visual and NIR spectra. Anim. BMC Genomics 19, 107 (2018). Sci. Google Scholar. Glover, K. A. et al. Genome sequences of marine shrimp Exopalaemon carinicauda Holthuis provide insights into genome size evolution of Caridea. Bras. Another method to reduce the cost of genotyping is through imputation of genotypes, where most of the animals can be genotyped with a low-cost, low-density SNP panel. Front. 99, 7374. Multiplex genome engineering using CRISPR/Cas systems. The future of genetic engineering to provide essential dietary Genetic improvement of farmed tilapias: growth performance in a complete diallel cross experiment with eight strains of Oreochromis niloticus. Natl Acad. A. Genomics and disease resistance studies in livestock. Increasing the size of the families from 4,000 to 8,000 has also shown to be ineffective in capturing extra genetic gain (Nielsen etal., 2011; Sonesson and degrd, 2016). 89, 630638. (2010). doi: 10.1007/s10126-008-9173-y, Legarra, A., Aguilar, I., and Misztal, I. Nat. The basic principles for implementing genomic selection (see Figure 1) involve a training population in which animals are phenotyped and genotyped, and SNP effects estimated using a range of statistical models (Taylor, 2014). You, W. & Hedgecock, D. Boom-and-bust production cycles in animal seafood aquaculture. BMC Genom. 49, 15 (2017). 5, 247 (2014). The selection of breeding individuals for genetic improvement of a trait of interest based on genetic markers linked to a quantitative trait locus affecting that trait. doi: 10.1111/j.1365-2109.1994.tb00668.x, Tiezzi, F., and Maltecca, C. (2015). Genetics 157, 18191829 (2001). This is a preview of subscription content, access via your institution. Neural Netw. (2017). Tsai, H.-Y. Khang, P. Van, Phuong, T. H., Dat, N. K., Knibb, W. & Nguyen, N. H. An 8-year breeding program for Asian seabass Lates calcarifer: genetic evaluation, experiences, and challenges. Sci. A., and Meuwissen, T. H. E. (2012). doi: 10.1038/hdy.2009.171, Houston, R. D., Taggart, J. Resour. Front. Morphological analysis of Trichomycterus areolatus Valenciennes, 1846 from southern Chilean rivers using a truss-based system (Siluriformes, Trichomycteridae). Genomics 111, 127132 (2019). doi: 10.1186/1297-9686-39-3-301, Sonesson, A. K., and Meuwissen, T. H. E. (2009). Has no genetic basis. doi: 10.1016/j.margen.2011.08.006. Sel. In the context of genomic selection, accuracy is the correlation between the estimated genomic breeding values and the true breeding values. A phylogenomic framework, evolutionary timeline and genomic resources for comparative studies of decapod crustaceans. Beyond that, even using the combination of 10,000 loci and different QTL sizes (100, 400, and 2,000) did not really increase the genetic gain by great margins after 15 generations (Liu etal., 2015).
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