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      Advances in genetic improvement for salmon and trout aquaculture: the Chilean situation and prospects

      1 , 1 , 2 , 3 , 4 , 5

      Reviews in Aquaculture

      Wiley

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          Genome editing. The new frontier of genome engineering with CRISPR-Cas9.

          The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics. Copyright © 2014, American Association for the Advancement of Science.
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            Mapping genes for complex traits in domestic animals and their use in breeding programmes.

            Genome-wide panels of SNPs have recently been used in domestic animal species to map and identify genes for many traits and to select genetically desirable livestock. This has led to the discovery of the causal genes and mutations for several single-gene traits but not for complex traits. However, the genetic merit of animals can still be estimated by genomic selection, which uses genome-wide SNP panels as markers and statistical methods that capture the effects of large numbers of SNPs simultaneously. This approach is expected to double the rate of genetic improvement per year in many livestock systems.
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              The Atlantic salmon genome provides insights into rediploidization.

              The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.
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                Author and article information

                Journal
                Reviews in Aquaculture
                Rev Aquacult
                Wiley
                1753-5123
                1753-5131
                March 18 2019
                May 2019
                April 25 2019
                May 2019
                : 11
                : 2
                : 340-353
                Affiliations
                [1 ]Benchmark Genetics Chile Puerto Montt Chile
                [2 ]Programa de Doctorado en Ciencias en Bioeconomía Pesquera y Acuícola Centro Interdisciplinario de Ciencias Marinas del Instituto Politécnico Nacional La Paz México
                [3 ]Facultad de Ciencias Agronómicas Universidad de Chile Santiago Chile
                [4 ]Facultad de Ciencias Veterinarias y Pecuarias Universidad de Chile Santiago Chile
                [5 ]Núcleo Milenio INVASAL Concepción Chile
                Article
                10.1111/raq.12335
                © 2019

                http://creativecommons.org/licenses/by/4.0/

                http://doi.wiley.com/10.1002/tdm_license_1.1

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