A refinement to gene editing in Atlantic salmon using asymmetrical oligonucleotide donors

Ah, Straume; Kjærner-Semb, Erik; Ko, Skaftnesmo; Güralp, Hilal; Lillico, Simon; Wargelius, Anna; Edvardsen, Rolf B.

doi:10.1101/2021.02.08.430296

Cited by 11 publications

(14 citation statements)

References 33 publications

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“…focus for fine-mapping with genome editing technology, whereby effects of the two missense mutations and the top-associated SNPs from previous association studies could be delineated.Single base editing of the known missense mutations and topassociated SNPs could introduce novel genotype combinations and help to more finely map and/or validate causal mutations at the vgll3 locus. Some success with single base editing in Atlantic salmon has been accomplished, whereby 30%-60% efficiency was achieved(Straume et al, 2021), suggesting editing of vgll3 SNPs may be feasible. Alternatively, identifying individuals carrying natural recombinant alleles at the vgll3 locus may be possible, but this may require genotyping and scanning a large number individuals from many source populations, followed by rearing of males and females to maturation age.As genome assembly and genomic data production for species in the wild becomes easier, the number of candidate loci linked to association and/selection signals is likely to rise.…”

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confidence: 99%

Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large‐effect locus

et al. 2021

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Efforts to understand the genetic underpinnings of phenotypic variation are becoming more and more frequent in molecular ecology. Such efforts often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing, an ecologically important trait, occurs in a genomic region including two genes, vgll3 and akap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, thus enabling delineation of the influence of variation at these two genes on early maturation.By rearing 5,895 males to maturation age, of which 81% had recombinant vgll3/akap11 allelic combinations, we found that vgll3 single nucleotide polymorphism (SNP) variation was strongly associated with early maturation, whereas there was little or no association between akap11 SNP variation and early maturation. These findings provide strong evidence supporting vgll3 as the primary candidate gene in the chromosome 25 locus for influencing early maturation. This will help guide future research for understanding the genetic processes controlling early maturation. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying ecologically important phenotypic diversity.

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confidence: 99%

Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large‐effect locus

et al. 2021

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“…Single base editing of the known missense mutation and top-associated SNPs could introduce novel genotype combinations and help to more finely map and/or validate causal mutations at the vgll3 locus. Some success with single base editing in Atlantic salmon has been accomplished, whereby 30% to 60% efficiency was achieved (Straume et al 2021), suggesting editing of vgll3 SNPs may be feasible. Alternatively, identifying individuals carrying natural recombinant alleles at the vgll3 locus may be possible, however this may require genotyping and scanning a large number individuals from many source populations, followed by rearing of males and females to maturation age.…”

Section: Discussionmentioning

confidence: 99%

Refining the genomic location of SNP variation affecting Atlantic salmon maturation timing at a key large-effect locus

Sinclair-Waters

Piavchenko

Ruokolainen

et al. 2021

Preprint

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Efforts to understand the genetic underpinnings of phenotypic variation often lead to the identification of candidate regions showing signals of association and/or selection. These regions may contain multiple genes and therefore validation of which genes are actually responsible for the signal is required. In Atlantic salmon (Salmo salar), a large-effect locus for maturation timing occurs in a genomic region including two candidate genes, vgll3 and akap11, but data for clearly determining which of the genes (or both) contribute to the association have been lacking. Here, we take advantage of natural recombination events detected between the two candidate genes in a salmon broodstock to reduce linkage disequilibrium at the locus, and thus enabling delineation of the influence of variation at these two genes on maturation timing. By rearing 5895 males to maturation age, of which 81% had recombinant vgll3/akap11 allelic combinations, we found that vgll3 SNP variation was strongly associated with maturation timing, whereas there was little or no association between akap11 SNP variation and maturation timing. These findings provide strong evidence supporting vgll3 as the primary candidate gene in the chromosome 25 locus for influencing maturation timing. This will help guide future research for understanding the genetic processes controlling maturation timing. This also exemplifies the utility of natural recombinants to more precisely map causal variation underlying phenotypic diversity.

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“…The most targeted traits for GE in fish aquaculture are reproduction and development (eg. Jin et al 2020;Straume et al 2021), growth (eg. Sun et al 2020), pigmentation (eg.…”

Section: Introductionmentioning

confidence: 99%

“…In several studies CRISPR/Cas9 have been used to edit different genes in Atlantic salmon (Datsomor et al 2019a, b;Edvardsen et al 2014;Güralp et al 2020;Straume et al 2020Straume et al , 2021Wargelius et al 2016) aimed at mitigating some of the problems of salmon aquaculture. For example, CRISPR/Cas9 has been used to develop a sterile salmon through knockout of the dead end (dnd) gene; the aim being to prevent hybridization and potential gene introgression of escapee farmed salmon into wild populations (Güralp et al 2020;Wargelius et al 2016).…”

Section: Introductionmentioning

confidence: 99%

“…In addition, editing of non-coding sequences to induce deletion of large fragments of microRNA and 3untranslated regions (3UTRs) has been conducted in tilapia ); this is one out of few studies using finfish species to attempt homology directed repair (HDR). Others are in Atlantic salmon targeting pigmentation (Straume et al 2020) and sterility (Straume et al 2021); and in farmed carp (Labeo rohita) (Chakrapani et al 2016) and channel catfish (Ictalurus punctatus) (Elaswad et al 2018a, b) targeting disease resistance and insertion of transgenes (Simora et al 2020).…”

Section: Introductionmentioning

confidence: 99%

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Sustainable use of CRISPR/Cas in fish aquaculture: the biosafety perspective

et al. 2021

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Aquaculture is becoming the primary source of seafood for human diets, and farmed fish aquaculture is one of its fastest growing sectors. The industry currently faces several challenges including infectious and parasitic diseases, reduced viability, fertility reduction, slow growth, escapee fish and environmental pollution. The commercialization of the growth-enhanced AquAdvantage salmon and the CRISPR/Cas9-developed tilapia (Oreochromis niloticus) proffers genetic engineering and genome editing tools, e.g. CRISPR/Cas, as potential solutions to these challenges. Future traits being developed in different fish species include disease resistance, sterility, and enhanced growth. Despite these notable advances, off-target effect and non-clarification of trait-related genes among other technical challenges hinder full realization of CRISPR/Cas potentials in fish breeding. In addition, current regulatory and risk assessment frameworks are not fit-for purpose regarding the challenges of CRISPR/Cas notwithstanding that public and regulatory acceptance are key to commercialization of products of the new technology. In this study, we discuss how CRISPR/Cas can be used to overcome some of these limitations focusing on diseases and environmental release in farmed fish aquaculture. We further present technical limitations, regulatory and risk assessment challenges of the use of CRISPR/Cas, and proffer research strategies that will provide much-needed data for regulatory decisions, risk assessments, increased public awareness and sustainable applications of CRISPR/Cas in fish aquaculture with emphasis on Atlantic salmon (Salmo salar) breeding.

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A refinement to gene editing in Atlantic salmon using asymmetrical oligonucleotide donors

Cited by 11 publications

References 33 publications

Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large‐effect locus

Refining the genomic location of single nucleotide polymorphism variation affecting Atlantic salmon maturation timing at a key large‐effect locus

Refining the genomic location of SNP variation affecting Atlantic salmon maturation timing at a key large-effect locus

Sustainable use of CRISPR/Cas in fish aquaculture: the biosafety perspective

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