Genetic improvement technologies to support the sustainable growth of UK aquaculture

Regan, Tim; Bean, Tim P.; Ellis, Tim; Davie, Andrew; Carboni, Stefano; Migaud, Hervé; Houston, Ross D.

doi:10.1111/raq.12553

Cited by 34 publications

(25 citation statements)

References 199 publications

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“…The availability of this reference genome will not only increase interest in Mytilidae as a model for ecological and evolutionary research, but will be also a valuable tool for breeding programmes [ 21 ]. The discovery of multiple duplication events will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies.…”

Section: Introductionmentioning

confidence: 99%

Evidence of multiple genome duplication events in Mytilus evolution

et al. 2022

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Background Molluscs remain one significantly under-represented taxa amongst available genomic resources, despite being the second-largest animal phylum and the recent advances in genomes sequencing technologies and genome assembly techniques. With the present work, we want to contribute to the growing efforts by filling this gap, presenting a new high-quality reference genome for Mytilus edulis and investigating the evolutionary history within the Mytilidae family, in relation to other species in the class Bivalvia. Results Here we present, for the first time, the discovery of multiple whole genome duplication events in the Mytilidae family and, more generally, in the class Bivalvia. In addition, the calculation of evolution rates for three species of the Mytilinae subfamily sheds new light onto the taxa evolution and highlights key orthologs of interest for the study of Mytilus species divergences. Conclusions The reference genome presented here will enable the correct identification of molecular markers for evolutionary, population genetics, and conservation studies. Mytilidae have the capability to become a model shellfish for climate change adaptation using genome-enabled systems biology and multi-disciplinary studies of interactions between abiotic stressors, pathogen attacks, and aquaculture practises.

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Section: Introductionmentioning

confidence: 99%

Evidence of multiple genome duplication events in Mytilus evolution

et al. 2022

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“…Recently, there have been advances in the development and application of genomic selection for genetic improvement in aquaculture species (Boudry et al, 2021 ; Houston et al, 2020 ; Lhorente et al, 2019 ; Norris, 2017 ; Regan et al, 2021 ; Symonds et al, 2019 ; Zenger et al, 2019 ), including Atlantic salmon ( Salmo salar ) (Lhorente et al, 2019 ; Regan et al, 2021 ). The use of genomic selection in aquaculture breeding programs has the potential to drive high rates of genetic gain, while also controlling inbreeding and diversity, due to the high fecundity of species and potentially low effective population sizes within breeding programs.…”

Section: Introductionmentioning

confidence: 99%

Commercial implementation of genomic selection in Tasmanian Atlantic salmon: Scheme evolution and validation

Verbyla

Kube

Evans

2021

Evolutionary Applications

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Genomic information was included for the first time in the prediction of breeding values for Atlantic salmon within the Australian Salmon Enterprises of Tasmania Pty Ltd selective breeding program in 2016. The process to realize genomic selection in the breeding program begun in 2014 with the scheme finalized and fully implemented for the first time in 2018. The high potential of within family selection to accelerate genetic gain, something not possible using the traditional pedigree‐based approach, provided the impetus for implementation. Efficient and effective genotyping platforms are essential for genomic selection. Genotype data from high density arrays revealed extensive persistence of linkage disequilibrium in the Tasmania Atlantic salmon population, resulting in high accuracies of both imputation and genomic breeding values when using imputed data. Consequently, a low‐density novel genotype‐by‐sequence assay was designed and incorporated into the scheme. Through the use of a static high‐ and dynamic low‐density genotyping platforms, an optimized genotyping scheme was devised and implemented such that all individuals in every year class are genotyped efficiently while maximizing the genetic gains and minimizing costs. The increase in the rates of genetic gain attributed to the implementation of genomic selection is significant across both the breeding programs primary and secondary traits. Substantial improvement in the ability to select parents prior to progeny testing is observed across multiple years. The resultant economic impacts for the industry are considerable based on the increases in genetic gain for traits achieved within the breeding program and the use of genomic selection for commercial production.

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“…In the review article focussing on the UK aquaculture, Regan et al (2021) summarized the success via selective breeding in obtaining Atlantic salmon with some important economic traits, including fast growth, delayed sexual maturity, and disease resistance against infectious pancreatic necrosis virus (IPNV). It was also introduced in this review paper that a series of economically important traits, such as growth, year-round growth, survival, fillet colour, sexual maturation, nutritional requirement, feed conversion efficiency, environmental sensitivity and disease resistance have been the cores of research and developmental programmes in the United Kingdom.…”

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confidence: 99%