Genomic prediction of host resistance to sea lice in farmed Atlantic salmon populations

Selective breeding is increasingly recognized as a key component of sustainable production of aquaculture species. The uptake of genomic technology in aquaculture breeding has traditionally lagged behind terrestrial farmed animals. However, the rapid development and application of sequencing technologies has allowed aquaculture to narrow the gap, leading to substantial genomic resources for all major aquaculture species. While high‐density single‐nucleotide polymorphism (SNP) arrays for some species have been developed recently, direct genotyping by sequencing (GBS) techniques have underpinned many of the advances in aquaculture genetics and breeding to date. In particular, restriction‐site associated DNA sequencing (RAD‐Seq) and subsequent variations have been extensively applied to generate population‐level SNP genotype data. These GBS techniques are not dependent on prior genomic information such as a reference genome assembly for the species of interest. As such, they have been widely utilized by researchers and companies focussing on nonmodel aquaculture species with relatively small research communities. Applications of RAD‐Seq techniques have included generation of genetic linkage maps, performing genome‐wide association studies, improvements of reference genome assemblies and, more recently, genomic selection for traits of interest to aquaculture like growth, sex determination or disease resistance. In this review, we briefly discuss the history of GBS, the nuances of the various GBS techniques, bioinformatics approaches and application of these techniques to various aquaculture species.

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“…; Tsai et al . , ; Vallejo et al . ) data, demonstrating the clear advantages over pedigree‐based methods.…”

Section: Applications Of Rad Sequencing In Aquaculturementioning

confidence: 99%

Applications of genotyping by sequencing in aquaculture breeding and genetics

Robledo

Palaiokostas

Bargelloni

et al. 2017

Reviews in Aquaculture

216

172

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“…In addition to inflicting substantial economic losses to farmed and wild fish, both species can be vectors for other pathogens. Resistance of Atlantic salmon to sea lice has been found as polygenic (Tsai et al, 2016a). A comparison of genomic selection methods was performed for C. rogercresseyi resistance based on genotyping with an SNP array .…”

Section: Domestication and Genomic Selectionmentioning

confidence: 99%

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Wenne

2017

Aquat. Living Resour.

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-An increase in aquatic animal production can be achieved by extending aquaculture areas geographically, utilizing new species for culture, and using new technologies. Among new technologies useful for the increase of aquaculture production is the application of genetics and genomics. New molecular tools that benefit aquaculture have been developed. There has been a large number of experimental and review papers published concerning molecular markers and the range of their applications, including aquaculture and food product analyses. Analysis of single nucleotide polymorphisms (SNPs) has emerged as genotyping technology with wide and significant applications in aquaculture. SNPs can be used for construction of genetic linkage maps, finding quantitative trait loci (QTL) for useful traits like growth, body weight, grilsing, thermal and low oxygen tolerance, resistance to stress and diseases, mapping sex determination loci and identification of progeny in selection and chromosome manipulation experiments, assessment of genomic selectionand marker assisted selection in aquaculture. Genome-wide association studies (GWAS) facilitate the finding associations between SNPs and a trait in related or unrelated specimens. However, many traits are complex and can be controlled by number of QTL. Genotyping by genome reduction complexity sequencing emerged as an efficient and applicable technology in genomic selection. Identification of genes, sequences and nucleotides (substitutions) directly influencing phenotypic variations opens the possibility of marker-assisted selection for desirable characters in culture. SNP and QTL associations can be enhanced using genome editing technology. Examples of successful applications of SNPs in aquaculture of fish, crustacean and mollusk species, representing most geographic areas, and ecological risks assessment are reviewed.

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“…; Tsai et al. ). In particular, within‐family genomic evaluation has been proposed for aquaculture programmes as large family sizes are available and high levels of linkage disequilibrium (LD) within families can be attained with a limited number of markers (Lillehammer, Meuwissen, & Sonesson, ).…”

Section: Introductionmentioning

confidence: 97%

Accuracy of genomic within‐family selection in aquaculture breeding programmes

Toro

Saura²,

Fernández³

et al. 2017

J Animal Breeding Genetics

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SummaryIn aquaculture breeding programmes, selection within families cannot be applied for traits that cannot be recorded on the candidates (e.g., disease resistance or fillet quality). However, this problem can be overcome if genomic evaluation is used. Within-family genomic evaluation has been proposed for these programmes as large family sizes are available and substantial levels of linkage disequilibrium (LD) within families can be attained with a limited number of markers even in populations in global linkage equilibrium. Here, we compare by computer simulation: (i) within-family and population-wide LD; and (ii) the accuracy of withinfamily genomic selection when genomic evaluations are carried out either at the population level or within families. The population simulated was composed by a varying number of families of full-sibs (half for training and half for testing). The results indicate that, to practice within-family selection, performing the genomic evaluation separately for each family using only molecular information from the family could be recommended for populations either in linkage equilibrium or with a low level of disequilibrium.

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Genomic prediction of host resistance to sea lice in farmed Atlantic salmon populations

Cited by 191 publications

References 34 publications

Applications of genotyping by sequencing in aquaculture breeding and genetics

Applications of genotyping by sequencing in aquaculture breeding and genetics

Single nucleotide polymorphism markers with applications in aquaculture and assessment of its impact on natural populations

Accuracy of genomic within‐family selection in aquaculture breeding programmes

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