Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia (Oreochromis niloticus) Population

Barría, Agustín; Benzie, John A. H.; Houston, Ross D.; Koning, Dirk-Jan de; Verdal, Hugues de

doi:10.3389/fgene.2021.737906

Cited by 24 publications

(13 citation statements)

References 104 publications

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“…Whilst Al-Tobasei et al (2021) found a similar trend when using between 500–1000 SNPs for fillet yield traits. To date, the utilization of low-density panels to decrease the cost of genomic evaluations has also been tested in several aquaculture species, including Atlantic salmon ( Salmo salar ) ( Tsai et al, 2016 ; Correa et al, 2017 ), rainbow trout ( Yoshida et al, 2018 ; Al-Tobasei et al, 2021 ), and Nile tilapia ( Oreochromis niloticus ) ( Yoshida et al, 2019 ; Barría et al, 2021 ), suggesting that the development of cost-effective strategies for applying GS will be key for shaping modern aquaculture breeding programs.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis)

et al. 2022

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The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed across Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to overexploitation and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was in the low-moderate range, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels was assessed. Genomic prediction accuracies using the full density panel were high (> 0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e., 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relatedness should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

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Section: Resultsmentioning

confidence: 99%

Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis)

et al. 2022

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“…Whilst Al-Tobasei et al (2021) found a similar trend when using between 500-1000 SNPs for fillet yield traits. To date, the utilization of low-density panels to decrease the cost of genomic evaluations has also been tested in several aquaculture species, including Atlantic salmon ( Salmo salar ) (Correa et al 2017; Tsai et al 2016), rainbow trout (Yoshida et al 2018; Al-Tobasei et al 2021), and Nile tilapia ( Oreochromis niloticus ) (Barría et al 2021; Yoshida et al 2019), suggesting that the development of cost-effective strategies for applying GS will be key for shaping modern aquaculture breeding programs.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

Peñaloza

Barría

Papadopoulou

et al. 2022

Preprint

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The European flat oyster (Ostrea edulis) is a bivalve mollusc that was once widely distributed in Europe and represented an important food resource for humans for centuries. Populations of O. edulis experienced a severe decline across their biogeographic range mainly due to anthropogenic activities and disease outbreaks. To restore the economic and ecological benefits of European flat oyster populations, extensive protection and restoration efforts are in place within Europe. In line with the increasing interest in supporting restoration and oyster farming through the breeding of stocks with enhanced performance, the present study aimed to evaluate the potential of genomic selection for improving growth traits in a European flat oyster population obtained from successive mass-spawning events. Four growth-related traits were evaluated: total weight (TW), shell height (SH), shell width (SW) and shell length (SL). The heritability of the growth traits was moderate-low, with estimates of 0.45, 0.37, 0.22, and 0.32 for TW, SH, SW and SL, respectively. A genome-wide association analysis revealed a largely polygenic genetic architecture for the four growth traits, with two distinct QTLs detected on chromosome 4. To investigate whether genomic selection can be implemented in flat oyster breeding at a reduced cost, the utility of low-density SNP panels (down to 100 SNPs) was assessed. Genomic prediction accuracies using the full density panel were high (>0.83 for all traits). The evaluation of the effect of reducing the number of markers used to predict genomic breeding values revealed that similar selection accuracies could be achieved for all traits with 2K SNPs as for a full panel containing 4,577 SNPs. Only slight reductions in accuracies were observed at the lowest SNP density tested (i.e. 100 SNPs), likely due to a high relatedness between individuals being included in the training and validation sets during cross-validation. Overall, our results suggest that the genetic improvement of growth traits in oysters is feasible. Nevertheless, and although low-density SNP panels appear as a promising strategy for applying GS at a reduced cost, additional populations with different degrees of genetic relationship should be assessed to derive estimates of prediction accuracies to be expected in practical breeding programmes.

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“…To further develop the GIFT strain and to enable future improvements, several studies have been investigating the genetic bases underlying traits of economic interest. As a consequence, Quantitative Trait Loci (QTL) associated with sex determination [11], Tilapia Lake Virus resistance [12, 13], feed efficiency [14], adaptation to oxygen stress [15] in the GIFT strain have now been identified.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus

Etherington

Nash

Ciezarek

et al. 2022

Preprint

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BackgroundThe Nile tilapia (Oreochromis niloticus) is the third most important freshwater fish for aquaculture. Its success is directly linked to continuous breeding efforts focusing on production traits such as growth rate and weight. Among those elite strains, the Genetically Improved Farmed Tilapia (GIFT) programme initiated by WorldFish is now distributed worldwide. To accelerate the development of the GIFT strain through genomic selection, a high-quality reference genome is necessary.FindingsUsing a combination of short (10X Genomics) and long read (PacBio HiFi, PacBio CLR) sequencing and a genetic map for the GIFT strain, we generated a chromosome level genome assembly for the GIFT. Using genomes of two closely related species (O. mossambicus, O. aureus), we characterised the extent of introgression between these species and O. niloticus that has occurred during the breeding process. Over 11Mb of O. mossambicus genomic material could be identified within the GIFT genome, including genes associated with immunity but also with traits of interest such as growth rate.ConclusionBecause of the breeding history of elite strains, current reference genomes might not be the most suitable to support further studies into the GIFT strain. We generated a chromosome level assembly of the GIFT strain, characterising its mixed origins, and the potential contributions of introgressed regions to selected traits.

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Genomic Selection and Genome-wide Association Study for Feed-Efficiency Traits in a Farmed Nile Tilapia (Oreochromis niloticus) Population

Cited by 24 publications

References 104 publications

Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis)

Genome-Wide Association and Genomic Prediction of Growth Traits in the European Flat Oyster (Ostrea edulis)

Genome-wide association and genomic prediction of growth traits in the European flat oyster (Ostrea edulis)

Chromosome-level genome sequence of the Genetically Improved Farmed Tilapia (GIFT, Oreochromis niloticus) highlights regions of introgression with O. mossambicus

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