Genetic diversity and heritability of economically important traits in captive Australasian snapper (Chrysophrys auratus)

Ashton, David T.; Hilario, Elena; Jaksons, Peter; Ritchie, Peter A.; Wellenreuther, Maren

doi:10.1016/j.aquaculture.2019.02.034

Cited by 28 publications

(34 citation statements)

References 40 publications

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“…The most possible explanation is that our sampling frequency of offspring was incomplete relative to the whole spawning periods, which could lead to a loss of genetic diversity and low parental contribution [ 49 ]. Moreover, since our samples come from grown-up fish instead of eggs or larvae directly, the different survival rates of progeny—which are influenced by the management practices, cannibalism and family genotype—could also result in a bias parental contribution [ 38 , 74 ]. More complete sampling and longer-term tracking is needed to clarify this issue.…”

Section: Discussionmentioning

confidence: 99%

“…It has been proposed that GBS data is one of the best options for cost-effective SNP discovery and parentage analysis [ 36 ]. Even so, the application of GBS for parentage analysis is still insufficient: only several related researches have been made for shellfish (blue mussel Mytilus galloprovincialis ) [ 37 ], fish (Florida bass Micropterus floridanus [ 14 ], Australasian snapper Chrysophrys auratus [ 38 ], arctic charr Salvelinus alpinus [ 39 ]) and plant (Scots pine Pinus sylvestris [ 40 ], radiata pine Pinus radiata [ 41 ]). Despite the increase in reports of parentage analysis using GBS recently, it should still be improved for related studies to take more advantage of GBS-based techniques and bioinformatic pipelines.…”

Section: Introductionmentioning

confidence: 99%

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Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Weng

Yang

Wang

et al. 2021

Genes

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Pedigree information is necessary for the maintenance of diversity for wild and captive populations. Accurate pedigree is determined by molecular marker-based parentage analysis, which may be influenced by the polymorphism and number of markers, integrity of samples, relatedness of parents, or different analysis programs. Here, we described the first development of 208 single nucleotide polymorphisms (SNPs) and 11 microsatellites for giant grouper (Epinephelus lanceolatus) taking advantage of Genotyping-by-sequencing (GBS), and compared the power of SNPs and microsatellites for parentage and relatedness analysis, based on a mixed family composed of 4 candidate females, 4 candidate males and 289 offspring. CERVUS, PAPA and COLONY were used for mutually verification. We found that SNPs had a better potential for relatedness estimation, exclusion of non-parentage and individual identification than microsatellites, and > 98% accuracy of parentage assignment could be achieved by 100 polymorphic SNPs (MAF cut-off < 0.4) or 10 polymorphic microsatellites (mean Ho = 0.821, mean PIC = 0.651). This study provides a reference for the development of molecular markers for parentage analysis taking advantage of next-generation sequencing, and contributes to the molecular breeding, fishery management and population conservation.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Weng

Yang

Wang

et al. 2021

Genes

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“…Australasian snapper (Pagrus auratus) in New Zealand. Rapid generation of de novo genome maps 41 , transcriptomes 42 , GBS methods 41,43 and estimation of genetic diversity and genetic parameters 43 were applied to inform the selection of base populations, retention of genetic diversity during domestication, and investigations into the biology of production traits.…”

Section: An Example Of Genomics-enabled Domestication Of a New Targetmentioning

confidence: 99%

Harnessing genomics to fast-track genetic improvement in aquaculture

et al. 2020

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Aquaculture is the fastest growing farmed food sector and will soon become the primary source of fish and shellfish for human diets. In contrast to crops and livestock, production is derived from numerous, exceptionally diverse species that are typically in the early stages of domestication. Genetic improvement of production traits via well-designed, managed breeding programmes has great potential to help meet the rising seafood demand driven by human population growth. Supported by continuous advances in sequencing and bioinformatics, genomics is increasingly being applied across the broad range of aquaculture species and at all stages of the domestication process to optimize selective breeding. In the future, combining genomic selection with biotechnological innovations, such as genome editing and surrogate broodstock technologies, may further expedite genetic improvement in aquaculture.

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“…A strategy for reducing these negative effects, while enhancing wild snapper stock productivity, is the development of captive production. Although there is not yet commercial aquaculture of the species, research programmes intending to develop Australian snapper into a profitable and sustainable aquaculture species exist in New Zealand and Australia (Ashton et al . 2019a; Catanach et al .…”

Section: Introductionmentioning

confidence: 99%

Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus)

Wellenreuther

Sandoval‐Castillo

Beheregaray

2021

Preprint

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Growth is one of the most important traits of an organism. For exploited species, this trait has ecological and evolutionary consequences as well as economical and conservation significance. Rapid changes in growth rate associated with anthropogenic stressors have been reported for several marine fishes, but little is known about the genetic basis of growth traits in teleosts. We used reduced genome representation data and genome-wide association approaches to identify growth-related genetic variation in the commercially, recreationally, and culturally important Australian snapper (Chrysophrys auratus, Sparidae). Based on 17,490 high-quality SNPs and 363 individuals representing extreme growth phenotypes from 15,000 fish of the same age and reared under identical conditions in a sea pen, we identified 100 unique candidates that were annotated to 51 proteins. We documented a complex polygenic nature of growth in the species that included several loci with small effects and a few loci with larger effects. Overall heritability was high (75.7%), reflected in the high accuracy of the genomic prediction for the phenotype (small vs large). Although the SNPs were distributed across the genome, most candidates (60%) clustered on chromosome 16, which also explains the largest proportion of heritability (16.4%). This study demonstrates that reduced genome representation SNPs and the right bioinformatic tools provide a cost-efficient approach to identify growth-related loci and to describe genomic architectures of complex quantitative traits. Our results help to inform captive aquaculture breeding programmes and are of relevance to monitor growth-related evolutionary shifts in wild populations in response to anthropogenic pressures.

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Genetic diversity and heritability of economically important traits in captive Australasian snapper (Chrysophrys auratus)

Cited by 28 publications

References 40 publications

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

Harnessing genomics to fast-track genetic improvement in aquaculture

Genomic prediction of growth in a commercially, recreationally, and culturally important marine resource, the Australian snapper (Chrysophrys auratus)

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