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Roche J, Griot R, Allal F, Besson M, Haffray P, Patrice P, Phocas F, Vandeputte M. APIS: an updated parentage assignment software managing triploids induced from diploid parents. G3 (BETHESDA, MD.) 2024; 14:jkae143. [PMID: 38954534 PMCID: PMC11304945 DOI: 10.1093/g3journal/jkae143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2024] [Revised: 05/11/2024] [Accepted: 06/13/2024] [Indexed: 07/04/2024]
Abstract
In aquaculture, sterile triploids are commonly used for production as sterility gives them potential gains in growth, yields, and quality. However, they cannot be reproduced, and DNA parentage assignment to their diploid or tetraploid parents is required to estimate breeding values for triploid phenotypes. No publicly available software has the ability to assign triploids to their parents. Here, we updated the R package APIS to support triploids induced from diploid parents. First, we created new exclusion and likelihood tables that account for the double allelic contribution of the dam and the recombination that can occur during female meiosis. As the effective recombination rate of each marker with the centromere is usually unknown, we set it at 0.5 and found that this value maximizes the assignment rate even for markers with high or low recombination rates. The number of markers needed for a high true assignment rate did not strongly depend on the proportion of missing parental genotypes. The assignment power was however affected by the quality of the markers (minor allele frequency, call rate). Altogether, 96-192 SNPs were required to have a high parentage assignment rate in a real rainbow trout dataset of 1,232 triploid progenies from 288 parents. The likelihood approach was more efficient than exclusion when the power of the marker set was limiting. When more markers were used, exclusion was more advantageous, with sensitivity reaching unity, very low false discovery rate (<0.01), and excellent specificity (0.96-0.99). Thus, APIS provides an efficient solution to assign triploids to their diploid parents.
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Affiliation(s)
- Julien Roche
- SYSAAF (French Poultry and Aquaculture Breeders Technical Centre), 35042 Rennes, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Ronan Griot
- SYSAAF (French Poultry and Aquaculture Breeders Technical Centre), 35042 Rennes, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, 34250 Palavas-les-Flots, France
| | - François Allal
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, 34250 Palavas-les-Flots, France
| | - Mathieu Besson
- SYSAAF (French Poultry and Aquaculture Breeders Technical Centre), 35042 Rennes, France
| | - Pierrick Haffray
- SYSAAF (French Poultry and Aquaculture Breeders Technical Centre), 35042 Rennes, France
| | - Pierre Patrice
- SYSAAF (French Poultry and Aquaculture Breeders Technical Centre), 35042 Rennes, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Marc Vandeputte
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, INRAE, 34250 Palavas-les-Flots, France
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Xia L, Shi M, Li H, Zhang W, Cheng Y, Xia XQ. PMSeeker: A Scheme Based on the Greedy Algorithm and the Exhaustive Algorithm to Screen Low-Redundancy Marker Sets for Large-Scale Parentage Assignment with Full Parental Genotyping. BIOLOGY 2024; 13:100. [PMID: 38392318 PMCID: PMC10886308 DOI: 10.3390/biology13020100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 01/30/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
Parentage assignment is a genetic test that utilizes genetic characteristics, such as molecular markers, to identify the parental relationships within populations, which, in commercial fish farming, are almost always large and where full information on potential parents is known. To accurately find the true parents, the genotypes of all loci in the parentage marker set (PMS) are required for each individual being tested. With the same accuracy, a PMS containing a smaller number of markers will undoubtedly save experimental costs. Thus, this study established a scheme to screen low-redundancy PMSs using the exhaustive algorithm and greedy algorithm. When screening PMSs, the greedy algorithm selects markers based on the parental dispersity index (PDI), a uniquely defined metric that outperforms the probability of exclusion (PE). With the conjunctive use of the two algorithms, non-redundant PMSs were found for more than 99.7% of solvable cases in three groups of random sample experiments in this study. Then, a low-redundancy PMS can be composed using two or more of these non-redundant PMSs. This scheme effectively reduces the number of markers in PMSs, thus conserving human and experimental resources and laying the groundwork for the widespread implementation of parentage assignment technology in economic species breeding.
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Affiliation(s)
- Lei Xia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mijuan Shi
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Heng Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanting Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yingyin Cheng
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Xiao-Qin Xia
- State Key Laboratory of Freshwater Ecology and Biotechnology, Hubei Hongshan Laboratory, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture and Rural Affairs, The Innovation Academy of Seed Design, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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Fraslin C, Robledo D, Kause A, Houston RD. Potential of low-density genotype imputation for cost-efficient genomic selection for resistance to Flavobacterium columnare in rainbow trout (Oncorhynchus mykiss). Genet Sel Evol 2023; 55:59. [PMID: 37580697 PMCID: PMC10424455 DOI: 10.1186/s12711-023-00832-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 07/26/2023] [Indexed: 08/16/2023] Open
Abstract
BACKGROUND Flavobacterium columnare is the pathogen agent of columnaris disease, a major emerging disease that affects rainbow trout aquaculture. Selective breeding using genomic selection has potential to achieve cumulative improvement of the host resistance. However, genomic selection is expensive partly because of the cost of genotyping large numbers of animals using high-density single nucleotide polymorphism (SNP) arrays. The objective of this study was to assess the efficiency of genomic selection for resistance to F. columnare using in silico low-density (LD) panels combined with imputation. After a natural outbreak of columnaris disease, 2874 challenged fish and 469 fish from the parental generation (n = 81 parents) were genotyped with 27,907 SNPs. The efficiency of genomic prediction using LD panels was assessed for 10 panels of different densities, which were created in silico using two sampling methods, random and equally spaced. All LD panels were also imputed to the full 28K HD panel using the parental generation as the reference population, and genomic predictions were re-evaluated. The potential of prioritizing SNPs that are associated with resistance to F. columnare was also tested for the six lower-density panels. RESULTS The accuracies of both imputation and genomic predictions were similar with random and equally-spaced sampling of SNPs. Using LD panels of at least 3000 SNPs or lower-density panels (as low as 300 SNPs) combined with imputation resulted in accuracies that were comparable to those of the 28K HD panel and were 11% higher than the pedigree-based predictions. CONCLUSIONS Compared to using the commercial HD panel, LD panels combined with imputation may provide a more affordable approach to genomic prediction of breeding values, which supports a more widespread adoption of genomic selection in aquaculture breeding programmes.
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Affiliation(s)
- Clémence Fraslin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Antti Kause
- Natural Resources Institute Finland (Luke), Myllytie 1, 31600, Jokioinen, Finland
| | - Ross D Houston
- Benchmark Genetics, Edinburgh Technopole, 1 Pioneer Building, Penicuik, EH26 0GB, UK
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Carrier A, Gilbert I, Leclerc P, Duchesne M, Robert C. Characterization of the genetic pool of the Canadienne dairy cattle breed. Genet Sel Evol 2023; 55:32. [PMID: 37161364 PMCID: PMC10170705 DOI: 10.1186/s12711-023-00793-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/15/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND Canadienne cattle are the oldest breed of dairy cattle in North America. The Canadienne breed originates from cattle that were brought to America by the mid-seventeenth century French settlers. The herd book was established in 1886 and the current breed characteristics include dark coat color, small size compared to the modern Holstein breed, and overall rusticity shaped by the harsh environmental conditions that were prevalent during the settlement of North America. The Canadienne breed is an invaluable genetic resource due to its high resilience, longevity and fertility. However, it is heavily threatened with a current herd limited to an estimated 1200 registered animals, of which less than 300 are fullblood. To date, no effort has been made to document the genetic pool of this heritage breed in order to preserve it. RESULTS In this project, we used genomic data, which allow a precise description of the genetic makeup of a population, to provide valuable information on the genetic diversity of this heritage breed and suggest management options for its long-term viability. Using a panel that includes 640,000 single nucleotide polymorphisms (SNPs), we genotyped 190 animals grouped into six purity ranges. Unsupervised clustering analyses revealed three genetically distinct groups among those with the higher levels of purity. The observed heterozygosity was higher than expected even in the 100% purebreds. Comparison with Holstein genotypes showed significantly shorter runs of homozygosity for the Canadienne breed, which was unexpected due to the high inbreeding value calculated from pedigree data. CONCLUSIONS Overall, our data indicate that the fullblood gene pool of the Canadienne breed is more diversified than expected and that bloodline management could promote breed sustainability. In its current state, the Canadienne is not a dead-end breed but remains highly vulnerable due to its small population size.
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Affiliation(s)
- Alexandra Carrier
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada
- Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, Canada
- Dé̇partement des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
| | - Isabelle Gilbert
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada
- Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, Canada
- Dé̇partement des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada
| | - Pierre Leclerc
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada
- Dé̇partement d'obstétrique, gynécologie et reproduction, Faculté de médecine, Université Laval, QC, Québec, Canada
| | - Mario Duchesne
- Association de Mise en Valeur de La Race Bovine Canadienne (AVRBC), Québec, QC, Canada
| | - Claude Robert
- Centre de recherche en reproduction, développement et santé intergénérationnelle, Université Laval, Québec, QC, Canada.
- Institut sur la nutrition et les aliments fonctionnels, Université Laval, Québec, QC, Canada.
- Dé̇partement des sciences animales, Faculté des sciences de l'agriculture et de l'alimentation, Université Laval, Québec, QC, Canada.
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Wenne R. Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations. Genes (Basel) 2023; 14:genes14040808. [PMID: 37107566 PMCID: PMC10138012 DOI: 10.3390/genes14040808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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6
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Carrier A, Prunier J, Poisson W, Trottier-Lavoie M, Gilbert I, Cavedon M, Pokharel K, Kantanen J, Musiani M, Côté SD, Albert V, Taillon J, Bourret V, Droit A, Robert C. Design and validation of a 63K genome-wide SNP-genotyping platform for caribou/reindeer (Rangifer tarandus). BMC Genomics 2022; 23:687. [PMID: 36199020 PMCID: PMC9533608 DOI: 10.1186/s12864-022-08899-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 09/15/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Development of large single nucleotide polymorphism (SNP) arrays can make genomic data promptly available for conservation problematic. Medium and high-density panels can be designed with sufficient coverage to offer a genome-wide perspective and the generated genotypes can be used to assess different genetic metrics related to population structure, relatedness, or inbreeding. SNP genotyping could also permit sexing samples with unknown associated metadata as it is often the case when using non-invasive sampling methods favored for endangered species. Genome sequencing of wild species provides the necessary information to design such SNP arrays. We report here the development of a SNP-array for endangered Rangifer tarandus using a multi-platform sequencing approach from animals found in diverse populations representing the entire circumpolar distribution of the species. RESULTS From a very large comprehensive catalog of SNPs detected over the entire sample set (N = 894), a total of 63,336 SNPs were selected. SNP selection accounted for SNPs evenly distributed across the entire genome (~ every 50Kb) with known minor alleles across populations world-wide. In addition, a subset of SNPs was selected to represent rare and local alleles found in Eastern Canada which could be used for ecotype and population assignments - information urgently needed for conservation planning. In addition, heterozygosity from SNPs located in the X-chromosome and genotyping call-rate of SNPs located into the SRY gene of the Y-chromosome yielded an accurate and robust sexing assessment. All SNPs were validated using a high-throughput SNP-genotyping chip. CONCLUSION This design is now integrated into the first genome-wide commercially available genotyping platform for Rangifer tarandus. This platform would pave the way to future genomic investigation of populations for this endangered species, including estimation of genetic diversity parameters, population assignments, as well as animal sexing from genetic SNP data for non-invasive samples.
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Affiliation(s)
- Alexandra Carrier
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Julien Prunier
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Quebec City, Québec, Canada
| | - William Poisson
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Mallorie Trottier-Lavoie
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Isabelle Gilbert
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada.,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada.,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada
| | - Maria Cavedon
- Department of biological sciences, Faculty of Science, University of Calgary, Calgary, Canada
| | | | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Marco Musiani
- Department of Biological, Geological and Environmental Sciences (BiGeA), University of Bologna, Bologna, Italy
| | - Steeve D Côté
- Département de biologie - Faculté de sciences et génie, Caribou Ungava, Université Laval, Quebec City, Québec, Canada
| | - Vicky Albert
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Joëlle Taillon
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Vincent Bourret
- Ministère des Forêts, de la Faune et des Parcs du Québec (MFFP), Quebec City, Québec, Canada
| | - Arnaud Droit
- Département de médecine moléculaire, Faculté de médecine, Université Laval, Quebec City, Québec, Canada
| | - Claude Robert
- Département de sciences animales, Faculté de l'agriculture et d'alimentation, Université Laval, Quebec City, Québec, Canada. .,Centre de recherche en reproduction, développement et santé intergénérationnelle (CRDSI), Quebec City, Québec, Canada. .,Réseau Québécois en reproduction (RQR), Saint-Hyacinthe, Québec, Canada.
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Animal board invited review: Widespread adoption of genetic technologies is key to sustainable expansion of global aquaculture. Animal 2022; 16:100642. [PMID: 36183431 PMCID: PMC9553672 DOI: 10.1016/j.animal.2022.100642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 08/31/2022] [Accepted: 09/02/2022] [Indexed: 11/23/2022] Open
Abstract
The extent of application of genetic technologies to aquaculture production varies widely by species and geography. Achieving a more universal application of seed derived from scientifically based breeding programmes is an important goal in order to meet increasing global demands for seafood production. This article reviews the status of genetic technologies across the world’s top 10 highly produced species. Opportunities and barriers to achieving broad-scale uptake of genetic technologies in global aquaculture are discussed. A future outlook for potential disruptive genetic technologies and how they might affect global aquaculture production is given.
Aquaculture production comprises a diverse range of species, geographies, and farming systems. The application of genetics and breeding technologies towards improved production is highly variable, ranging from the use of wild-sourced seed through to advanced family breeding programmes augmented by genomic techniques. This technical variation exists across some of the most highly produced species globally, with several of the top ten global species by volume generally lacking well-managed breeding programmes. Given the well-documented incremental and cumulative benefits of genetic improvement on production, this is a major missed opportunity. This short review focusses on (i) the status of application of selective breeding in the world’s most produced aquaculture species, (ii) the range of genetic technologies available and the opportunities they present, and (iii) a future outlook towards realising the potential contribution of genetic technologies to aquaculture sustainability and global food security.
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What Can Genetics Do for the Control of Infectious Diseases in Aquaculture? Animals (Basel) 2022; 12:ani12172176. [PMID: 36077896 PMCID: PMC9454762 DOI: 10.3390/ani12172176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Infectious diseases place an economic burden on aquaculture and a limitation to its growth. This state-of-the-art review describes the application of genetics and genomics as novel tools to control infectious disease in aquaculture. Abstract Infectious diseases place an economic burden on aquaculture and a limitation to its growth. An innovative approach to mitigate their impact on production is breeding for disease resistance: selection for domestication, family-based selection, marker-assisted selection, and more recently, genomic selection. Advances in genetics and genomics approaches to the control of infectious diseases are key to increasing aquaculture efficiency, profitability, and sustainability and to reducing its environmental footprint. Interaction and co-evolution between a host and pathogen can, however, turn breeding to boost infectious disease resistance into a potential driver of pathogenic change. Parallel molecular characterization of the pathogen and its virulence and antimicrobial resistance genes is therefore essential to understand pathogen evolution over time in response to host immunity, and to apply appropriate mitigation strategies.
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9
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Abstract
To date, genomic prediction has been conducted in about 20 aquaculture species, with a preference for intra-family genomic selection (GS). For every trait under GS, the increase in accuracy obtained by genomic estimated breeding values instead of classical pedigree-based estimation of breeding values is very important in aquaculture species ranging from 15% to 89% for growth traits, and from 0% to 567% for disease resistance. Although the implementation of GS in aquaculture is of little additional investment in breeding programs already implementing sib testing on pedigree, the deployment of GS remains sparse, but could be boosted by adaptation of cost-effective imputation from low-density panels. Moreover, GS could help to anticipate the effect of climate change by improving sustainability-related traits such as production yield (e.g., carcass or fillet yields), feed efficiency or disease resistance, and by improving resistance to environmental variation (tolerance to temperature or salinity variation). This chapter synthesized the literature in applications of GS in finfish, crustaceans and molluscs aquaculture in the present and future breeding programs.
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Affiliation(s)
- François Allal
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France.
| | - Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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10
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Linking Pedigree Information to the Gene Expression Phenotype to Understand Differential Family Survival Mechanisms in Highly Fecund Fish: A Case Study in the Larviculture of Pacific Bluefin Tuna. Curr Issues Mol Biol 2021; 43:2098-2110. [PMID: 34940119 PMCID: PMC8929136 DOI: 10.3390/cimb43030145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 11/16/2022] Open
Abstract
Mass spawning in fish culture often brings about a marked variance in family size, which can cause a reduction in effective population sizes in seed production for stock enhancement. This study reports an example of combined pedigree information and gene expression phenotypes to understand differential family survival mechanisms in early stages of Pacific bluefin tuna, Thunnus orientalis, in a mass culture tank. Initially, parentage was determined using the partial mitochondrial DNA control region sequence and 11 microsatellite loci at 1, 10, 15, and 40 days post-hatch (DPH). A dramatic proportional change in the families was observed at around 15 DPH; therefore, transcriptome analysis was conducted for the 15 DPH larvae using a previously developed oligonucleotide microarray. This analysis successfully addressed the family-specific gene expression phenotypes with 5739 differentially expressed genes and highlighted the importance of expression levels of gastric-function-related genes at the developmental stage for subsequent survival. This strategy demonstrated herein can be broadly applicable to species of interest in aquaculture to comprehend the molecular mechanism of parental effects on offspring survival, which will contribute to the optimization of breeding technologies.
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11
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Griot R, Allal F, Phocas F, Brard-Fudulea S, Morvezen R, Haffray P, François Y, Morin T, Bestin A, Bruant JS, Cariou S, Peyrou B, Brunier J, Vandeputte M. Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, the European Sea Bass ( Dicentrarchus labrax) and the Gilthead Sea Bream ( Sparus aurata). Front Genet 2021; 12:665920. [PMID: 34335683 PMCID: PMC8317601 DOI: 10.3389/fgene.2021.665920] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Disease outbreaks are a major threat to the aquaculture industry, and can be controlled by selective breeding. With the development of high-throughput genotyping technologies, genomic selection may become accessible even in minor species. Training population size and marker density are among the main drivers of the prediction accuracy, which both have a high impact on the cost of genomic selection. In this study, we assessed the impact of training population size as well as marker density on the prediction accuracy of disease resistance traits in European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata). We performed a challenge to nervous necrosis virus (NNV) in two sea bass cohorts, a challenge to Vibrio harveyi in one sea bass cohort and a challenge to Photobacterium damselae subsp. piscicida in one sea bream cohort. Challenged individuals were genotyped on 57K-60K SNP chips. Markers were sampled to design virtual SNP chips of 1K, 3K, 6K, and 10K markers. Similarly, challenged individuals were randomly sampled to vary training population size from 50 to 800 individuals. The accuracy of genomic-based (GBLUP model) and pedigree-based estimated breeding values (EBV) (PBLUP model) was computed for each training population size using Monte-Carlo cross-validation. Genomic-based breeding values were also computed using the virtual chips to study the effect of marker density. For resistance to Viral Nervous Necrosis (VNN), as one major QTL was detected, the opportunity of marker-assisted selection was investigated by adding a QTL effect in both genomic and pedigree prediction models. As training population size increased, accuracy increased to reach values in range of 0.51-0.65 for full density chips. The accuracy could still increase with more individuals in the training population as the accuracy plateau was not reached. When using only the 6K density chip, accuracy reached at least 90% of that obtained with the full density chip. Adding the QTL effect increased the accuracy of the PBLUP model to values higher than the GBLUP model without the QTL effect. This work sets a framework for the practical implementation of genomic selection to improve the resistance to major diseases in European sea bass and gilthead sea bream.
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Affiliation(s)
- Ronan Griot
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, Rennes, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | - François Allal
- MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Romain Morvezen
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, Rennes, France
| | | | | | - Thierry Morin
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Viral Fish Diseases Unit, National Reference Laboratory for Regulated Fish Diseases, Technopôle Brest-Iroise, Plouzané, France
| | | | | | | | - Bruno Peyrou
- Ecloserie Marine de Gravelines-Ichtus, Gravelines, France
| | - Joseph Brunier
- Ecloserie Marine de Gravelines-Ichtus, Gravelines, France
| | - Marc Vandeputte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
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12
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Pincot DDA, Ledda M, Feldmann MJ, Hardigan MA, Poorten TJ, Runcie DE, Heffelfinger C, Dellaporta SL, Cole GS, Knapp SJ. Social network analysis of the genealogy of strawberry: retracing the wild roots of heirloom and modern cultivars. G3-GENES GENOMES GENETICS 2021; 11:6117203. [PMID: 33772307 PMCID: PMC8022721 DOI: 10.1093/g3journal/jkab015] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 12/12/2020] [Indexed: 01/22/2023]
Abstract
The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of the highly admixed populations from which heirloom and modern cultivars have emerged. To develop deeper insights into the three-century-long domestication history of strawberry, we reconstructed the genealogy as deeply as possible—pedigree records were assembled for 8,851 individuals, including 2,656 cultivars developed since 1775. The parents of individuals with unverified or missing pedigree records were accurately identified by applying an exclusion analysis to array-genotyped single-nucleotide polymorphisms. We identified 187 wild octoploid and 1,171 F. × ananassa founders in the genealogy, from the earliest hybrids to modern cultivars. The pedigree networks for cultivated strawberry are exceedingly complex labyrinths of ancestral interconnections formed by diverse hybrid ancestry, directional selection, migration, admixture, bottlenecks, overlapping generations, and recurrent hybridization with common ancestors that have unequally contributed allelic diversity to heirloom and modern cultivars. Fifteen to 333 ancestors were predicted to have transmitted 90% of the alleles found in country-, region-, and continent-specific populations. Using parent–offspring edges in the global pedigree network, we found that selection cycle lengths over the past 200 years of breeding have been extraordinarily long (16.0-16.9 years/generation), but decreased to a present-day range of 6.0-10.0 years/generation. Our analyses uncovered conspicuous differences in the ancestry and structure of North American and European populations, and shed light on forces that have shaped phenotypic diversity in F. × ananassa.
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Affiliation(s)
- Dominique D A Pincot
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mirko Ledda
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Mitchell J Feldmann
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Michael A Hardigan
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Thomas J Poorten
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Daniel E Runcie
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Christopher Heffelfinger
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Stephen L Dellaporta
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | - Glenn S Cole
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
| | - Steven J Knapp
- Department of Plant Sciences, University of California, Davis, Davis, CA 95616, USA
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13
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Maximum likelihood parentage assignment using quantitative genotypes. Heredity (Edinb) 2021; 126:884-895. [PMID: 33692533 DOI: 10.1038/s41437-021-00421-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/09/2022] Open
Abstract
The cost of parentage assignment precludes its application in many selective breeding programmes and molecular ecology studies, and/or limits the circumstances or number of individuals to which it is applied. Pooling samples from more than one individual, and using appropriate genetic markers and algorithms to determine parental contributions to pools, is one means of reducing the cost of parentage assignment. This paper describes and validates a novel maximum likelihood (ML) parentage-assignment method, that can be used to accurately assign parentage to pooled samples of multiple individuals-previously published ML methods are applicable to samples of single individuals only-using low-density single nucleotide polymorphism (SNP) 'quantitative' (also referred to as 'continuous') genotype data. It is demonstrated with simulated data that, when applied to pools, this 'quantitative maximum likelihood' method assigns parentage with greater accuracy than established maximum likelihood parentage-assignment approaches, which rely on accurate discrete genotype calls; exclusion methods; and estimating parental contributions to pools by solving the weighted least squares problem. Quantitative maximum likelihood can be applied to pools generated using either a 'pooling-for-individual-parentage-assignment' approach, whereby each individual in a pool is tagged or traceable and from a known and mutually exclusive set of possible parents; or a 'pooling-by-phenotype' approach, whereby individuals of the same, or similar, phenotype/s are pooled. Although computationally intensive when applied to large pools, quantitative maximum likelihood has the potential to substantially reduce the cost of parentage assignment, even if applied to pools comprised of few individuals.
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14
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Couch AJ, Dyer F, Lintermans M. Multi-year pair-bonding in Murray cod ( Maccullochella peelii). PeerJ 2020; 8:e10460. [PMID: 33354425 PMCID: PMC7733648 DOI: 10.7717/peerj.10460] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 11/10/2020] [Indexed: 01/20/2023] Open
Abstract
Mating strategies in fishes are known to include polygyny, polyandry and monogamy and provide valuable insights regarding powerful evolutionary forces such as sexual selection. Monogamy is a complex of mating systems that has been relatively neglected. Previous work on mating strategies in fishes has often been based on observation and focused on marine species rather than freshwater fishes. SNPs are increasingly being used as a molecular ecology tool in non-model organisms, and methods of probabilistic genetic analysis of such datasets are becoming available for use in the absence of parental genotypes. This approach can be used to infer mating strategies. The long-term pair bonding seen in mammals, reptiles and birds has not been recorded in freshwater fishes-in every other respect an extremely diverse group. This study shows that multi-year pair bonding occurs in an Australian Percichthyid fish that exhibits paternal care of eggs and larvae. Using SNPs, full sibling pairs of larvae were found over multiple years in a three-year study. Stable isotope signatures of the larvae support the genetic inference that full sibling pairs shared a common mother, the ultimate source of that isotopic signature during oogenesis. Spatial and temporal clustering also suggests that the full sibling larvae are unlikely to be false positive identifications of the probabilistic identification of siblings. For the first time, we show multi-year pair bonding in a wild freshwater fish. This will have important conservation and management implications for the species. This approach could provide insights into many behavioural, ecological and evolutionary questions, particularly if this is not a unique case. Our findings are likely to initiate interest in seeking more examples of monogamy and alternative mating strategies in freshwater fishes, particularly if others improve methods of analysis of SNP data for identification of siblings in the absence of parental genotypes.
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Affiliation(s)
- Alan J Couch
- Centre for Applied Water Science, University of Canberra, Canberra, ACT, Australia
| | - Fiona Dyer
- Centre for Applied Water Science, University of Canberra, Canberra, ACT, Australia
| | - Mark Lintermans
- Centre for Applied Water Science, University of Canberra, Canberra, ACT, Australia
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15
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D'Ambrosio J, Morvezen R, Brard-Fudulea S, Bestin A, Acin Perez A, Guéméné D, Poncet C, Haffray P, Dupont-Nivet M, Phocas F. Genetic architecture and genomic selection of female reproduction traits in rainbow trout. BMC Genomics 2020; 21:558. [PMID: 32795250 PMCID: PMC7430828 DOI: 10.1186/s12864-020-06955-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/27/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Rainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, to determine the genetic architecture of these traits by the identification of quantitative trait loci (QTL), and to assess the expected efficiency of a pedigree-based selection (BLUP) or genomic selection for these traits. RESULTS A pedigreed population of 1343 trout were genotyped for 57,000 SNP markers and phenotyped for seven traits at 2 years of age: spawning date, female body weight before and after spawning, the spawn weight and the egg number of the spawn, the egg average weight and average diameter. Genetic parameters were estimated in multi-trait linear animal models. Heritability estimates were moderate, varying from 0.27 to 0.44. The female body weight was not genetically correlated to any of the reproduction traits. Spawn weight showed strong and favourable genetic correlation with the number of eggs in the spawn and individual egg size traits, but the egg number was uncorrelated to the egg size traits. The genome-wide association studies showed that all traits were very polygenic since less than 10% of the genetic variance was explained by the cumulative effects of the QTLs: for any trait, only 2 to 4 QTLs were detected that explained in-between 1 and 3% of the genetic variance. Genomic selection based on a reference population of only one thousand individuals related to candidates would improve the efficiency of BLUP selection from 16 to 37% depending on traits. CONCLUSIONS Our genetic parameter estimates made unlikely the hypothesis that selection for growth could induce any indirect improvement for female reproduction traits. It is thus important to consider direct selection for spawn weight for improving egg production traits in rainbow trout breeding programs. Due to the low proportion of genetic variance explained by the few QTLs detected for each reproduction traits, marker assisted selection cannot be effective. However genomic selection would allow significant gains of accuracy compared to pedigree-based selection.
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Affiliation(s)
- J D'Ambrosio
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - R Morvezen
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - S Brard-Fudulea
- SYSAAF, Section Avicole, Centre INRAE Val de Loire, 37380, Nouzilly, France
| | - A Bestin
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - A Acin Perez
- Viviers de Sarrance, Pisciculture Labedan, 64490, Sarrance, France
| | - D Guéméné
- SYSAAF, Section Avicole, Centre INRAE Val de Loire, 37380, Nouzilly, France
| | - C Poncet
- Université Clermont-Auvergne, INRAE, GDEC, 63039, Clermont-Ferrand, France
| | - P Haffray
- SYSAAF, Station INRAE-LPGP, Campus de Beaulieu, 35042, Rennes cedex, France
| | - M Dupont-Nivet
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - F Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
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16
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Development and validation of a RAD-Seq target-capture based genotyping assay for routine application in advanced black tiger shrimp (Penaeus monodon) breeding programs. BMC Genomics 2020; 21:541. [PMID: 32758142 PMCID: PMC7430818 DOI: 10.1186/s12864-020-06960-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 07/29/2020] [Indexed: 11/26/2022] Open
Abstract
Background The development of genome-wide genotyping resources has provided terrestrial livestock and crop industries with the unique ability to accurately assess genomic relationships between individuals, uncover the genetic architecture of commercial traits, as well as identify superior individuals for selection based on their specific genetic profile. Utilising recent advancements in de-novo genome-wide genotyping technologies, it is now possible to provide aquaculture industries with these same important genotyping resources, even in the absence of existing genome assemblies. Here, we present the development of a genome-wide SNP assay for the Black Tiger shrimp (Penaeus monodon) through utilisation of a reduced-representation whole-genome genotyping approach (DArTseq). Results Based on a single reduced-representation library, 31,262 polymorphic SNPs were identified across 650 individuals obtained from Australian wild stocks and commercial aquaculture populations. After filtering to remove SNPs with low read depth, low MAF, low call rate, deviation from HWE, and non-Mendelian inheritance, 7542 high-quality SNPs were retained. From these, 4236 high-quality genome-wide loci were selected for baits-probe development and 4194 SNPs were included within a finalized target-capture genotype-by-sequence assay (DArTcap). This assay was designed for routine and cost effective commercial application in large scale breeding programs, and demonstrates higher confidence in genotype calls through increased call rate (from 80.2 ± 14.7 to 93.0% ± 3.5%), increased read depth (from 20.4 ± 15.6 to 80.0 ± 88.7), as well as a 3-fold reduction in cost over traditional genotype-by-sequencing approaches. Conclusion Importantly, this assay equips the P. monodon industry with the ability to simultaneously assign parentage of communally reared animals, undertake genomic relationship analysis, manage mate pairings between cryptic family lines, as well as undertake advance studies of genome and trait architecture. Critically this assay can be cost effectively applied as P. monodon breeding programs transition to undertaking genomic selection.
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17
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Houston RD, Bean TP, Macqueen DJ, Gundappa MK, Jin YH, Jenkins TL, Selly SLC, Martin SAM, Stevens JR, Santos EM, Davie A, Robledo D. Harnessing genomics to fast-track genetic improvement in aquaculture. Nat Rev Genet 2020; 21:389-409. [PMID: 32300217 DOI: 10.1038/s41576-020-0227-y] [Citation(s) in RCA: 129] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2020] [Indexed: 12/12/2022]
Abstract
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 crop and livestock production, aquaculture 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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Affiliation(s)
- Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK.
| | - Tim P Bean
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Daniel J Macqueen
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Manu Kumar Gundappa
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
| | - Tom L Jenkins
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | | | | | - Jamie R Stevens
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Eduarda M Santos
- Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, UK
| | - Andrew Davie
- Institute of Aquaculture, University of Stirling, Stirling, UK
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, UK
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18
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Smits M, Enez F, Ferraresso S, Dalla Rovere G, Vetois E, Auvray JF, Genestout L, Mahla R, Arcangeli G, Paillard C, Haffray P, Bargelloni L. Potential for Genetic Improvement of Resistance to Perkinsus olseni in the Manila Clam, Ruditapes philippinarum, Using DNA Parentage Assignment and Mass Spawning. Front Vet Sci 2020; 7:579840. [PMID: 33195590 PMCID: PMC7649815 DOI: 10.3389/fvets.2020.579840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/08/2020] [Indexed: 02/05/2023] Open
Abstract
The Manila clam Ruditapes philippinarum, a major cultured shellfish species, is threatened by infection with the microparasite Perkinsus olseni, whose prevalence increases with high water temperatures. Under the current trend of climate change, the already severe effects of this parasitic infection might rapidly increase the frequency of mass mortality events. Treating infectious diseases in bivalves is notoriously problematic, therefore selective breeding for resistance represents a key strategy for mitigating the negative impact of pathogens. A crucial step in initiating selective breeding is the estimation of genetic parameters for traits of interest, which relies on the ability to record parentage and accurate phenotypes in a large number of individuals. Here, to estimate the heritability of resistance against P. olseni, a field experiment mirroring conditions in industrial clam production was set up, a genomic tool was developed for parentage assignment, and parasite load was determined through quantitative PCR. A mixed-family cohort of potentially 1,479 clam families was produced in a hatchery by mass spawning of 53 dams and 57 sires. The progenies were seeded in a commercial clam production area in the Venice lagoon, Italy, where high prevalence of P. olseni had previously been reported. Growth and parasite load were monitored every month and, after 1 year, more than 1,000 individuals were collected for DNA samples and phenotype recording. A pooled sequencing approach was carried out using DNA samples from the hatchery broodstock and from a Venice lagoon clam population, providing candidate markers used to develop a 245-SNP panel. Parentage assignment for 246 F1 individuals showed sire and dam representation were high (75 and 85%, respectively), indicating a very limited risk of inbreeding. Moderate heritability (0.23 ± 0.11-0.35 ± 0.13) was estimated for growth traits (shell length, shell weight, total weight), while parasite load showed high heritability, estimated at 0.51 ± 0.20. No significant genetic correlations were found between growth-associated traits and parasite load. Overall, the preliminary results provided by this study show high potential for selecting clams resistant to parasite load. Breeding for resistance may help limit the negative effects of climate change on clam production, as the prevalence of the parasite is predicted to increase under a future scenario of higher temperatures. Finally, the limited genetic correlation between resistance and growth suggests that breeding programs could incorporate dual selection without negative interactions.
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Affiliation(s)
- Morgan Smits
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
- Morgan Smits
| | - Florian Enez
- Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
| | - Emilie Vetois
- Société Atlantique de Mariculture (SATMAR), Gatteville-Phare, France
| | | | | | - Rachid Mahla
- Labogena, Domaine de Vilvert, Jouy en Josas, France
| | - Giuseppe Arcangeli
- National Reference Centre for Fish, Crustacean and Mollusc Pathology, Italian Health Authority and Research Organization for Animal Health and Food Safety (IZSVe), Legnaro, Italy
| | - Christine Paillard
- Laboratory of Marine Environmental Sciences (LEMAR), Institut Universitaire Européen de la Mer, Plouzané, France
| | - Pierrick Haffray
- Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Campus de Beaulieu, Rennes, France
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science (BCA), University of Padova, Legnaro, Italy
- *Correspondence: Luca Bargelloni
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19
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Vandeputte M, Bugeon J, Bestin A, Desgranges A, Allamellou JM, Tyran AS, Allal F, Dupont-Nivet M, Haffray P. First Evidence of Realized Selection Response on Fillet Yield in Rainbow Trout Oncorhynchus mykiss, Using Sib Selection or Based on Correlated Ultrasound Measurements. Front Genet 2019; 10:1225. [PMID: 31921286 PMCID: PMC6933014 DOI: 10.3389/fgene.2019.01225] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/05/2019] [Indexed: 11/13/2022] Open
Abstract
Fillet yield, the proportion of edible fillet relative to body weight, is a major trait to improve in fish sold processed, as it has a direct impact on profitability and can simultaneously decrease the environmental impact of producing a given amount of fillet. However, it is difficult to improve by selective breeding, because it cannot be measured on live breeding candidates, its phenotypic variation is low, and, as a ratio, it is not normally distributed and a same change in fillet yield can be the result of different changes in fillet weight and body weight. Residual headless gutted carcass weight (rHGCW) is heritable and highly genetically correlated to Fillet% in rainbow trout, and can be predicted by the ratio of abdominal wall thickness to depth of the peritoneal cavity (E8/E23), measured on live fish by ultrasound tomography. We selected broodstock based on rHGCW, measured on sibs of the selection candidates, on ultrasound measurements (E8/E23) measured on the selection candidates, or a combination of both. Seven broodstock groups were selected: fish with 15% highest (rHGCW+) or lowest (rHGCW−) EBV for rHGCW, with 15% highest (E8/E23+) or lowest (E8/E23−) EBV for E8/E23, with both rHGCW+ and E8/E23+ (Both+) or rHGCW− and E8/E23− (Both−), or with close to zero EBVs for both traits (Mid). Seven corresponding groups of offspring were produced and reared communally. At harvest size (1.5 kg mean weight), 1,561 trout were slaughtered, measured for the traits of interest, and pedigreed with DNA fingerprinting. Offspring from groups Both+, rHGCW+ and E8/E23+ had a higher EBV for rHGCW than the control group, while down-selected groups had a lower EBV. Looking at the phenotypic mean for Fillet% (correlated response), up-selected fish had more fillet than down-selected fish. The highest difference was between Both+ (69.36%) and Both− (68.20%), a 1.16% units difference in fillet percentage. The change in Fillet% was explained by an opposite change in Viscera%, while Head% remained stable. Selection using sib information on rHGCW was on average more efficient than selection using the candidates’ own E8/E23 phenotypes, and downward selection (decreasing Fillet%) was more efficient than upward selection.
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Affiliation(s)
- Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,MARBEC, Université de Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | | | | | | | | | | | - François Allal
- MARBEC, Université de Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
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20
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Griot R, Allal F, Brard‐Fudulea S, Morvezen R, Haffray P, Phocas F, Vandeputte M. APIS: An auto‐adaptive parentage inference software that tolerates missing parents. Mol Ecol Resour 2019; 20:579-590. [DOI: 10.1111/1755-0998.13103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 10/01/2019] [Accepted: 10/09/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Ronan Griot
- SYSAAF Station LPGP/INRA Rennes France
- GABI INRA AgroParisTech Université Paris‐Saclay Jouy-en-Josas France
| | - François Allal
- MARBEC Ifremer CNRS IRD Univ. Montpellier Palavas‐les‐Flots France
| | | | | | | | - Florence Phocas
- GABI INRA AgroParisTech Université Paris‐Saclay Jouy-en-Josas France
| | - Marc Vandeputte
- GABI INRA AgroParisTech Université Paris‐Saclay Jouy-en-Josas France
- MARBEC Ifremer CNRS IRD Univ. Montpellier Palavas‐les‐Flots France
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21
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Foote A, Simma D, Khatkar M, Raadsma H, Guppy J, Coman G, Giardina E, Jerry D, Zenger K, Wade N. Considerations for Maintaining Family Diversity in Commercially Mass-Spawned Penaeid Shrimp: A Case Study on Penaeus monodon. Front Genet 2019; 10:1127. [PMID: 31781174 PMCID: PMC6861421 DOI: 10.3389/fgene.2019.01127] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 10/17/2019] [Indexed: 12/05/2022] Open
Abstract
Skewed family distributions are common in aquaculture species that are highly fecund, communally (mass) spawned, and/or communally reared. The magnitude of skews pose challenges for maintaining family-specific genetic diversity, as increased resources are required to detect individuals from underrepresented families, or reliably determine relative survival as a measure of family performance. There is limited understanding of family skews or changes in family proportion of communally reared shrimp under commercial rearing conditions and particularly how this may affect genotyping strategies to recover family performance data in breeding programs. In this study, three separate batches of shrimp, Penaeus monodon, were communally spawned and reared, and then sampled as larvae when ponds were stocked at 30 days of culture (DOC) and as juveniles from commercial ponds during harvest at 150 DOC. A total of 199 broodstock contributed to the 5,734 progeny that were genotyped with a custom multiplex single nucleotide polymorphism (SNP) panel, and family assignments were cross-referenced using two parentage assignment methods, CERVUS and COLONY. A total of 121 families were detected, with some families contributing up to 11% of progeny at 30 DOC and up to 18% of progeny at harvest. Significant changes were detected for 20% of families from 30 to 150 DOC, with up to a 9% change in relative contribution. Family skew data was applied in several models to determine the optimal sample size to detect families, along with the ability to detect changes in relative family contribution over time. Results showed that an order of magnitude increase in sampling was required to capture the lowest represented 25% of families, as well as significantly improve the accuracy to determine changes in family proportion from 30 to 150 DOC. Practical measures may be implemented at the hatchery to reduce family skews; a cost-effective measure may be to address the initial magnitude differences in viable progeny produced among families, by pooling equal quantities of hatched larvae from each family. This study demonstrates the relationships between skews in families under commercial conditions, the ability to accurately detect families, and the balance of sampling effort and genotyping cost in highly fecund species such as shrimp.
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Affiliation(s)
- Andrew Foote
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,Aquaculture Program, CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - David Simma
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Mehar Khatkar
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Sciences, University of Sydney, Camden, NSW, Australia
| | - Herman Raadsma
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Sciences, University of Sydney, Camden, NSW, Australia
| | - Jarrod Guppy
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Greg Coman
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Aquaculture Program, CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Erika Giardina
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Seafarms Group Ltd., Flying Fish Point, QLD, Australia
| | - Dean Jerry
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Kyall Zenger
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Nick Wade
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Aquaculture Program, CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
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22
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Chen H, Wang D, Duan X, Liu S, Chen D, Li Y. Hatchery-reared enhancement program for silver carp ( Hypophthalmichthys molitrix) in the middle Yangtze River: monitoring the effectiveness based on parentage analysis. PeerJ 2019; 7:e6836. [PMID: 31119073 PMCID: PMC6507896 DOI: 10.7717/peerj.6836] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 03/23/2019] [Indexed: 11/20/2022] Open
Abstract
Introduction A hatchery-reared silver carp (Hypophthalmichthys molitrix) program has been intensively carried out since 2010 to enhance the rapidly declining fisheries production in the middle Yangtze River. However, only a little information regarding the effectiveness of the enhancement program has been reported. In this context, this study investigates on an enhancement program through monitoring the efficacy based on parentage analysis. Methods A total of 1,529 hatchery-reared fish and 869 larvae were sampled from the middle Yangtze River in 2016 and 2017 and were genotyped by thirteen microsatellite loci. Based on the results of parentage analysis the larvae were divided into three populations: (1) larvae population with both parents being hatchery-reared fish (=R), (2) larvae population with only a male or a female parent being hatchery-reared fish (=H), and (3) larvae population with no hatchery-reared fish parent (=W). The following analyses were also carried out: (1) assessing the contribution of hatchery-reared offspring to larval resources, and (2) evaluating the genetic effect of stock enhancement on the wild population. Results In total, 10.37% and 11.56% of larvae were identified as the offspring produced by hatchery-reared fish released in 2016 and 2017, respectively. In 2017, some of the larvae were assigned unambiguously to hatchery-reared fish released in 2016. In terms of the number of offspring produced, the hatchery-reared fish have shown significant variations. No significant differences were found among all the larvae populations concerning genetic parameters for diversity. High levels of genetic diversity of all larvae populations were obtained. Low F STvalues obtained from pairwise F ST analysis, as well as the analysis of molecular variance (AMOVA), revealed high genetic structural similarity among all the larvae populations. The genetic composition of the W larvae population in 2017 was different from that of all other larvae populations (all larvae populations in 2016, and R and H larvae populations in 2017), as demonstrated from the results of STRUCTURE and PCA analyses. Conclusion It was demonstrated that hatchery-reared fish are successful in producing the offspring in the natural environment during multiple years, which might assist in increasing the abundance of larvae. The hatchery-reared fish had variations in terms of the success rates on reproduction. Also, the hatchery-reared enhancement program had no significant effect on the genetic diversity or the genetic structure of wild populations. However, the genetic component of the W larvae population in 2017 was changed as compared to 2016, which was not due to the hatchery-reared enhancement program for silver carp. This could be due to flooding, but the specific causes need further studies. Our results clearly show the necessity to continuously inspect the genetic impact of the enhancement program so that historical information can be utilized for further research.
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Affiliation(s)
- Huijuan Chen
- College of Animal Science and Technology, Southwest University, Chongqing, China.,Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Dengqiang Wang
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Xinbin Duan
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Shaoping Liu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Daqing Chen
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, China
| | - Yun Li
- College of Animal Science and Technology, Southwest University, Chongqing, China
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23
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Aguiar JDP, Fazzi-Gomes PF, Hamoy IG, Dos Santos SE, Sampaio I. Tracing individuals and populations of the tambaqui, Colossoma macropomum (Cuvier, 1818), from Brazilian hatcheries using microsatellite markers. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2019; 99:2998-3004. [PMID: 30478936 DOI: 10.1002/jsfa.9513] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 11/21/2018] [Accepted: 11/22/2018] [Indexed: 06/09/2023]
Abstract
BACKGROUND In recent years, tracing of alimentary produce of animal origin has become increasingly important, for economic, food safety and ecological reasons. The tambaqui, Colossoma macropomum, is the native fish most farmed in Brazil. The reliable identification of the origin of tambaquis (wild or farmed) offered for sale to the general public has become necessary to satisfy regulatory norms and uphold consumer confidence. Molecular methods based on the analysis of DNA sequences have often been used to evaluate the potential for tracing farmed fish, given their reliability and precision. RESULTS Full likelihood and Bayesian approaches proved to be the most efficient for the identification, respectively, of individuals and populations for most of the fish sampled from seven hatcheries and one wild stock. The exclusion method and genetic distances were the least effective approaches for the identification of individuals and populations. The Bayesian method identified correctly more than 99% of the fry from most stocks, except those of the Santarém hatchery and River Amazon wild stock, which presented the best results for individual identification. CONCLUSIONS The identification of populations was effective for most hatcheries, although the identification of individuals from most stocks was hampered by the reduced genetic variability. © 2018 Society of Chemical Industry.
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Affiliation(s)
- Jonas da Paz Aguiar
- Laboratory of Genetics and Molecular Biology, Institute of Coastal Studies, Federal University of Pará, Belém, Brazil
| | - Paola F Fazzi-Gomes
- Laboratory of Applied Genetics, Institute of Socio-environmental Studies and Hydrological Resources, Federal Rural University of the Amazon, Belém, Brazil
| | - Igor G Hamoy
- Laboratory of Applied Genetics, Institute of Socio-environmental Studies and Hydrological Resources, Federal Rural University of the Amazon, Belém, Brazil
| | - Sidney Eb Dos Santos
- Laboratory of Human and Medical Genetics, Institute of Biological Sciences, Federal University of Pará, Belém, Brazil
| | - Iracilda Sampaio
- Laboratory of Genetics and Molecular Biology, Institute of Coastal Studies, Federal University of Pará, Belém, Brazil
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24
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Vandeputte M, Gagnaire PA, Allal F. The European sea bass: a key marine fish model in the wild and in aquaculture. Anim Genet 2019; 50:195-206. [PMID: 30883830 PMCID: PMC6593706 DOI: 10.1111/age.12779] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/17/2019] [Indexed: 01/13/2023]
Abstract
The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype‐by‐environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large‐scale aquaculture productions.
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Affiliation(s)
- M Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,MARBEC, Ifremer-CNRS-IRD-UM, Université de Montpellier, 34250, Palavas-les-Flots, France
| | - P-A Gagnaire
- Institut des Sciences de l'Evolution de Montpellier, UMR5554 UM-CNRS-IRD-EPHE, Place Eugène Bataillon, 34095, Montpellier, France.,Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - F Allal
- MARBEC, Ifremer-CNRS-IRD-UM, Université de Montpellier, 34250, Palavas-les-Flots, France
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25
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Vendrami DLJ, Houston RD, Gharbi K, Telesca L, Gutierrez AP, Gurney‐Smith H, Hasegawa N, Boudry P, Hoffman JI. Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oysters ( Crassostrea gigas) revealed by genome-wide SNP data. Evol Appl 2019; 12:519-534. [PMID: 30847007 PMCID: PMC6383735 DOI: 10.1111/eva.12736] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 11/02/2018] [Accepted: 11/05/2018] [Indexed: 01/10/2023] Open
Abstract
Cultivated bivalves are important not only because of their economic value, but also due to their impacts on natural ecosystems. The Pacific oyster (Crassostrea gigas) is the world's most heavily cultivated shellfish species and has been introduced to all continents except Antarctica for aquaculture. We therefore used a medium-density single nucleotide polymorphism (SNP) array to investigate the genetic structure of this species in Europe, where it was introduced during the 1960s and has since become a prolific invader of coastal ecosystems across the continent. We analyzed 21,499 polymorphic SNPs in 232 individuals from 23 localities spanning a latitudinal cline from Portugal to Norway and including the source populations of Japan and Canada. We confirmed the results of previous studies by finding clear support for a southern and a northern group, with the former being indistinguishable from the source populations indicating the absence of a pronounced founder effect. We furthermore conducted a large-scale comparison of oysters sampled from the wild and from hatcheries to reveal substantial genetic differences including significantly higher levels of inbreeding in some but not all of the sampled hatchery cohorts. These findings were confirmed by a smaller but representative SNP dataset generated using restriction site-associated DNA sequencing. We therefore conclude that genomic approaches can generate increasingly detailed insights into the genetics of wild and hatchery produced Pacific oysters.
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Affiliation(s)
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth LaboratoriesUniversity of EdinburghEdinburghUK
| | - Luca Telesca
- Department of Earth SciencesUniversity of CambridgeCambridgeUK
- British Antarctic Survey, High CrossCambridgeUK
| | - Alejandro P. Gutierrez
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Helen Gurney‐Smith
- Department of Fisheries and AquacultureVancouver Island UniversityNanaimoBritish ColumbiaCanada
| | - Natsuki Hasegawa
- National Research Institute of AquacultureJapan Fisheries Research AgencyMinami‐IseJapan
| | - Pierre Boudry
- IfremerLaboratoire des Sciences de l’Environnement Marin (UBO/CNRS/IRD/Ifremer)PlouzanéFrance
| | - Joseph I. Hoffman
- Department of Animal BehaviorBielefeld UniversityBielefeldGermany
- British Antarctic Survey, High CrossCambridgeUK
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26
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Zenger KR, Khatkar MS, Jones DB, Khalilisamani N, Jerry DR, Raadsma HW. Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters. Front Genet 2019; 9:693. [PMID: 30728827 PMCID: PMC6351666 DOI: 10.3389/fgene.2018.00693] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs (pearl oysters, Pinctada maxima) and marine shrimp (Litopenaeus vannamei and Penaeus monodon). The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. We highlight the pitfalls and offer the solutions to the genotyping by sequencing approach and the building of appropriate genetic resources to undertake genomic selection from first-hand experience. We describe the potential to capture large-scale commercial phenotypes based on image analysis and artificial intelligence through machine learning, as inputs for calculation of genomic breeding values. The application of genomic selection over traditional aquatic breeding programs offers significant advantages through being able to accurately predict complex polygenic traits including disease resistance; increasing rates of genetic gain; minimizing inbreeding; and negating potential limiting effects of genotype by environment interactions. Further practical advantages of genomic selection through the use of large-scale communal mating and rearing systems are highlighted, as well as presenting rate-limiting steps that impact on attaining maximum benefits from adopting genomic selection. Genomic selection is now at the tipping point where commercial applications can be readily adopted and offer significant short- and long-term solutions to sustainable and profitable aquaculture industries.
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Affiliation(s)
- Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
| | - Mehar S Khatkar
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Nima Khalilisamani
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University Singapore, Singapore, Singapore
| | - Herman W Raadsma
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
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27
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Guppy JL, Jones DB, Jerry DR, Wade NM, Raadsma HW, Huerlimann R, Zenger KR. The State of " Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization. Front Genet 2018; 9:282. [PMID: 30123237 PMCID: PMC6085479 DOI: 10.3389/fgene.2018.00282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022] Open
Abstract
Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. "Omics" based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from "omics" studies has not yet been completely realized. Integration between the multiple "omics" resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging "omics" based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of "omics" resources in penaeid aquaculture.
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Affiliation(s)
- Jarrod L. Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - David B. Jones
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Dean R. Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Nicholas M. Wade
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Aquaculture Program, CSIRO Agriculture & Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Herman W. Raadsma
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - Roger Huerlimann
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Kyall R. Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
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28
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Robledo D, Palaiokostas C, Bargelloni L, Martínez P, Houston R. Applications of genotyping by sequencing in aquaculture breeding and genetics. REVIEWS IN AQUACULTURE 2018; 10:670-682. [PMID: 30220910 PMCID: PMC6128402 DOI: 10.1111/raq.12193] [Citation(s) in RCA: 106] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/27/2016] [Indexed: 05/18/2023]
Abstract
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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Affiliation(s)
- Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Christos Palaiokostas
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food ScienceUniversity of PadovaLegnaroPadovaItaly
| | - Paulino Martínez
- Department of ZoologyGenetics and Physical AnthropologyFaculty of VeterinaryUniversity of Santiago de CompostelaLugoSpain
| | - Ross Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghMidlothianUK
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29
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Hollenbeck CM, Johnston IA. Genomic Tools and Selective Breeding in Molluscs. Front Genet 2018; 9:253. [PMID: 30073016 PMCID: PMC6058216 DOI: 10.3389/fgene.2018.00253] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 06/25/2018] [Indexed: 11/13/2022] Open
Abstract
The production of most farmed molluscs, including mussels, oysters, scallops, abalone, and clams, is heavily dependent on natural seed from the plankton. Closing the lifecycle of species in hatcheries can secure independence from wild stocks and enables long-term genetic improvement of broodstock through selective breeding. Genomic techniques have the potential to revolutionize hatchery-based selective breeding by improving our understanding of the characteristics of mollusc genetics that can pose a challenge for intensive aquaculture and by providing a new suite of tools for genetic improvement. Here we review characteristics of the life history and genetics of molluscs including high fecundity, self-fertilization, high genetic diversity, genetic load, high incidence of deleterious mutations and segregation distortion, and critically assess their impact on the design and effectiveness of selective breeding strategies. A survey of the results of current breeding programs in the literature show that selective breeding with inbreeding control is likely the best strategy for genetic improvement of most molluscs, and on average growth rate can be improved by 10% per generation and disease resistance by 15% per generation across the major farmed species by implementing individual or family-based selection. Rapid advances in sequencing technology have resulted in a wealth of genomic resources for key species with the potential to greatly improve hatchery-based selective breeding of molluscs. In this review, we catalog the range of genomic resources currently available for molluscs of aquaculture interest and discuss the bottlenecks, including lack of high-quality reference genomes and the relatively high cost of genotyping, as well as opportunities for applying genomics-based selection.
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Affiliation(s)
- Christopher M Hollenbeck
- School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, United Kingdom
| | - Ian A Johnston
- School of Biology, Scottish Oceans Institute, University of St Andrews, St Andrews, United Kingdom.,Xelect Ltd, St Andrews, United Kingdom
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30
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Palaiokostas C, Kocour M, Prchal M, Houston RD. Accuracy of Genomic Evaluations of Juvenile Growth Rate in Common Carp ( Cyprinus carpio) Using Genotyping by Sequencing. Front Genet 2018; 9:82. [PMID: 29593780 PMCID: PMC5859378 DOI: 10.3389/fgene.2018.00082] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 02/26/2018] [Indexed: 01/03/2023] Open
Abstract
Cyprinids are the most important group of farmed fish globally in terms of production volume, with common carp (Cyprinus carpio) being one of the most valuable species of the group. The use of modern selective breeding methods in carp is at a formative stage, implying a large scope for genetic improvement of key production traits. In the current study, a population of 1,425 carp juveniles, originating from a partial factorial cross between 40 sires and 20 dams, was used for investigating the potential of genomic selection (GS) for juvenile growth, an exemplar polygenic production trait. RAD sequencing was used to identify and genotype SNP markers for subsequent parentage assignment, construction of a medium density genetic map (12,311 SNPs), genome-wide association study (GWAS), and testing of GS. A moderate heritability was estimated for body length of carp at 120 days (as a proxy of juvenile growth) of 0.33 (s.e. 0.05). No genome-wide significant QTL was identified using a single marker GWAS approach. Genomic prediction of breeding values outperformed pedigree-based prediction, resulting in 18% improvement in prediction accuracy. The impact of reduced SNP densities on prediction accuracy was tested by varying minor allele frequency (MAF) thresholds, with no drop in prediction accuracy until the MAF threshold is set <0.3 (2,744 SNPs). These results point to the potential for GS to improve economically important traits in common carp breeding programs.
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Affiliation(s)
- Christos Palaiokostas
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Martin Kocour
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Martin Prchal
- Faculty of Fisheries and Protection of Waters, South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses, University of South Bohemia in České Budějovice, Vodňany, Czechia
| | - Ross D Houston
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
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Tan B, Grattapaglia D, Wu HX, Ingvarsson PK. Genomic relationships reveal significant dominance effects for growth in hybrid Eucalyptus. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 267:84-93. [PMID: 29362102 DOI: 10.1016/j.plantsci.2017.11.011] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Revised: 11/15/2017] [Accepted: 11/24/2017] [Indexed: 05/23/2023]
Abstract
Non-additive genetic effects can be effectively exploited in control-pollinated families with the availability of genome-wide markers. We used 41,304 SNP markers and compared pedigree vs. marker-based genetic models by analysing height, diameter, basic density and pulp yield for Eucalyptus urophylla × E.grandis control-pollinated families represented by 949 informative individuals. We evaluated models accounting for additive, dominance, and first-order epistatic interactions (additive by additive, dominance by dominance, and additive by dominance). We showed that the models can capture a large proportion of the genetic variance from dominance and epistasis for growth traits as those components are typically not independent. We also showed that we could partition genetic variances more precisely when using relationship matrices derived from markers compared to using only pedigree information. In addition, phenotypic prediction accuracies were only slightly increased by including dominance effects for growth traits since estimates of non-additive variances yielded rather high standard errors. This novel result improves our current understanding of the architecture of quantitative traits and recommends accounting for dominance variance when developing genomic selection strategies in hybrid Eucalyptus.
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Affiliation(s)
- Biyue Tan
- Department of Ecology and Environmental Science, Umeå University, SE-901 87, Umeå, Sweden; Biomaterials Division, Stora Enso AB, SE-131 04, Nacka, Sweden
| | - Dario Grattapaglia
- EMBRAPA Genetic Resources and Biotechnology-EPqB, 70770-910, Brasilia, DF, Brazil; Universidade Católica de Brasília- SGAN, 916 modulo B, Brasilia, DF, 70790-160, Brazil
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden
| | - Pär K Ingvarsson
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden.
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Ferrari S, Horri K, Allal F, Vergnet A, Benhaim D, Vandeputte M, Chatain B, Bégout ML. Heritability of Boldness and Hypoxia Avoidance in European Seabass, Dicentrarchus labrax. PLoS One 2016; 11:e0168506. [PMID: 27992517 PMCID: PMC5167369 DOI: 10.1371/journal.pone.0168506] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/01/2016] [Indexed: 11/19/2022] Open
Abstract
To understand the genetic basis of coping style in European seabass, fish from a full factorial mating (10 females x 50 males) were reared in common garden and individually tagged. Individuals coping style was characterized through behavior tests at four different ages, categorizing fish into proactive or reactive: a hypoxia avoidance test (at 255 days post hatching, dph) and 3 risk-taking tests (at 276, 286 and 304 dph). We observed significant heritability of the coping style, higher for the average of risk-taking scores (h2 = 0.45 ± 0.14) than for the hypoxia avoidance test (h2 = 0.19 ± 0.10). The genetic correlations between the three risk-taking scores were very high (rA = 0.96–0.99) showing that although their repeatability was moderately high (rP = 0.64–0.72), successive risk-taking tests evaluated the same genetic variation. A mild genetic correlation between the results of the hypoxia avoidance test and the average of risk-taking scores (0.45 ± 0.27) suggested that hypoxia avoidance and risk-taking tests do not address exactly the same behavioral and physiological responses. Genetic correlations between weight and risk taking traits showed negative values whatever the test used in our population i.e. reactive individual weights were larger. The results of this quantitative genetic analysis suggest a potential for the development of selection programs based on coping styles that could increase seabass welfare without altering growth performances. Overall, it also contributes to a better understanding of the origin and the significance of individual behavioral differences.
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Affiliation(s)
- Sébastien Ferrari
- Ifremer, Fisheries laboratory, Place Gaby Coll, L’Houmeau, France
- * E-mail: (SF); (MLB)
| | - Khaled Horri
- Ifremer, MARBEC UMR9190, Chemin de Maguelone, Palavas-les-Flots, France
| | - François Allal
- Ifremer, MARBEC UMR9190, Chemin de Maguelone, Palavas-les-Flots, France
| | - Alain Vergnet
- Ifremer, MARBEC UMR9190, Chemin de Maguelone, Palavas-les-Flots, France
| | - David Benhaim
- Laboratoire universitaire des sciences appliquées de Cherbourg, Normandie Univ, UNICAEN, LUSAC, Cherbourg, France
- Conservatoire National des Arts et Métiers. Intechmer, Cherbourg, France
| | - Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
- Ifremer, L3AS, Chemin de Maguelone, Palavas-les-Flots, France
| | - Béatrice Chatain
- Ifremer, MARBEC UMR9190, Chemin de Maguelone, Palavas-les-Flots, France
| | - Marie-Laure Bégout
- Ifremer, Fisheries laboratory, Place Gaby Coll, L’Houmeau, France
- * E-mail: (SF); (MLB)
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33
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Yáñez JM, Newman S, Houston RD. Genomics in aquaculture to better understand species biology and accelerate genetic progress. Front Genet 2015; 6:128. [PMID: 25883603 PMCID: PMC4381651 DOI: 10.3389/fgene.2015.00128] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 03/17/2015] [Indexed: 11/13/2022] Open
Affiliation(s)
- José M Yáñez
- Faculty of Veterinary and Animal Sciences, University of Chile Santiago, Chile ; Aquainnovo Puerto Montt, Chile
| | | | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh Midlothian, UK
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