1
|
Angelakopoulos R, Tsipourlianos A, Giannoulis T, Mamuris Z, Moutou KA. MassArray Genotyping as a Selection Tool for Extending the Shelf-Life of Fresh Gilthead Sea Bream and European Seabass. Animals (Basel) 2024; 14:205. [PMID: 38254374 PMCID: PMC10812826 DOI: 10.3390/ani14020205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 12/12/2023] [Accepted: 01/06/2024] [Indexed: 01/24/2024] Open
Abstract
In modern aquaculture, genomics-driven breeding programs have emerged as powerful tools for optimizing fish quality. This study focused on two emblematic Mediterranean fish species, the European seabass (Dicentrarchus labrax) and the gilthead sea bream (Sparus aurata), with a primary aim of exploring the genetic basis of white muscle/fillet degradation in fresh fish following harvest. We identified 57 and 44 missense SNPs in gilthead sea bream and European seabass, respectively, located within genes encoding for endogenous proteases responsible for fillet quality. These SNPs were cherry-picked based on their strategic location within the catalytic/regulatory domains of endogenous proteases that are expressed in the white muscle. Using MassArray technology, we successfully associated differentiated enzymatic activity of those endogenous proteases post-harvest as a phenotypic trait with genetic polymorphism of six SNPs in gilthead sea bream and nine in European seabass. These findings can be valuable attributes in selective breeding programs toward the extension of freshness and shelf life of these species. The integration of MassArray technology into breeding programs offers a cost-effective strategy for harnessing the potential of these genetic variants to enhance the overall quality of the final product. Recognizing that fresh fish perishability is a challenge, extending shelf-life is pivotal in reducing losses and production costs.
Collapse
Affiliation(s)
- Rafael Angelakopoulos
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Andreas Tsipourlianos
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Themistoklis Giannoulis
- Laboratory of Biology, Genetics and Bioinformatics, Department of Animal Science, University of Thessaly, Greece Gaiopolis, 41334 Larissa, Greece;
| | - Zissis Mamuris
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| | - Katerina A. Moutou
- Laboratory of Genetics, Comparative and Evolutionary Biology, Department of Biochemistry and Biotechnology, School of Medical Sciences, University of Thessaly, Viopolis, Mezourlo, 41500 Larissa, Greece; (R.A.); (A.T.); (Z.M.)
| |
Collapse
|
2
|
Chessari G, Criscione A, Marletta D, Crepaldi P, Portolano B, Manunza A, Cesarani A, Biscarini F, Mastrangelo S. Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds. Sci Rep 2024; 14:3. [PMID: 38168531 PMCID: PMC10762050 DOI: 10.1038/s41598-023-49125-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/04/2023] [Indexed: 01/05/2024] Open
Abstract
Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north-south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.
Collapse
Affiliation(s)
- Giorgio Chessari
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Andrea Criscione
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy.
| | - Donata Marletta
- Dipartimento Agricoltura, Alimentazione e Ambiente, University of Catania, Via Santa Sofia 100, 95123, Catania, Italy
| | - Paola Crepaldi
- Dipartimento Scienze Agrarie e Ambientali, Produzione, Territorio, Agroenergia, University of Milan, Via Giovanni Celoria 2, 20133, Milan, Italy
| | - Baldassare Portolano
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
| | - Arianna Manunza
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Viale Italia 39, 07100, Sassari, Italy
- Animal and Dairy Science Department, University of Georgia, 425 River Road, 30602, Athens, GA, USA
| | - Filippo Biscarini
- CNR, Institute of Agricultural Biology and Biotechnology (IBBA), Via Bassini 15, 20133, Milan, Italy
| | - Salvatore Mastrangelo
- Dipartimento Scienze Agrarie, Alimentari e Forestali, University of Palermo, Viale delle Scienze, 90128, Palermo, Italy
| |
Collapse
|
3
|
Moulistanos A, Nikolaou T, Sismanoglou S, Gkagkavouzis K, Karaiskou N, Antonopoulou E, Triantafyllidis A, Papakostas S. Investigating the role of genetic variation in vgll3 and six6 in the domestication of gilthead seabream ( Sparus aurata Linnaeus) and European seabass ( Dicentrarchus labrax Linnaeus). Ecol Evol 2023; 13:e10727. [PMID: 38020694 PMCID: PMC10654472 DOI: 10.1002/ece3.10727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 12/01/2023] Open
Abstract
Gene function conservation is crucial in molecular ecology, especially for key traits like growth and maturation in teleost fish. The vgll3 and six6 genes are known to influence age-at-maturity in Atlantic salmon, but their impact on other fish species is poorly understood. Here, we investigated the association of vgll3 and six6 in the domestication of gilthead seabream and European seabass, both undergoing selective breeding for growth-related traits in the Mediterranean. We analysed two different sets of samples using two different genotyping approaches. The first dataset comprised farmed and wild populations from Greece, genotyped for SNPs within the two genes ('gene-level genotyping'). The second dataset examined 300-600 k SNPs located in the chromosomes of the two genes, derived from a meta-analysis of a Pool-Seq experiment involving farmed and wild populations distributed widely across the Mediterranean ('chromosome-level genotyping'). The gene-level analysis revealed a statistically significant allele frequency differences between farmed and wild populations on both genes in each species. This finding was partially supported by the chromosome-level analysis, identifying highly differentiated regions may be involved in the domestication process at varying distances from the candidate genes. Noteworthy genomic features were found, such as a CpG island in gilthead seabream and novel candidate genes in European seabass, warranting further investigation. These findings support a putative role of vgll3 and six6 in the maturation and growth of gilthead seabream and European seabass, emphasizing the need for further research on their conserved function.
Collapse
Affiliation(s)
- Aristotelis Moulistanos
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Theopisti Nikolaou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
| | - Smaragda Sismanoglou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
| | - Konstantinos Gkagkavouzis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Nikoleta Karaiskou
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Efthimia Antonopoulou
- Department of Zoology, School of BiologyAristotle University of ThessalonikiThessalonikiGreece
| | - Alexandros Triantafyllidis
- Department of Genetics, Development & Molecular Biology, School of Biology, Faculty of ScienceAristotle University of ThessalonikiThessalonikiGreece
- Genomics and Epigenomics Translational Research (GENeTres)Center for Interdisciplinary Research and Innovation (CIRI‐AUTH), Balkan CenterThessalonikiGreece
| | - Spiros Papakostas
- Department of Science and TechnologyInternational Hellenic UniversityThessalonikiGreece
| |
Collapse
|
4
|
Gutierrez AP, Selly SLC, Pountney SM, Taggart JB, Kokkinias P, Cavrois-Rogacki T, Fernandez EJ, Migaud H, Lein I, Davie A, Bekaert M. Development of genomic markers associated to growth-related traits and sex determination in lumpfish (Cyclopterus lumpus). Genomics 2023; 115:110721. [PMID: 37769819 DOI: 10.1016/j.ygeno.2023.110721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/19/2023] [Accepted: 09/25/2023] [Indexed: 10/02/2023]
Abstract
Cleaner fish species have gained great importance in the control of sea lice, among them, lumpfish (Cyclopterus lumpus) has become one of the most popular. Lumpfish life cycle has been closed, and hatchery reproduction is now possible, however, current production is reliant on wild caught broodstock to meet the increasing demand. Selective breeding practices are called to play an important role in the successful breeding of most aquaculture species, including lumpfish. In this study we analysed a lumpfish population for the identification of genomic markers linked to production traits. Sequencing of RAD libraries allowed us to identify, 7193 informative markers within the sampled individuals. Genome wide association analysis for sex, weight, condition factor and standard length was performed. One single major QTL region was identified for sex, while nine QTL regions were detected for weight, and three QTL regions for standard length. A total of 177 SNP markers of interest (from QTL regions) and 399 high Fst SNP markers were combined in a low-density panel, useful to obtain relevant genetic information from lumpfish populations. Moreover, a robust combined subset of 29 SNP markers (10 associated to sex, 14 to weight and 18 to standard length) provided over 90% accuracy in predicting the animal's phenotype by machine learning. Overall, our findings provide significant insights into the genetic control of important traits in lumpfish and deliver important genomic resources that will facilitate the establishment of selective breeding programmes in lumpfish.
Collapse
Affiliation(s)
- Alejandro P Gutierrez
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Sarah-Louise Counter Selly
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Samuel M Pountney
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK; University of Victoria, Victoria, BC V8P 5C2, Canada
| | - John B Taggart
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Panagiotis Kokkinias
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | | | | | - Herve Migaud
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Ingrid Lein
- Nofima AS, Sjølsengvegen 22, Sunndalsøra 6600, Norway
| | - Andrew Davie
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK
| | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, Scotland, UK.
| |
Collapse
|
5
|
Montanari S, Deng C, Koot E, Bassil NV, Zurn JD, Morrison-Whittle P, Worthington ML, Aryal R, Ashrafi H, Pradelles J, Wellenreuther M, Chagné D. A multiplexed plant-animal SNP array for selective breeding and species conservation applications. G3 (Bethesda) 2023; 13:jkad170. [PMID: 37565490 PMCID: PMC10542201 DOI: 10.1093/g3journal/jkad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/15/2023] [Accepted: 06/30/2023] [Indexed: 08/12/2023]
Abstract
Reliable and high-throughput genotyping platforms are of immense importance for identifying and dissecting genomic regions controlling important phenotypes, supporting selection processes in breeding programs, and managing wild populations and germplasm collections. Amongst available genotyping tools, single nucleotide polymorphism arrays have been shown to be comparatively easy to use and generate highly accurate genotypic data. Single-species arrays are the most commonly used type so far; however, some multi-species arrays have been developed for closely related species that share single nucleotide polymorphism markers, exploiting inter-species cross-amplification. In this study, the suitability of a multiplexed plant-animal single nucleotide polymorphism array, including both closely and distantly related species, was explored. The performance of the single nucleotide polymorphism array across species for diverse applications, ranging from intra-species diversity assessments to parentage analysis, was assessed. Moreover, the value of genotyping pooled DNA of distantly related species on the single nucleotide polymorphism array as a technique to further reduce costs was evaluated. Single nucleotide polymorphism performance was generally high, and species-specific single nucleotide polymorphisms proved suitable for diverse applications. The multi-species single nucleotide polymorphism array approach reported here could be transferred to other species to achieve cost savings resulting from the increased throughput when several projects use the same array, and the pooling technique adds another highly promising advancement to additionally decrease genotyping costs by half.
Collapse
Affiliation(s)
- Sara Montanari
- The New Zealand Institute for Plant and Food Research Ltd, Motueka 7198, New Zealand
| | - Cecilia Deng
- The New Zealand Institute for Plant and Food Research Ltd, Auckland 1025, New Zealand
| | - Emily Koot
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North 4410, New Zealand
| | - Nahla V Bassil
- USDA-ARS National Clonal Germplasm Repository, Corvallis, OR 97333, USA
| | - Jason D Zurn
- Department of Plant Pathology, Kansas State University, Manhattan, KS 66506, USA
| | | | | | - Rishi Aryal
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | - Hamid Ashrafi
- Department of Horticultural Science, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd, Nelson 7010, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - David Chagné
- The New Zealand Institute for Plant and Food Research Ltd, Palmerston North 4410, New Zealand
| |
Collapse
|
6
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
7
|
Faggion S, Carnier P, Franch R, Babbucci M, Pascoli F, Dalla Rovere G, Caggiano M, Chavanne H, Toffan A, Bargelloni L. Viral nervous necrosis resistance in gilthead sea bream (Sparus aurata) at the larval stage: heritability and accuracy of genomic prediction with different training and testing settings. Genet Sel Evol 2023; 55:22. [PMID: 37013478 PMCID: PMC10069116 DOI: 10.1186/s12711-023-00796-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 03/21/2023] [Indexed: 04/05/2023] Open
Abstract
BACKGROUND The gilthead sea bream (Sparus aurata) has long been considered resistant to viral nervous necrosis (VNN), until recently, when significant mortalities caused by a reassortant nervous necrosis virus (NNV) strain were reported. Selective breeding to enhance resistance against NNV might be a preventive action. In this study, 972 sea bream larvae were subjected to a NNV challenge test and the symptomatology was recorded. All the experimental fish and their parents were genotyped using a genome-wide single nucleotide polymorphism (SNP) array consisting of over 26,000 markers. RESULTS Estimates of pedigree-based and genomic heritabilities of VNN symptomatology were consistent with each other (0.21, highest posterior density interval at 95% (HPD95%): 0.1-0.4; 0.19, HPD95%: 0.1-0.3, respectively). The genome-wide association study suggested one genomic region, i.e., in linkage group (LG) 23 that might be involved in sea bream VNN resistance, although it was far from the genome-wide significance threshold. The accuracies (r) of the predicted estimated breeding values (EBV) provided by three Bayesian genomic regression models (Bayes B, Bayes C, and Ridge Regression) were consistent and on average were equal to 0.90 when assessed in a set of cross-validation (CV) procedures. When genomic relationships between training and testing sets were minimized, accuracy decreased greatly (r = 0.53 for a validation based on genomic clustering, r = 0.12 for a validation based on a leave-one-family-out approach focused on the parents of the challenged fish). Classification of the phenotype using the genomic predictions of the phenotype or using the genomic predictions of the pedigree-based, all data included, EBV as classifiers was moderately accurate (area under the ROC curve 0.60 and 0.66, respectively). CONCLUSIONS The estimate of the heritability for VNN symptomatology indicates that it is feasible to implement selective breeding programs for increased resistance to VNN of sea bream larvae/juveniles. Exploiting genomic information offers the opportunity of developing prediction tools for VNN resistance, and genomic models can be trained on EBV using all data or phenotypes, with minimal differences in classification performance of the trait phenotype. In a long-term view, the weakening of the genomic ties between animals in the training and test sets leads to decreased genomic prediction accuracies, thus periodical update of the reference population with new data is mandatory.
Collapse
Affiliation(s)
- Sara Faggion
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy.
| | - Paolo Carnier
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Francesco Pascoli
- Division of Comparative Biomedical Sciences, OIE Reference Centre for Viral Encephalopathy and Retinopathy, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Padova, Italy
| | - Giulia Dalla Rovere
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| | - Massimo Caggiano
- Panittica Italia Società Agricola S.R.L., Strada del Procaccio, 72016, Torre Canne di Fasano, Italy
| | - Hervé Chavanne
- Panittica Italia Società Agricola S.R.L., Strada del Procaccio, 72016, Torre Canne di Fasano, Italy
| | - Anna Toffan
- Division of Comparative Biomedical Sciences, OIE Reference Centre for Viral Encephalopathy and Retinopathy, Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), Padova, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Viale dell'Università, 16, 35020, Legnaro, PD, Italy
| |
Collapse
|
8
|
Bertolini F, Ribani A, Capoccioni F, Buttazzoni L, Bovo S, Schiavo G, Caggiano M, Rothschild MF, Fontanesi L. Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei. Genes (Basel) 2023; 14:genes14040839. [PMID: 37107597 PMCID: PMC10137967 DOI: 10.3390/genes14040839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/21/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.
Collapse
Affiliation(s)
- Francesca Bertolini
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
- Correspondence:
| | - Anisa Ribani
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Fabrizio Capoccioni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Luca Buttazzoni
- Centro di Ricerca “Zootecnia e Acquacoltura”, Consiglio per la Ricerca in Agricoltura e l’Analisi dell’Economia Agraria (CREA), 00198 Roma, Italy
| | - Samuele Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Giuseppina Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| | - Massimo Caggiano
- Panittica Italia Società Agricola Srl, Torre Canne di Fasano, 72016 Brindisi, Italy
| | - Max F. Rothschild
- Department of Animal Science, Iowa State University, Ames, IA 50011-3150, USA
| | - Luca Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, 40127 Bologna, Italy
| |
Collapse
|
9
|
Houston RD, Kriaridou C, Robledo D. 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] [What about the content of this article? (0)] [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.
Collapse
|
10
|
Zhu K, Li Y, Wu W, Liu B, Guo H, Zhang N, Guo L, Zhang D. Isolation and characterization of 112 SNP markers in Yellowfin seabream (Acanthopagrus latus) using RAD sequencing. CONSERV GENET RESOUR. [DOI: 10.1007/s12686-022-01265-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
|
11
|
Vela-Avitúa S, Thorland I, Bakopoulos V, Papanna K, Dimitroglou A, Kottaras E, Leonidas P, Guinand B, Tsigenopoulos CS, Aslam ML. Genetic Basis for Resistance Against Viral Nervous Necrosis: GWAS and Potential of Genomic Prediction Explored in Farmed European Sea Bass ( Dicentrarchus labrax). Front Genet 2022; 13:804584. [PMID: 35401661 PMCID: PMC8992836 DOI: 10.3389/fgene.2022.804584] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
Viral nervous necrosis (VNN) is an infectious disease caused by the red-spotted grouper nervous necrosis virus (RGNNV) in European sea bass and is considered a serious concern for the aquaculture industry with fry and juveniles being highly susceptible. To understand the genetic basis for resistance against VNN, a survival phenotype through the challenge test against the RGNNV was recorded in populations from multiple year classes (YC2016 and YC2017). A total of 4,851 individuals from 181 families were tested, and a subset (n∼1,535) belonging to 122 families was genotyped using a ∼57K Affymetrix Axiom array. The survival against the RGNNV showed low to moderate heritability with observed scale estimates of 0.18 and 0.25 obtained using pedigree vs. genomic information, respectively. The genome-wide association analysis showed a strong signal of quantitative trait loci (QTL) at LG12 which explained ∼33% of the genetic variance. The QTL region contained multiple genes (ITPK1, PLK4, HSPA4L, REEP1, CHMP2, MRPL35, and SCUBE) with HSPA4L and/or REEP1 genes being highly relevant with a likely effect on host response in managing disease-associated symptoms. The results on the accuracy of predicting breeding values presented 20–43% advantage in accuracy using genomic over pedigree-based information which varied across model types and applied validation schemes.
Collapse
Affiliation(s)
- Sergio Vela-Avitúa
- Benchmark Genetics Norway AS (formerly Akvaforsk Genetics Center AS), Sunndalsøra, Norway
| | - Ingunn Thorland
- Benchmark Genetics Norway AS (formerly Akvaforsk Genetics Center AS), Sunndalsøra, Norway
| | - Vasileios Bakopoulos
- Laboratory of Ichthyology, Aquaculture and Diseases of Aquatic Animals, Department of Marine Sciences, University of The Aegean, Mytilene, Greece
| | | | | | | | | | - Bruno Guinand
- CNRS, IRD, EPHE, ISEM, Université de Montpellier, Montpellier, France
| | - Costas S Tsigenopoulos
- Biotechnology and Aquaculture (IMBBC), Hellenic Centre for Marine Research (HCMR), Institute of Marine Biology, Heraklion, Greece
| | | |
Collapse
|
12
|
Liu Y, Cheng J, Xia Y, Li X, Liu Y, Liu PF. Response mechanism of gut microbiome and metabolism of European seabass (Dicentrarchus labrax) to temperature stress. Sci Total Environ 2022; 813:151786. [PMID: 34942265 DOI: 10.1016/j.scitotenv.2021.151786] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 11/08/2021] [Accepted: 11/14/2021] [Indexed: 05/10/2023]
Abstract
In animals, the gut microbiome is vital to growth, and changes in the composition of these microbial communities may affect growth and adaptability to the environment. Temperature is another important factor that influences the healthy growth of animals. To date, the mechanism by which juvenile European seabass (Dicentrarchus labrax) and their symbiotic flora adapt to changes in environmental temperature is not well understood. Therefore, we evaluated the effect of temperature on the gut microbiota and metabolism of European seabass juveniles. We used 16S rRNA gene amplicon sequencing and non-targeted liquid chromatography with tandem mass spectrometry (LC-MS/MS)-based metabolomics to study the gut microbes of European seabass after 60 days of rearing of water temperature at 10 °C (T1), 15 °C (T2) and 20 °C (T3). At the phylum level, the abundance of the gut microbiota did not differ significantly among the three groups after 60 days of cultivation. At the genus level, however, the abundance of Faecalibacterium, Filifactor, Butyricicoccus, and Erysipelotrichaceae UCG-006 in the intestines differed significantly among the temperature groups. Compared with T2, the relative abundance of Filifactor in T1 was significantly increased, while Faecalibacterium was significantly decreased, while the relative abundance of Butyricicoccus and Erysipelotrichaceae UCG-006 in T3 was significantly increased. The LC-MS/MS analysis revealed 107 metabolites in the 10 °C group and 68 metabolites in the 20 °C group that differed significantly from those in the intestines of fish in the 15 °C control group. These metabolites are closely related to several metabolic pathways, including amino acid metabolism, glucose and lipid metabolism, and the tricarboxylic acid cycle. Correlation analysis of the Intestine microbiota, metabolic pathways, and metabolites identified metabolic pathways and metabolites that were strongly related to the observed significant differences in the microbiome among the temperature groups. These results show that temperature can induce significant changes in the gut microbiota and metabolism of European seabass juveniles, and that significant changes in metabolites may be mediated through the interaction of the microbiome and metabolic pathways.
Collapse
Affiliation(s)
- Yanyun Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China
| | - Jianxin Cheng
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Life Science, Liaoning Normal University, Dalian 116081, China
| | - Yuqing Xia
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; School of Marine Sciences, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Xiaohao Li
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China
| | - Ying Liu
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116023, China; Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China
| | - Peng-Fei Liu
- Key Laboratory of Environment Controlled Aquaculture (Dalian Ocean University) Ministry of Education, 116023, China; College of Marine Technology and Environment, Dalian Ocean University, Dalian 116023, China.
| |
Collapse
|
13
|
Ratcliffe FC, Garcia de Leaniz C, Consuegra S. MHC class I-α population differentiation in a commercial fish, the European sea bass (Dicentrarchus labrax). Anim Genet 2022; 53:340-351. [PMID: 35274334 PMCID: PMC9314080 DOI: 10.1111/age.13184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 01/13/2022] [Accepted: 02/20/2022] [Indexed: 01/29/2023]
Abstract
Identifying population structuring in highly fecund marine species with high dispersal rates is challenging, but critical for conservation and stock delimitation for fisheries management. European sea bass (Dicentrarchus labrax) is a commercial species of fisheries and aquaculture relevance whose stocks are declining in the North Atlantic, despite management measures to protect them and identifying their fine population structure is needed for managing their exploitation. As for other marine fishes, neutral genetic markers indicate that eastern Atlantic sea bass form a panmictic population and is currently managed as arbitrarily divided stocks. The genes of the major histocompatibility complex (MHC) are key components of the adaptive immune system and ideal candidates to assess fine structuring arising from local selective pressures. We used Illumina sequencing to characterise allelic composition and signatures of selection at the MHC class I-α region of six D. labrax populations across the Atlantic range. We found high allelic diversity driven by positive selection, corresponding to moderate supertype diversity, with 131 alleles clustering into four to eight supertypes, depending on the Bayesian information criterion threshold applied, and a mean number of 13 alleles per individual. Alleles could not be assigned to particular loci, but private alleles allowed us to detect regional genetic structuring not found previously using neutral markers. Our results suggest that MHC markers can be used to detect cryptic population structuring in marine species where neutral markers fail to identify differentiation. This is particularly critical for fisheries management, and of potential use for selective breeding or identifying escapes from sea farms.
Collapse
Affiliation(s)
- Frances C Ratcliffe
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| | | | - Sofia Consuegra
- Department of Biosciences, College of Science, Swansea University, Swansea, UK
| |
Collapse
|
14
|
Difford GF, Díaz-Gil C, Sánchez-Moya A, Aslam ML, Horn SS, Ruyter B, Herlin M, Lopez M, Sonesson AK. Genomic and Phenotypic Agreement Defines the Use of Microwave Dielectric Spectroscopy for Recording Muscle Lipid Content in European Seabass ( Dicentrarchus labrax). Front Genet 2021; 12:671491. [PMID: 34527016 PMCID: PMC8435770 DOI: 10.3389/fgene.2021.671491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 08/06/2021] [Indexed: 11/13/2022] Open
Abstract
Recording the fillet lipid percentage in European seabass is crucial to control lipid deposition as a means toward improving production efficiency and product quality. The reference method for recording lipid content is solvent lipid extraction and is the most accurate and precise method available. However, it is costly, requires sacrificing the fish and grinding the fillet sample which limits the scope of applications, for example grading of fillets, recording live fish or selective breeding of fish with own phenotypes are all limited. We tested a rapid, cost effective and non-destructive handheld microwave dielectric spectrometer (namely the Distell fat meter) against the reference method by recording both methods on 313 European seabass (Dicentrarchus labrax). The total method agreement between the dielectric spectrometer and the reference method was assessed by Lin’s concordance correlation coefficient (CCC), which was low to moderate CCC = 0.36–0.63. We detected a significant underestimation in accuracy of lipid percentage 22–26% by the dielectric spectrometer and increased imprecision resulting in the coefficient of variation (CV) doubling for dielectric spectrometer CV = 40.7–46% as compared to the reference method 27–31%. Substantial genetic variation for fillet lipid percentage was found for both the reference method (h2 = 0.59) and dielectric spectroscopy (h2 = 0.38–0.58), demonstrating that selective breeding is a promising method for controlling fillet lipid content. Importantly, the genetic correlation (rg) between the dielectric spectrometer and the reference method was positive and close to unity (rg = 0.96), demonstrating the dielectric spectrometer captures practically all the genetic variation in the reference method. These findings form the basis of defining the scope of applications and experimental design for using dielectric spectroscopy for recording fillet lipid content in European seabass and validate its use for selective breeding.
Collapse
Affiliation(s)
| | | | - Albert Sánchez-Moya
- Department of Cell Biology, Physiology, and Immunology, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | | | | | | | | | | | | |
Collapse
|
15
|
Miccoli A, Buonocore F, Picchietti S, Scapigliati G. The sea bass Dicentrarchus labrax as a marine model species in immunology: Insights from basic and applied research. Aquaculture and Fisheries 2021. [DOI: 10.1016/j.aaf.2021.09.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|