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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.
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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
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Difford GF, Haugen JE, Aslam ML, Johansen LH, Breiland MW, Hillestad B, Baranski M, Boison S, Moghadam H, Jacq C. Variation in volatile organic compounds in Atlantic salmon mucus is associated with resistance to salmon lice infection. Sci Rep 2022; 12:4839. [PMID: 35318390 PMCID: PMC8940922 DOI: 10.1038/s41598-022-08872-z] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Accepted: 03/08/2022] [Indexed: 01/14/2023] Open
Abstract
Salmon lice are ectoparasites that threaten wild and farmed salmonids. Artificial selection of salmon for resistance to the infectious copepodid lice stage currently relies on in vivo challenge trials on thousands of salmon a year. We challenged 5750 salmon with salmon lice (Lepeophtheirus salmonis) from two distinct farmed strains of salmon in two separate trials. We found that volatile organic compounds (VOC), 1-penten-3-ol, 1-octen-3-ol and 6-methyl-5-hepten-2-one in the mucus of the salmon host after salmon lice infection, were significantly associated with lice infection numbers across a range of water temperatures (5 °C, 10 °C, 17 °C). Some VOCs (benzene, 1-octen-3-ol and 3,5,5-trimethyl-2-hexene) were significantly different between lines divergently selected for salmon lice resistance. In a combined population assessment, selected VOCs varied between families in the range of 47- 59% indicating a genetic component and were positively correlated to the salmon hosts estimated breeding values 0.59–0.74. Mucosal VOC phenotypes could supplement current breeding practices and have the potential to be a more direct and ethical proxy for salmon lice resistance provided they can be measured prior to lice infestation.
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Affiliation(s)
- G F Difford
- Breeding and Genetics Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, 1430, Ås, Norway.
| | - J-E Haugen
- Food and Health Nofima, Norwegian Institute for Food, Fisheries and Aquaculture Research, Osloveien 1, 1430, Ås, Norway
| | - M L Aslam
- Breeding and Genetics Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, 1430, Ås, Norway
| | - L H Johansen
- Fish Health Nofima, Norwegian Institute for Food, Fisheries and Aquaculture Research, Muninbakken 9, 9019, Tromsø, Norway
| | - M W Breiland
- Fish Health Nofima, Norwegian Institute for Food, Fisheries and Aquaculture Research, Muninbakken 9, 9019, Tromsø, Norway
| | - B Hillestad
- Benchmark Genetics Norway AS, Sandviksboder 3A, Bergen, Norway.,Viking Aqua AS, Sandevegen 631, 5997, Ånneland, Norway
| | - M Baranski
- Mowi Genetics AS, Sandviksboder 77AB, Bergen, Norway
| | - S Boison
- Mowi Genetics AS, Sandviksboder 77AB, Bergen, Norway
| | - H Moghadam
- Benchmark Genetics Norway AS, Sandviksboder 3A, Bergen, Norway
| | - C Jacq
- Breeding and Genetics Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, 1430, Ås, Norway.,Blue Analytics AS, Kong Christian Frederiks plass 3, 5006, Bergen, Norway
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Saura M, Caballero A, Santiago E, Fernández A, Morales-González E, Fernández J, Cabaleiro S, Millán A, Martínez P, Palaiokostas C, Kocour M, Aslam ML, Houston RD, Prchal M, Bargelloni L, Tzokas K, Haffray P, Bruant JS, Villanueva B. Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes. Genet Sel Evol 2021; 53:85. [PMID: 34742227 PMCID: PMC8572424 DOI: 10.1186/s12711-021-00680-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 10/22/2021] [Indexed: 11/15/2022] Open
Abstract
Background The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. Methods Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. Results Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. Conclusions Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00680-9.
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Affiliation(s)
- María Saura
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain.
| | - Armando Caballero
- Centro de Investigación Mariña, Facultade de Bioloxía, Universidade de Vigo, 36310, Vigo, Spain
| | - Enrique Santiago
- Departamento de Biología Funcional, Universidad de Oviedo, C/ Julián Clavería s/n, 33006, Oviedo, Spain
| | - Almudena Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
| | | | - Jesús Fernández
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
| | - Santiago Cabaleiro
- CETGA, Cluster de Acuicultura de Galicia, Punta do Couso s/n, 15695, Aguiño-Ribeira, Spain
| | | | - Paulino Martínez
- Departament of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, 27002, Lugo, Spain
| | - Christos Palaiokostas
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Martin Kocour
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | | | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Martin Prchal
- South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Faculty of Fisheries and Protection of Waters, University of South Bohemia in České Budějovice, Zátiší 728/II, 389 25, Vodňany, Czech Republic
| | - Luca Bargelloni
- Universitá degli Studi di Padova, Via 8 Febbraio 1848, 2, 35122, Padova, PD, Italy
| | - Kostas Tzokas
- Andromeda Group SA, Leof. Lavriou 99, 190 02, Peania, Greece
| | - Pierrick Haffray
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
| | | | - Beatriz Villanueva
- Departamento de Mejora Genética Animal, INIA-CSIC, Ctra. de La Coruña, km 7.5, 28040, Madrid, Spain
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Peñaloza C, Manousaki T, Franch R, Tsakogiannis A, Sonesson AK, Aslam ML, Allal F, Bargelloni L, Houston RD, Tsigenopoulos CS. Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata). Genomics 2021; 113:2096-2107. [PMID: 33933591 PMCID: PMC8276775 DOI: 10.1016/j.ygeno.2021.04.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/30/2021] [Accepted: 04/27/2021] [Indexed: 12/23/2022]
Abstract
SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both selective breeding and population genomic research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding programmes increasingly underpin stock supply for this industry, genomic selection is not yet widespread. Genomic selection has major potential to expedite genetic gain, particularly for traits practically impossible to measure on selection candidates, such as disease resistance and fillet characteristics. The aim of our study was to design a combined-species 60 K SNP array for European seabass and gilthead seabream, and to test its performance on farmed and wild populations from numerous locations throughout the species range. To achieve this, high coverage Illumina whole-genome sequencing of pooled samples was performed for 24 populations of European seabass and 27 populations of gilthead seabream. This resulted in a database of ~20 million SNPs per species, which were then filtered to identify high-quality variants and create the final set for the development of the ‘MedFish’ SNP array. The array was then tested by genotyping a subset of the discovery populations, highlighting a high conversion rate to functioning polymorphic assays on the array (92% in seabass; 89% in seabream) and repeatability (99.4–99.7%). The platform interrogates ~30 K markers in each species, includes features such as SNPs previously shown to be associated with performance traits, and is enriched for SNPs predicted to have high functional effects on proteins. The array was demonstrated to be effective at detecting population structure across a wide range of fish populations from diverse geographical origins, and to examine the extent of haplotype sharing among Mediterranean farmed fish populations. In conclusion, the new MedFish array enables efficient and accurate high-throughput genotyping for genome-wide distributed SNPs for each fish species, and will facilitate stock management, population genomics approaches, and acceleration of selective breeding through genomic selection. Α 60 K SNP array (MedFish) was designed for European seabass and gilthead seabream from wild and domesticated populations. The array exhibited a high conversion rate (92% in seabass; 89% in seabream) and repeatability (99.4 and 99.7%). The MedFish array is expected to facilitate stock management and acceleration of selective breeding via genomic selection.
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Affiliation(s)
- C Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - T Manousaki
- Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece
| | - R Franch
- Padova University, Via Ugo Bassi, 58yB, I-35131 Padova, Italy
| | - A Tsakogiannis
- Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece
| | - A K Sonesson
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, PO Box 210, N-1432 Ås, Norway
| | - M L Aslam
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, PO Box 210, N-1432 Ås, Norway
| | - F Allal
- MARBEC, University of Montpellier, Ifremer, CNRS, IRD, 34250 Palavas-les-Flots, France
| | - L Bargelloni
- Padova University, Via Ugo Bassi, 58yB, I-35131 Padova, Italy
| | - R D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK.
| | - C S Tsigenopoulos
- Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece.
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5
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Robinson NA, Krasnov A, Burgerhout E, Johnsen H, Moghadam HK, Hillestad B, Aslam ML, Baranski M, Boison SA. Response of the Salmon Heart Transcriptome to Pancreas Disease: Differences Between High- and Low-Ranking Families for Resistance. Sci Rep 2020; 10:868. [PMID: 31964968 PMCID: PMC6972705 DOI: 10.1038/s41598-020-57786-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2019] [Accepted: 01/07/2020] [Indexed: 12/30/2022] Open
Abstract
Pancreas disease caused by salmonid alphaviruses leads to severe losses in Atlantic salmon aquaculture. The aim of our study was to gain a better understanding of the biological differences between salmon with high and low genomic breeding values (H-gEBV and L-gEBV respectively) for pancreas disease resistance. Fish from H- and L-gEBV families were challenged by intraperitoneal injection of salmonid alphavirus or co-habitation with infected fish. Mortality was higher with co-habitation than injection, and for L- than H-gEBV. Heart for RNA-seq and histopathology was collected before challenge and at four- and ten-weeks post-challenge. Heart damage was less severe in injection-challenged H- than L-gEBV fish at week 4. Viral load was lower in H- than L-gEBV salmon after co-habitant challenge. Gene expression differences between H- and L-gEBV manifested before challenge, peaked at week 4, and moderated by week 10. At week 4, H-gEBV salmon showed lower expression of innate antiviral defence genes, stimulation of B- and T-cell immune function, and weaker stress responses. Retarded resolution of the disease explains the higher expression of immune genes in L-gEBV at week 10. Results suggest earlier mobilization of acquired immunity better protects H-gEBV salmon by accelerating clearance of the virus and resolution of the disease.
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Affiliation(s)
- N A Robinson
- Breeding and Genetics, Nofima, Ås, 1430, Norway. .,Sustainable Aquaculture Laboratory- Temperate and Tropical (SALTT), School of BioSciences, The University of Melbourne, Parkville, 3010, Australia.
| | - A Krasnov
- Breeding and Genetics, Nofima, Ås, 1430, Norway
| | | | - H Johnsen
- Breeding and Genetics, Nofima, Ås, 1430, Norway
| | | | | | - M L Aslam
- Breeding and Genetics, Nofima, Ås, 1430, Norway
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Pauletto M, Manousaki T, Ferraresso S, Babbucci M, Tsakogiannis A, Louro B, Vitulo N, Quoc VH, Carraro R, Bertotto D, Franch R, Maroso F, Aslam ML, Sonesson AK, Simionati B, Malacrida G, Cestaro A, Caberlotto S, Sarropoulou E, Mylonas CC, Power DM, Patarnello T, Canario AVM, Tsigenopoulos C, Bargelloni L. Genomic analysis of Sparus aurata reveals the evolutionary dynamics of sex-biased genes in a sequential hermaphrodite fish. Commun Biol 2018; 1:119. [PMID: 30271999 PMCID: PMC6123679 DOI: 10.1038/s42003-018-0122-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 07/27/2018] [Indexed: 12/13/2022] Open
Abstract
Sexual dimorphism is a fascinating subject in evolutionary biology and mostly results from sex-biased expression of genes, which have been shown to evolve faster in gonochoristic species. We report here genome and sex-specific transcriptome sequencing of Sparus aurata, a sequential hermaphrodite fish. Evolutionary comparative analysis reveals that sex-biased genes in S. aurata are similar in number and function, but evolved following strikingly divergent patterns compared with gonochoristic species, showing overall slower rates because of stronger functional constraints. Fast evolution is observed only for highly ovary-biased genes due to female-specific patterns of selection that are related to the peculiar reproduction mode of S. aurata, first maturing as male, then as female. To our knowledge, these findings represent the first genome-wide analysis on sex-biased loci in a hermaphrodite vertebrate species, demonstrating how having two sexes in the same individual profoundly affects the fate of a large set of evolutionarily relevant genes.
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Affiliation(s)
- Marianna Pauletto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Tereza Manousaki
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Alexandros Tsakogiannis
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Bruno Louro
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134, Verona, Italy
| | - Viet Ha Quoc
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Roberta Carraro
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Daniela Bertotto
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Rafaella Franch
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Francesco Maroso
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | | | | | | | | | - Alessandro Cestaro
- Research and Innovation Centre, Fondazione Edmund Mach, via Edmund Mach 1, 38010, San Michele all'Adige, Trento, Italy
| | - Stefano Caberlotto
- Valle Cà Zuliani Società Agricola Srl, Via Timavo 76, 34074, Monfalcone, Gorizia, Italy
| | - Elena Sarropoulou
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Costantinos C Mylonas
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Deborah M Power
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy
| | - Adelino V M Canario
- CCMAR-Centro de Ciências do Mar, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Costas Tsigenopoulos
- Institute of Marine Biology, Biotechnology and Aquaculture ó, Hellenic Centre for Marine Research, Thalassocosmos, Former US Base at Gournes, 715 00, Heraklion, Greece
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, viale dell'Università, 16 35020, Legnaro, Italy.
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Aslam ML, Carraro R, Bestin A, Cariou S, Sonesson AK, Bruant JS, Haffray P, Bargelloni L, Meuwissen THE. Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing. BMC Genet 2018; 19:43. [PMID: 29996763 PMCID: PMC6042378 DOI: 10.1186/s12863-018-0631-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [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: 12/01/2017] [Accepted: 06/25/2018] [Indexed: 12/11/2022] Open
Abstract
Background Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90–100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males). This group of 1187 individuals represented 177 full-sib families with 1–49 sibs per family, which were challenged with virulent Phdp for a duration of 18 days, and mortalities were recorded within this duration. Tissue samples were collected from the parents and the recorded offspring for DNA extraction, library preparation using 2b-RAD and genotyping by sequencing. Genotypic data was used to develop a linkage map, genome wide association analysis and for the estimation of breeding values. Results The analysis of genetic variation for resistance against Phdp revealed moderate genomic heritability with estimates of ~ 0.32. A genome-wide association analysis revealed a quantitative trait locus (QTL) including 11 SNPs at linkage group 17 presenting significant association to the trait with p-value crossing genome-wide Bonferroni corrected threshold P ≤ 2.22e-06. The proportion total genetic variance explained by the single top most significant SNP was ranging from 13.28–16.14% depending on the method used to compute the variance. The accuracies of predicting breeding values obtained using genomic vs. pedigree information displayed 19–24% increase when using genomic information. Conclusion The current study demonstrates that SNPs-based genotyping of a sea bream population with 2b-RAD approach is effective at capturing the genetic variation for resistance against Phdp. Prediction accuracies obtained using genomic information were significantly higher than the accuracies obtained using pedigree information which highlights the importance and potential of genomic selection in commercial breeding programs. Electronic supplementary material The online version of this article (10.1186/s12863-018-0631-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Anastasia Bestin
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
| | | | | | | | - Pierrick Haffray
- SYSAAF, French poultry and aquaculture breeders, 35042, Rennes Cedex, France
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Nowell RW, Elsworth B, Oostra V, Zwaan BJ, Wheat CW, Saastamoinen M, Saccheri IJ, van’t Hof AE, Wasik BR, Connahs H, Aslam ML, Kumar S, Challis RJ, Monteiro A, Brakefield PM, Blaxter M. A high-coverage draft genome of the mycalesine butterfly Bicyclus anynana. Gigascience 2017; 6:1-7. [PMID: 28486658 PMCID: PMC5493746 DOI: 10.1093/gigascience/gix035] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 04/28/2017] [Accepted: 05/07/2017] [Indexed: 12/24/2022] Open
Abstract
The mycalesine butterfly Bicyclus anynana, the "Squinting bush brown," is a model organism in the study of lepidopteran ecology, development, and evolution. Here, we present a draft genome sequence for B. anynana to serve as a genomics resource for current and future studies of this important model species. Seven libraries with insert sizes ranging from 350 bp to 20 kb were constructed using DNA from an inbred female and sequenced using both Illumina and PacBio technology; 128 Gb of raw Illumina data was filtered to 124 Gb and assembled to a final size of 475 Mb (∼×260 assembly coverage). Contigs were scaffolded using mate-pair, transcriptome, and PacBio data into 10 800 sequences with an N50 of 638 kb (longest scaffold 5 Mb). The genome is comprised of 26% repetitive elements and encodes a total of 22 642 predicted protein-coding genes. Recovery of a BUSCO set of core metazoan genes was almost complete (98%). Overall, these metrics compare well with other recently published lepidopteran genomes. We report a high-quality draft genome sequence for Bicyclus anynana. The genome assembly and annotated gene models are available at LepBase (http://ensembl.lepbase.org/index.html).
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Affiliation(s)
- Reuben W. Nowell
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Ben Elsworth
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Vicencio Oostra
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Bas J. Zwaan
- Laboratory of Genetics, Wageningen University, Wageningen, the Netherlands
| | | | - Marjo Saastamoinen
- Metapopulation Research Centre, Department of Biosciences, University of Helsinki, Helsinki, Finland
| | - Ilik J. Saccheri
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Arjen E. van’t Hof
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK
| | - Bethany R. Wasik
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
| | - Heidi Connahs
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Muhammad L. Aslam
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Sujai Kumar
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Richard J. Challis
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Antónia Monteiro
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA
- Department of Biological Sciences, National University of Singapore, Singapore 117543
- Yale-NUS College, Singapore 138609
| | | | - Mark Blaxter
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3FL, UK
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Aslam ML, Bastiaansen JW, Megens HJ, Crooijmans RP, Nasreen F, Blomberg LA, Van Tassell CP, Sonstegard TS, Schroeder SG, Groenen MA, Long JA. Genome-wide candidate regions for selective sweeps revealed through massive parallel sequencing of DNA across ten turkey populations. BMC Genet 2014; 15:117. [PMID: 25421611 PMCID: PMC4253982 DOI: 10.1186/s12863-014-0117-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 10/22/2014] [Indexed: 12/02/2022] Open
Abstract
Background The domestic turkey (Meleagris gallopavo) is an important agricultural species that is largely used as a meat-type bird. Characterizing genetic variation in populations of domesticated species and associating these variation patterns with the evolution, domestication, and selective breeding is critical for understanding the dynamics of genomic change in these species. Intense selective breeding and population bottlenecks are expected to leave signatures in the genome of domesticated species, such as unusually low nucleotide diversity or the presence of exceptionally extended haplotype homozygosity. These patterns of variation in selected populations are highly useful to not only understand the consequences of selective breeding and population dynamics, but also to provide insights into biological mechanisms that may affect physiological processes important to bring changes in phenotype of interest. Results We observed 54 genomic regions in heritage and commercial turkey populations on 14 different chromosomes that showed statistically significant (P < 0.05) reduction in genomic variation indicating candidate selective sweeps. Areas with evidence of selective sweeps varied from 1.5 Mb to 13.8 Mb in length. Out of these 54 sweeps, 23 overlapped at least partially between two or more populations. Overlapping sweeps were found on 13 different chromosomes. The remaining 31 sweeps were population-specific and were observed on 12 different chromosomes, with 26 of these regions present only in commercial populations. Genes that are known to affect growth were enriched in the sweep regions. Conclusion The turkey genome showed large sweep regions. The relatively high number of sweep regions in commercial turkey populations compared to heritage varieties and the enrichment of genes important to growth in these regions, suggest that these sweeps are the result of intense selection in these commercial lines, moving specific haplotypes towards fixation. Electronic supplementary material The online version of this article (doi:10.1186/s12863-014-0117-4) contains supplementary material, which is available to authorized users.
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Aslam ML, Bastiaansen JWM, Elferink MG, Megens HJ, Crooijmans RPMA, Blomberg LA, Fleischer RC, Van Tassell CP, Sonstegard TS, Schroeder SG, Groenen MAM, Long JA. Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo). BMC Genomics 2012; 13:391. [PMID: 22891612 PMCID: PMC3496629 DOI: 10.1186/1471-2164-13-391] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/09/2012] [Indexed: 11/23/2022] Open
Abstract
Background The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Results Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. Conclusion The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.
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Affiliation(s)
- Muhammad L Aslam
- Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708WD Wageningen, The Netherlands.
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Aslam ML, Bastiaansen JWM, Crooijmans RPMA, Vereijken A, Groenen MAM. Whole genome QTL mapping for growth, meat quality and breast meat yield traits in turkey. BMC Genet 2011; 12:61. [PMID: 21745371 PMCID: PMC3142527 DOI: 10.1186/1471-2156-12-61] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2011] [Accepted: 07/11/2011] [Indexed: 12/02/2022] Open
Abstract
Background The turkey (Meleagris gallopavo) is an important agricultural species and is the second largest contributor to the world's poultry meat production. Demand of turkey meat is increasing very rapidly. Genetic markers linked to genes affecting quantitative traits can increase the selection response of animal breeding programs. The use of these molecular markers for the identification of quantitative trait loci, and subsequently fine-mapping of quantitative trait loci regions, allows for pinpointing of genes that underlie such economically important traits. Results The quantitative trait loci analyses of the growth curve, body weight, breast yield and the meat quality traits showed putative quantitative trait loci on 21 of the 27 turkey chromosomes covered by the linkage map. Forty-five quantitative trait loci were detected across all traits and these were found in 29 different regions on 21 chromosomes. Out of the 45 quantitative trait loci, twelve showed significant (p < 0.01) evidence of linkage while the remaining 33 showed suggestive evidence (p < 0.05) of linkage with different growth, growth curve, meat quality and breast yield traits. Conclusion A large number of quantitative trait loci were detected across the turkey genome, which affected growth, breast yield and meat quality traits. Pleiotropic effects or close linkages between quantitative trait loci were suggested for several of the chromosomal regions. The comparative analysis regarding the location of quantitative trait loci on different turkey, and on the syntenic chicken chromosomes, along with their phenotypic associations, revealed signs of functional conservation between these species.
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Affiliation(s)
- Muhammad L Aslam
- Animal Breeding and Genomics Centre, Wageningen University, 6709PG, Wageningen, The Netherlands.
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12
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Aslam ML, Bastiaansen JW, Crooijmans RP, Ducro BJ, Vereijken A, Groenen MA. Genetic variances, heritabilities and maternal effects on body weight, breast meat yield, meat quality traits and the shape of the growth curve in turkey birds. BMC Genet 2011; 12:14. [PMID: 21266032 PMCID: PMC3039623 DOI: 10.1186/1471-2156-12-14] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2010] [Accepted: 01/25/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Turkey is an important agricultural species and is largely used as a meat bird. In 2004, turkey represented 6.5% of the world poultry meat production. The world-wide turkey population has rapidly grown due to increased commercial farming. Due to the high demand for turkey meat from both consumers and industry global turkey stocks increased from 100 million in 1970 to over 276 million in 2004. This rapidly increasing importance of turkeys was a reason to design this study for the estimation of genetic parameters that control body weight, body composition, meat quality traits and parameters that shape the growth curve in turkey birds. RESULTS The average heritability estimate for body weight traits was 0.38, except for early weights that were strongly affected by maternal effects. This study showed that body weight traits, upper asymptote (a growth curve trait), percent breast meat and redness of meat had high heritability whereas heritabilities of breast length, breast width, percent drip loss, ultimate pH, lightness and yellowness of meat were medium to low. We found high positive genetic and phenotypic correlations between body weight, upper asymptote, most breast meat yield traits and percent drip loss but percent drip loss was found strongly negatively correlated with ultimate pH. Percent breast meat, however, showed genetic correlations close to zero with body weight traits and upper asymptote. CONCLUSION The results of this analysis and the growth curve from the studied population of turkey birds suggest that the turkey birds could be selected for breeding between 60 and 80 days of age in order to improve overall production and the production of desirable cuts of meat. The continuous selection of birds within this age range could promote high growth rates but specific attention to meat quality would be needed to avoid a negative impact on the quality of meat.
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Affiliation(s)
- Muhammad L Aslam
- Animal Breeding and Genomics Centre, Wageningen University, 6709PG, Wageningen, the Netherlands.
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Aslam ML, Bastiaansen JWM, Crooijmans RPMA, Vereijken A, Megens HJ, Groenen MAM. A SNP based linkage map of the turkey genome reveals multiple intrachromosomal rearrangements between the turkey and chicken genomes. BMC Genomics 2010; 11:647. [PMID: 21092123 PMCID: PMC3091770 DOI: 10.1186/1471-2164-11-647] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 11/20/2010] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND The turkey (Meleagris gallopavo) is an important agricultural species that is the second largest contributor to the world's poultry meat production. The genomic resources of turkey provide turkey breeders with tools needed for the genetic improvement of commercial breeds of turkey for economically important traits. A linkage map of turkey is essential not only for the mapping of quantitative trait loci, but also as a framework to enable the assignment of sequence contigs to specific chromosomes. Comparative genomics with chicken provides insight into mechanisms of genome evolution and helps in identifying rare genomic events such as genomic rearrangements and duplications/deletions. RESULTS Eighteen full sib families, comprising 1008 (35 F1 and 973 F2) birds, were genotyped for 775 single nucleotide polymorphisms (SNPs). Of the 775 SNPs, 570 were informative and used to construct a linkage map in turkey. The final map contains 531 markers in 28 linkage groups. The total genetic distance covered by these linkage groups is 2,324 centimorgans (cM) with the largest linkage group (81 loci) measuring 326 cM. Average marker interval for all markers across the 28 linkage groups is 4.6 cM. Comparative mapping of turkey and chicken revealed two inter-, and 57 intrachromosomal rearrangements between these two species. CONCLUSION Our turkey genetic map of 531 markers reveals a genome length of 2,324 cM. Our linkage map provides an improvement of previously published maps because of the more even distribution of the markers and because the map is completely based on SNP markers enabling easier and faster genotyping assays than the microsatellitemarkers used in previous linkage maps. Turkey and chicken are shown to have a highly conserved genomic structure with a relatively low number of inter-, and intrachromosomal rearrangements.
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Affiliation(s)
- Muhammad L Aslam
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
| | - John WM Bastiaansen
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
| | - Richard PMA Crooijmans
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
| | - Addie Vereijken
- Hendrix Genetics, Research & Technology Centre, 5830 AC, Boxmeer, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
| | - Martien AM Groenen
- Animal Breeding and Genomics Centre, Wageningen University,6709PG, Wageningen, The Netherlands
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