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Jung H, Ventura T, Chung JS, Kim WJ, Nam BH, Kong HJ, Kim YO, Jeon MS, Eyun SI. Twelve quick steps for genome assembly and annotation in the classroom. PLoS Comput Biol 2020; 16:e1008325. [PMID: 33180771 PMCID: PMC7660529 DOI: 10.1371/journal.pcbi.1008325] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Eukaryotic genome sequencing and de novo assembly, once the exclusive domain of well-funded international consortia, have become increasingly affordable, thus fitting the budgets of individual research groups. Third-generation long-read DNA sequencing technologies are increasingly used, providing extensive genomic toolkits that were once reserved for a few select model organisms. Generating high-quality genome assemblies and annotations for many aquatic species still presents significant challenges due to their large genome sizes, complexity, and high chromosome numbers. Indeed, selecting the most appropriate sequencing and software platforms and annotation pipelines for a new genome project can be daunting because tools often only work in limited contexts. In genomics, generating a high-quality genome assembly/annotation has become an indispensable tool for better understanding the biology of any species. Herein, we state 12 steps to help researchers get started in genome projects by presenting guidelines that are broadly applicable (to any species), sustainable over time, and cover all aspects of genome assembly and annotation projects from start to finish. We review some commonly used approaches, including practical methods to extract high-quality DNA and choices for the best sequencing platforms and library preparations. In addition, we discuss the range of potential bioinformatics pipelines, including structural and functional annotations (e.g., transposable elements and repetitive sequences). This paper also includes information on how to build a wide community for a genome project, the importance of data management, and how to make the data and results Findable, Accessible, Interoperable, and Reusable (FAIR) by submitting them to a public repository and sharing them with the research community.
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Affiliation(s)
- Hyungtaek Jung
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, Australia
- Centre for Agriculture and Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Tomer Ventura
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - J. Sook Chung
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, United States of America
| | - Woo-Jin Kim
- Genetics and Breeding Research Center, National Institute of Fisheries Science, Geoje, Korea
| | - Bo-Hye Nam
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Hee Jeong Kong
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Young-Ok Kim
- Biotechnology Research Division, National Institute of Fisheries Science, Busan, Korea
| | - Min-Seung Jeon
- Department of Life Science, Chung-Ang University, Seoul, Korea
| | - Seong-il Eyun
- Department of Life Science, Chung-Ang University, Seoul, Korea
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Gratacap RL, Jin YH, Mantsopoulou M, Houston RD. Efficient Genome Editing in Multiple Salmonid Cell Lines Using Ribonucleoprotein Complexes. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:717-724. [PMID: 32946000 PMCID: PMC7520412 DOI: 10.1007/s10126-020-09995-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/31/2020] [Indexed: 06/11/2023]
Abstract
Infectious and parasitic diseases have major negative economic and animal welfare impacts on aquaculture of salmonid species. Improved knowledge of the functional basis of host response and genetic resistance to these diseases is key to developing preventative and treatment options. Cell lines provide valuable models to study infectious diseases in salmonids, and genome editing using CRISPR/Cas systems provides an exciting avenue to evaluate the function of specific genes in those systems. While CRISPR/Cas editing has been successfully performed in a Chinook salmon cell line (CHSE-214), there are no reports to date of editing of cell lines derived from the most commercially relevant salmonid species Atlantic salmon and rainbow trout, which are difficult to transduce and therefore edit using lentivirus-mediated methods. In the current study, a method of genome editing of salmonid cell lines using ribonucleoprotein (RNP) complexes was optimised and tested in the most commonly used salmonid fish cell lines: Atlantic salmon (SHK-1 and ASK cell lines), rainbow trout (RTG-2) and Chinook salmon (CHSE-214). Electroporation of RNP based on either Cas9 or Cas12a was efficient at targeted editing of all the tested lines (typically > 90% cells edited), and the choice of enzyme expands the number of potential target sites for editing within the genomes of these species. These optimised protocols will facilitate functional genetic studies in salmonid cell lines, which are widely used as model systems for infectious diseases in aquaculture.
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Affiliation(s)
- Remi L Gratacap
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Marina Mantsopoulou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, EH25 9RG, UK.
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Identification of a Growth-Associated Single Nucleotide Polymorphism (SNP) in Cyclin C of the Giant Tiger Shrimp Penaeus monodon. Biochem Genet 2020; 59:114-133. [PMID: 32780225 DOI: 10.1007/s10528-020-09993-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 07/31/2020] [Indexed: 10/23/2022]
Abstract
The full-length cDNA of cyclin C of the giant tiger shrimp Penaeus monodon (PmCyC) was isolated by RACE-PCR. It was 1443 bp in length containing an open reading frame (ORF) of 804 bp and 267 deduced amino acids. Tissue distribution analysis indicated that PmCyC was more abundantly expressed in ovaries and testes than other tissues of female and male juveniles (P < 0.05). A pair of primers was designed, and an amplification product of 403 bp containing an intron of 123 bp was obtained. Polymorphism of amplified PmCyC gene segments of the 5th (3-month-old G5, N = 30) and 7th (5-month-old G7, N = 18) generations of domesticated juveniles was analyzed. Four conserved SNPs (T>C134, T>C188, G>A379, and T>C382) were found within the examined sequences. A TaqMan genotyping assay was developed for detection of a T>C134 SNP. Association analysis indicated that this SNP displayed significant association with body weight (P < 4.2e-10) and total length (P < 2e-09) of the examined G7 P. monodon (N = 419) with an allele substitution effect of 5.02 ± 0.78 g and 1.41 ± 0.19 cm, respectively. Juveniles with C/C134 (22.80 ± 2.51 g and 12.97 ± 0.53 cm, N = 19) and T/C134 (20.41 ± 0.93 g and 12.77 ± 0.21 cm, N = 129) genotypes exhibited a significantly greater average body weight and total length than those with a T/T134 genotype (14.72 ± 0.53 g and 11.37 ± 0.13 cm, N = 271) (P < 0.05).
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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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Development and Validation of an Open Access SNP Array for Nile Tilapia ( Oreochromis niloticus). G3-GENES GENOMES GENETICS 2020; 10:2777-2785. [PMID: 32532799 PMCID: PMC7407453 DOI: 10.1534/g3.120.401343] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tilapia are among the most important farmed fish species worldwide, and are fundamental for the food security of many developing countries. Several genetically improved Nile tilapia (Oreochromis niloticus) strains exist, such as the iconic Genetically Improved Farmed Tilapia (GIFT), and breeding programs typically follow classical pedigree-based selection. The use of genome-wide single-nucleotide polymorphism (SNP) data can enable an understanding of the genetic architecture of economically important traits and the acceleration of genetic gain via genomic selection. Due to the global importance and diversity of Nile tilapia, an open access SNP array would be beneficial for aquaculture research and production. In the current study, a ∼65K SNP array was designed based on SNPs discovered from whole-genome sequence data from a GIFT breeding nucleus population and the overlap with SNP datasets from wild fish populations and several other farmed Nile tilapia strains. The SNP array was applied to clearly distinguish between different tilapia populations across Asia and Africa, with at least ∼30,000 SNPs segregating in each of the diverse population samples tested. It is anticipated that this SNP array will be an enabling tool for population genetics and tilapia breeding research, facilitating consistency and comparison of results across studies.
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Gratacap RL, Regan T, Dehler CE, Martin SAM, Boudinot P, Collet B, Houston RD. Efficient CRISPR/Cas9 genome editing in a salmonid fish cell line using a lentivirus delivery system. BMC Biotechnol 2020; 20:35. [PMID: 32576161 PMCID: PMC7310381 DOI: 10.1186/s12896-020-00626-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 06/10/2020] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Genome editing is transforming bioscience research, but its application to non-model organisms, such as farmed animal species, requires optimisation. Salmonids are the most important aquaculture species by value, and improving genetic resistance to infectious disease is a major goal. However, use of genome editing to evaluate putative disease resistance genes in cell lines, and the use of genome-wide CRISPR screens is currently limited by a lack of available tools and techniques. RESULTS In the current study, we developed an optimised protocol using lentivirus transduction for efficient integration of constructs into the genome of a Chinook salmon (Oncorhynchus tshwaytcha) cell line (CHSE-214). As proof-of-principle, two target genes were edited with high efficiency in an EGFP-Cas9 stable CHSE cell line; specifically, the exogenous, integrated EGFP and the endogenous RIG-I locus. Finally, the effective use of antibiotic selection to enrich the successfully edited targeted population was demonstrated. CONCLUSIONS The optimised lentiviral-mediated CRISPR method reported here increases possibilities for efficient genome editing in salmonid cells, in particular for future applications of genome-wide CRISPR screens for disease resistance.
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Affiliation(s)
- Remi L Gratacap
- The Roslin Institute, University of Edinburgh, Easter Bush campus, Midlothian, UK.
| | - Tim Regan
- The Roslin Institute, University of Edinburgh, Easter Bush campus, Midlothian, UK
| | - Carola E Dehler
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
| | - Samuel A M Martin
- Institute of Biological and Environmental Sciences, University of Aberdeen, Aberdeen, UK
| | - Pierre Boudinot
- Virologie et Immunologie Moleculaires, Institut National de Recherche Agronomique (INRA), Universite Paris-Saclay, Jouy-en-Josas, France
| | - Bertrand Collet
- Virologie et Immunologie Moleculaires, Institut National de Recherche Agronomique (INRA), Universite Paris-Saclay, Jouy-en-Josas, France
| | - Ross D Houston
- The Roslin Institute, University of Edinburgh, Easter Bush campus, Midlothian, UK.
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Perry WB, Lindsay E, Payne CJ, Brodie C, Kazlauskaite R. The role of the gut microbiome in sustainable teleost aquaculture. Proc Biol Sci 2020; 287:20200184. [PMID: 32372688 PMCID: PMC7282919 DOI: 10.1098/rspb.2020.0184] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
As the most diverse vertebrate group and a major component of a growing global aquaculture industry, teleosts continue to attract significant scientific attention. The growth in global aquaculture, driven by declines in wild stocks, has provided additional empirical demand, and thus opportunities, to explore teleost diversity. Among key developments is the recent growth in microbiome exploration, facilitated by advances in high-throughput sequencing technologies. Here, we consider studies on teleost gut microbiomes in the context of sustainable aquaculture, which we have discussed in four themes: diet, immunity, artificial selection and closed-loop systems. We demonstrate the influence aquaculture has had on gut microbiome research, while also providing a road map for the main deterministic forces that influence the gut microbiome, with topical applications to aquaculture. Functional significance is considered within an aquaculture context with reference to impacts on nutrition and immunity. Finally, we identify key knowledge gaps, both methodological and conceptual, and propose promising applications of gut microbiome manipulation to aquaculture, and future priorities in microbiome research. These include insect-based feeds, vaccination, mechanism of pro- and prebiotics, artificial selection on the hologenome, in-water bacteriophages in recirculating aquaculture systems (RAS), physiochemical properties of water and dysbiosis as a biomarker.
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Affiliation(s)
- William Bernard Perry
- Molecular Ecology and Fisheries Genetics Laboratory, Bangor University, Bangor, Gwynedd LL57 2UW, UK
| | - Elle Lindsay
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | | | - Christopher Brodie
- Ecosystems and Environment Research Centre, University of Salford, Salford M5 4WT, UK.,School of Biological and Environmental Sciences, Liverpool John Moores University, Liverpool L3 5UG, UK
| | - Raminta Kazlauskaite
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow G12 8QQ, UK
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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: 125] [Impact Index Per Article: 31.3] [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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Tan MH, Gan HM, Lee YP, Grandjean F, Croft LJ, Austin CM. A Giant Genome for a Giant Crayfish ( Cherax quadricarinatus) With Insights Into cox1 Pseudogenes in Decapod Genomes. Front Genet 2020; 11:201. [PMID: 32211032 PMCID: PMC7069360 DOI: 10.3389/fgene.2020.00201] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/20/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Mun Hua Tan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Han Ming Gan
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Yin Peng Lee
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Frederic Grandjean
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267 Equipe Ecologie Evolution Symbiose, Poitiers, France
| | - Laurence J. Croft
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
| | - Christopher M. Austin
- Centre of Integrative Ecology, School of Life and Environmental Sciences Deakin University, Geelong, VIC, Australia
- Deakin Genomics Centre, Deakin University, Geelong, VIC, Australia
- School of Science, Monash University Malaysia, Petaling Jaya, Malaysia
- Genomics Facility, Tropical Medicine and Biology Platform, Monash University Malaysia, Petaling Jaya, Malaysia
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Kriaridou C, Tsairidou S, Houston RD, Robledo D. Genomic Prediction Using Low Density Marker Panels in Aquaculture: Performance Across Species, Traits, and Genotyping Platforms. Front Genet 2020; 11:124. [PMID: 32174974 PMCID: PMC7056899 DOI: 10.3389/fgene.2020.00124] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/03/2020] [Indexed: 01/21/2023] Open
Abstract
Genomic selection increases the rate of genetic gain in breeding programs, which results in significant cumulative improvements in commercially important traits such as disease resistance. Genomic selection currently relies on collecting genome-wide genotype data accross a large number of individuals, which requires substantial economic investment. However, global aquaculture production predominantly occurs in small and medium sized enterprises for whom this technology can be prohibitively expensive. For genomic selection to benefit these aquaculture sectors, more cost-efficient genotyping is necessary. In this study the utility of low and medium density SNP panels (ranging from 100 to 9,000 SNPs) to accurately predict breeding values was tested and compared in four aquaculture datasets with different characteristics (species, genome size, genotyping platform, family number and size, total population size, and target trait). The traits show heritabilities between 0.19–0.49, and genomic prediction accuracies using the full density panel of 0.55–0.87. A consistent pattern of genomic prediction accuracy was observed across species with little or no accuracy reduction until SNP density was reduced below 1,000 SNPs (prediction accuracies of 0.44–0.75). Below this SNP density, heritability estimates and genomic prediction accuracies tended to be lower and more variable (93% of maximum accuracy achieved with 1,000 SNPs, 89% with 500 SNPs, and 70% with 100 SNPs). A notable drop in accuracy was observed between 200 SNP panels (0.44–0.75) and 100 SNP panels (0.39–0.66). Now that a multitude of studies have highlighted the benefits of genomic over pedigree-based prediction of breeding values in aquaculture species, the results of the current study highlight that these benefits can be achieved at lower SNP densities and at lower cost, raising the possibility of a broader application of genetic improvement in smaller and more fragmented aquaculture settings.
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Affiliation(s)
- Christina Kriaridou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Smaragda Tsairidou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
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61
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Tao M, Liang Y, Zhang Y, Wang F. A novel WSSV responsive plasma protein from Litopenaeus vannamei contributes to hemocytes anti-apoptosis. Mol Immunol 2020; 120:113-121. [PMID: 32113131 DOI: 10.1016/j.molimm.2020.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 02/06/2020] [Accepted: 02/11/2020] [Indexed: 12/01/2022]
Abstract
Litopenaeus vannamei, as an important marine aquaculture species, has attracted more and more attentions in past several years. More recently people got its genome fine mapping, which unveiled a gene treasure. In this study, we have identified a novel trypsin-like protein which came from previous WSSV-infected shrimp plasma iTRAQ data. This protein is a 39 kDa protein with 363 amino acids. It contains a conserved trypsin-domain and could be strongly induced with WSSV infection. Interestingly, knockdown of this protein made shrimps vulnerable to WSSV infection. Further exploration unveiled that this fragility was probably due to the fact that knockdown of this protein could cause shrimp hemocytes apoptosis, which indicated that this protein played key roles in preventing shrimp hemocytes from apoptosis. To further explore how LvTLAP protected shrimp hemocytes from apoptosis, GST pull down assay was applied to screen LvTLAP interacting protein in shrimp plasma. L. vannamei growth and transformation-dependent-like protein (LvGTD-like protein) was identified as a LvTLAP interacting protein, which played proapoptotic roles in cells. Thus, a possible explanation for LvTLAP anti-apoptosis activity was that this protein could block LvGTD-like protein proapoptotic activity to protect shrimp hemocytes from death. In general, our study has uncovered a novel WSSV responsive shrimp plasma protein, which played key roles in shrimp hemocytes anti-apoptosis and shrimp against WSSV infection.
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Affiliation(s)
- Mengyuan Tao
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Yuqin Liang
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China
| | - Yueling Zhang
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China; Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China
| | - Fan Wang
- Department of Biology, College of Science, Shantou University, Shantou, 515063, China; Institute of Marine Sciences and Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, China; STU-UMT Joint Shellfish Research Laboratory, Shantou University, Shantou, 515063, China.
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Tsairidou S, Hamilton A, Robledo D, Bron JE, Houston RD. Optimizing Low-Cost Genotyping and Imputation Strategies for Genomic Selection in Atlantic Salmon. G3 (BETHESDA, MD.) 2020; 10:581-590. [PMID: 31826882 PMCID: PMC7003102 DOI: 10.1534/g3.119.400800] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/03/2019] [Indexed: 11/20/2022]
Abstract
Genomic selection enables cumulative genetic gains in key production traits such as disease resistance, playing an important role in the economic and environmental sustainability of aquaculture production. However, it requires genome-wide genetic marker data on large populations, which can be prohibitively expensive. Genotype imputation is a cost-effective method for obtaining high-density genotypes, but its value in aquaculture breeding programs which are characterized by large full-sibling families has yet to be fully assessed. The aim of this study was to optimize the use of low-density genotypes and evaluate genotype imputation strategies for cost-effective genomic prediction. Phenotypes and genotypes (78,362 SNPs) were obtained for 610 individuals from a Scottish Atlantic salmon breeding program population (Landcatch, UK) challenged with sea lice, Lepeophtheirus salmonis The genomic prediction accuracy of genomic selection was calculated using GBLUP approaches and compared across SNP panels of varying densities and composition, with and without imputation. Imputation was tested when parents were genotyped for the optimal SNP panel, and offspring were genotyped for a range of lower density imputation panels. Reducing SNP density had little impact on prediction accuracy until 5,000 SNPs, below which the accuracy dropped. Imputation accuracy increased with increasing imputation panel density. Genomic prediction accuracy when offspring were genotyped for just 200 SNPs, and parents for 5,000 SNPs, was 0.53. This accuracy was similar to the full high density and optimal density dataset, and markedly higher than using 200 SNPs without imputation. These results suggest that imputation from very low to medium density can be a cost-effective tool for genomic selection in Atlantic salmon breeding programs.
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Affiliation(s)
- Smaragda Tsairidou
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, United Kingdom,
| | - Alastair Hamilton
- Hendrix Genetics Aquaculture BV/ Netherlands Villa 'de Körver', Spoorstraat 695831 CK Boxmeer, The Netherlands, and
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, United Kingdom
| | - James E Bron
- Institute of Aquaculture, University of Stirling, FK9 4LA, United Kingdom
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, EH25 9RG, United Kingdom
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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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Liu G, Dong L, Gu L, Han Z, Zhang W, Fang M, Wang Z. Evaluation of Genomic Selection for Seven Economic Traits in Yellow Drum (Nibea albiflora). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:806-812. [PMID: 31745748 PMCID: PMC6890617 DOI: 10.1007/s10126-019-09925-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 09/25/2019] [Indexed: 05/27/2023]
Abstract
Yellow drum (Nibea albiflora) is an important maricultural fish in China, and genetic improvement is necessary for this species. This research evaluated the application of genomic selection methods to predict the genetic values of seven economic traits for yellow drum. Using genome-wide single-nucleotide polymorphisms (SNPs), we estimated the genetic parameters for seven traits, including body length (BL), swimming bladder index (SBI), swimming bladder weight (SBW), body thickness (BT), body height (BH), body length/body height ratio (LHR), and gonad weight index (GWI). The heritability estimates ranged from 0.309 to 0.843. We evaluated the prediction performance of various statistical methods, and no one method provided the highest predictive ability for all traits. We then evaluated and compared the use of genome-wide association study (GWAS)-informative SNPs and random SNPs for prediction and found that GWAS-informative SNPs obviously increased. It only needed 5 and 100 informative SNPs for LHR and BT to achieve almost the same predictive abilities as using genome-wide SNPs, and for BL, SBI, SBW, BH, and GWI, about 1000 to 3000 informative SNPs were needed to achieve whole-genome level predictive abilities. It can be concluded from the test results that breeders can use fewer SNPs to save the breeding costs of genomic selection for some traits.
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Affiliation(s)
- Guijia Liu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Linsong Dong
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Linlin Gu
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Zhaofang Han
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Wenjing Zhang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China
| | - Ming Fang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
| | - Zhiyong Wang
- Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture and Rural Affairs, Jimei University, Xiamen, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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65
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Nguyen NH, Phuthaworn C, Knibb W. Genomic prediction for disease resistance to Hepatopancreatic parvovirus and growth, carcass and quality traits in Banana shrimp Fenneropenaeus merguiensis. Genomics 2019; 112:2021-2027. [PMID: 31765824 DOI: 10.1016/j.ygeno.2019.11.014] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 11/12/2019] [Accepted: 11/19/2019] [Indexed: 01/12/2023]
Abstract
Conventional genetic improvement of disease resistance in aquatic animal species involves challenge tests or using qPCR to quantify viral load that is costly, time-consuming and causing biosecurity concerns. Recent developments in high throughput next generation genome sequencing platforms such as genotyping by sequencing (GBS) have opened new possibilities for improving disease traits based on DNA information. The principal aim of this study was thus to examine potential application of genomic selection to improve resistance to hepatopancreatic parvovirus (HPV) in banana shrimp Fenneropenaeus merguiensis. Specifically, we used a total of 9472 single nucleotide polymorphisms (SNPs) developed de novo from GBS platforms to assess accuracy of genomic prediction for HPV resistance and growth, carcass and quality-related traits in this white shrimp species. Our multi-locus mixed model analysis showed moderate heritabilities for HPV resistance (h2 = 0.46) and other traits studied (0.10 to 0.55). Genetic correlations of HPV titre with growth and carcass traits, estimated using SNPs markers, were negative (i.e., favourable), suggesting that selection for improved growth and carcass traits may have increased HPV resistance (i.e., reduced HPV titre). More importantly, our gBLUP model demonstrated that the accuracy of gBLUP prediction was moderate for HPV disease resistance (0.46). The genomic prediction accuracy was somewhat greater for growth and carcass related traits especially for body weight (0.76) and meat or tail weight (0.77). On the other hand, the prediction accuracy was from 0.25 to 0.41 for quality traits (raw and cooked colour and flesh streaks). Collectively, it is concluded that there are prospects to apply genomic selection in the genetic improvement for increased disease resistance, carcass and quality-related traits in this population of banana shrimp F. merguiensis.
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Affiliation(s)
- Nguyen Hong Nguyen
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland 4558, Australia.
| | - Chontida Phuthaworn
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland 4558, Australia
| | - Wayne Knibb
- Genecology Research Centre, School of Science and Engineering, University of the Sunshine Coast, Locked Bag 4, Maroochydore DC, Queensland 4558, Australia
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Hua K, Cobcroft JM, Cole A, Condon K, Jerry DR, Mangott A, Praeger C, Vucko MJ, Zeng C, Zenger K, Strugnell JM. The Future of Aquatic Protein: Implications for Protein Sources in Aquaculture Diets. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.oneear.2019.10.018] [Citation(s) in RCA: 254] [Impact Index Per Article: 50.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Gratacap RL, Wargelius A, Edvardsen RB, Houston RD. Potential of Genome Editing to Improve Aquaculture Breeding and Production. Trends Genet 2019; 35:672-684. [PMID: 31331664 DOI: 10.1016/j.tig.2019.06.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 06/21/2019] [Accepted: 06/26/2019] [Indexed: 02/02/2023]
Abstract
Aquaculture is the fastest growing food production sector and is rapidly becoming the primary source of seafood for human diets. Selective breeding programs are enabling genetic improvement of production traits, such as disease resistance, but progress is limited by the heritability of the trait and generation interval of the species. New breeding technologies, such as genome editing using CRISPR/Cas9 have the potential to expedite sustainable genetic improvement in aquaculture. Genome editing can rapidly introduce favorable changes to the genome, such as fixing alleles at existing trait loci, creating de novo alleles, or introducing alleles from other strains or species. The high fecundity and external fertilization of most aquaculture species can facilitate genome editing for research and application at a scale that is not possible in farmed terrestrial animals.
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Affiliation(s)
- Remi L Gratacap
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Anna Wargelius
- Institute of Marine Research, PO Box 1870, Nordnes, NO-5817 Bergen, Norway
| | | | - Ross D Houston
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK.
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