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Cox N, De Swaef E, Corteel M, Van Den Broeck W, Bossier P, Nauwynck HJ, Dantas-Lima JJ. Experimental Infection Models and Their Usefulness for White Spot Syndrome Virus (WSSV) Research in Shrimp. Viruses 2024; 16:813. [PMID: 38793694 PMCID: PMC11125927 DOI: 10.3390/v16050813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 05/14/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
White spot syndrome virus (WSSV) is marked as one of the most economically devastating pathogens in shrimp aquaculture worldwide. Infection of cultured shrimp can lead to mass mortality (up to 100%). Although progress has been made, our understanding of WSSV's infection process and the virus-host-environment interaction is far from complete. This in turn hinders the development of effective mitigation strategies against WSSV. Infection models occupy a crucial first step in the research flow that tries to elucidate the infectious disease process to develop new antiviral treatments. Moreover, since the establishment of continuous shrimp cell lines is a work in progress, the development and use of standardized in vivo infection models that reflect the host-pathogen interaction in shrimp is a necessity. This review critically examines key aspects of in vivo WSSV infection model development that are often overlooked, such as standardization, (post)larval quality, inoculum type and choice of inoculation procedure, housing conditions, and shrimp welfare considerations. Furthermore, the usefulness of experimental infection models for different lines of WSSV research will be discussed with the aim to aid researchers when choosing a suitable model for their research needs.
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Affiliation(s)
- Natasja Cox
- IMAQUA, 9080 Lochristi, Belgium; (E.D.S.); (M.C.); (J.J.D.-L.)
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium;
| | | | - Mathias Corteel
- IMAQUA, 9080 Lochristi, Belgium; (E.D.S.); (M.C.); (J.J.D.-L.)
| | - Wim Van Den Broeck
- Department of Morphology, Medical Imaging, Orthopedics, Physiotherapy and Nutrition, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium;
| | - Peter Bossier
- Laboratory of Aquaculture & Artemia Reference Center, Department of Animal Sciences and Aquatic Ecology, Faculty of Bioscience Engineering, Ghent University, 9000 Ghent, Belgium;
| | - Hans J. Nauwynck
- Laboratory of Virology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium;
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Mangabeira-Silva IS, Soares PET, Vieira da Silva YT, Rodrigues de Albuquerque BHD, Câmera de Oliveira MTF, Ferreira LAH, Bezerra de Souza MF, Vieira de Lucena D, Paiva Pereira JM, Pinheiro e Silva RP, Lanza DCF. Characterization of microsatellite markers in the coding regions of the Penaeus vannamei genome. PLoS One 2024; 19:e0289351. [PMID: 38696386 PMCID: PMC11065258 DOI: 10.1371/journal.pone.0289351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 07/18/2023] [Indexed: 05/04/2024] Open
Abstract
In this study, an extensive analysis of microsatellite markers (Single Tandem Repeats-STRs) in Penaeus vannamei was conducted at an advanced level. The markers were thoroughly examined, characterized, and specific markers located within coding regions were identified. Out of a total of 306 STRs, 117 were classified as perfect markers based on their single repeat motif. Among these perfect markers, 62 were found to be associated with predicted coding genes (mRNA), which were involved in various functions such as binding, catalytic activity, ATP-dependent activity, transcription, structural and molecular regulation. To validate the accuracy of the findings, a sample of nine markers was subjected to in vitro testing, which confirmed the presence of polymorphisms within the population. These results suggest the existence of different protein isoforms within the population, indicating the potential of these markers for application in both population and phenotype-genotype association studies. This innovative approach opens up new possibilities for investigating the impact of genomic plasticity in populations of P. vannamei.
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Affiliation(s)
- Iasmim Santos Mangabeira-Silva
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biotechnology, RENORBIO, Natal, RN, Brazil
| | - Paulo Eduardo Toscano Soares
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Yago Tomaz Vieira da Silva
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Beatriz Helena Dantas Rodrigues de Albuquerque
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Maryana Thalyta Ferreira Câmera de Oliveira
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | | | - Maria Fernanda Bezerra de Souza
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Danyllo Vieira de Lucena
- Postgraduate Program in Civil and Environmental Engineering, Federal University of Campina Grande, Campina Grande, PB, Brazil
| | | | | | - Daniel Carlos Ferreira Lanza
- Laboratory of Applied Molecular Biology—LAPLIC, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Postgraduate Program in Biotechnology, RENORBIO, Natal, RN, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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Toubanaki DK, Efstathiou A, Tzortzatos OP, Valsamidis MA, Papaharisis L, Bakopoulos V, Karagouni E. Nervous Necrosis Virus Modulation of European Sea Bass ( Dicentrarchus labrax, L.) Immune Genes and Transcriptome towards Establishment of Virus Carrier State. Int J Mol Sci 2023; 24:16613. [PMID: 38068937 PMCID: PMC10706053 DOI: 10.3390/ijms242316613] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/16/2023] [Accepted: 11/20/2023] [Indexed: 12/18/2023] Open
Abstract
Viral infections of teleost fish have great environmental and economic implications in aquaculture. Nervous necrosis virus (NNV) is a pathogen affecting more than 120 different species, causing high mortality and morbidity. Herein, we studied the course of NNV experimental infection of D. labrax, focusing on survivors which indicated viral carrier state. To determine the carrier state of D. labrax head kidney, we performed a gene expression analysis of selected immune-related genes and we profiled its transcriptome 14 days post infection (dpi). All tested genes showed clear differentiations in expression levels while most of them were up-regulated 14 dpi suggesting that their role is not limited in early antiviral responses, but they are also implicated in disease persistence. To gain a better understanding of the fish that survived the acute infection but still maintained a high viral load, we studied the differential expression of 124 up-regulated and 48 down-regulated genes in D. labrax head kidney, at 14 dpi. Concluding, the NNV virus persistent profile was assessed in D. labrax, where immune-related gene modification was intense (14 dpi) and the head kidney transcriptome profile at this time point offered a glimpse into host attempts to control the infection in asymptomatic carriers.
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Affiliation(s)
- Dimitra K. Toubanaki
- Immunology of Infection Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.K.T.); (A.E.); (O.-P.T.)
| | - Antonia Efstathiou
- Immunology of Infection Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.K.T.); (A.E.); (O.-P.T.)
| | - Odysseas-Panagiotis Tzortzatos
- Immunology of Infection Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.K.T.); (A.E.); (O.-P.T.)
| | - Michail-Aggelos Valsamidis
- Department of Marine Sciences, School of the Environment, University of the Aegean, University Hill, Lesvos, 81100 Mytilene, Greece; (M.-A.V.); (V.B.)
| | | | - Vasileios Bakopoulos
- Department of Marine Sciences, School of the Environment, University of the Aegean, University Hill, Lesvos, 81100 Mytilene, Greece; (M.-A.V.); (V.B.)
| | - Evdokia Karagouni
- Immunology of Infection Group, Department of Microbiology, Hellenic Pasteur Institute, 11521 Athens, Greece; (D.K.T.); (A.E.); (O.-P.T.)
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Robinson NA, Robledo D, Sveen L, Daniels RR, Krasnov A, Coates A, Jin YH, Barrett LT, Lillehammer M, Kettunen AH, Phillips BL, Dempster T, Doeschl‐Wilson A, Samsing F, Difford G, Salisbury S, Gjerde B, Haugen J, Burgerhout E, Dagnachew BS, Kurian D, Fast MD, Rye M, Salazar M, Bron JE, Monaghan SJ, Jacq C, Birkett M, Browman HI, Skiftesvik AB, Fields DM, Selander E, Bui S, Sonesson A, Skugor S, Østbye TK, Houston RD. Applying genetic technologies to combat infectious diseases in aquaculture. REVIEWS IN AQUACULTURE 2023; 15:491-535. [PMID: 38504717 PMCID: PMC10946606 DOI: 10.1111/raq.12733] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/24/2022] [Accepted: 08/16/2022] [Indexed: 03/21/2024]
Abstract
Disease and parasitism cause major welfare, environmental and economic concerns for global aquaculture. In this review, we examine the status and potential of technologies that exploit genetic variation in host resistance to tackle this problem. We argue that there is an urgent need to improve understanding of the genetic mechanisms involved, leading to the development of tools that can be applied to boost host resistance and reduce the disease burden. We draw on two pressing global disease problems as case studies-sea lice infestations in salmonids and white spot syndrome in shrimp. We review how the latest genetic technologies can be capitalised upon to determine the mechanisms underlying inter- and intra-species variation in pathogen/parasite resistance, and how the derived knowledge could be applied to boost disease resistance using selective breeding, gene editing and/or with targeted feed treatments and vaccines. Gene editing brings novel opportunities, but also implementation and dissemination challenges, and necessitates new protocols to integrate the technology into aquaculture breeding programmes. There is also an ongoing need to minimise risks of disease agents evolving to overcome genetic improvements to host resistance, and insights from epidemiological and evolutionary models of pathogen infestation in wild and cultured host populations are explored. Ethical issues around the different approaches for achieving genetic resistance are discussed. Application of genetic technologies and approaches has potential to improve fundamental knowledge of mechanisms affecting genetic resistance and provide effective pathways for implementation that could lead to more resistant aquaculture stocks, transforming global aquaculture.
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Affiliation(s)
- Nicholas A. Robinson
- Nofima ASTromsøNorway
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Rose Ruiz Daniels
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | - Andrew Coates
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Ye Hwa Jin
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Luke T. Barrett
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
- Institute of Marine Research, Matre Research StationMatredalNorway
| | | | | | - Ben L. Phillips
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Tim Dempster
- Sustainable Aquaculture Laboratory—Temperate and Tropical (SALTT)School of BioSciences, The University of MelbourneMelbourneVictoriaAustralia
| | - Andrea Doeschl‐Wilson
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Francisca Samsing
- Sydney School of Veterinary ScienceThe University of SydneyCamdenAustralia
| | | | - Sarah Salisbury
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | | | | | | | | | - Dominic Kurian
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesThe University of EdinburghEdinburghUK
| | - Mark D. Fast
- Atlantic Veterinary CollegeThe University of Prince Edward IslandCharlottetownPrince Edward IslandCanada
| | | | | | - James E. Bron
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Sean J. Monaghan
- Institute of AquacultureUniversity of StirlingStirlingScotlandUK
| | - Celeste Jacq
- Blue Analytics, Kong Christian Frederiks Plass 3BergenNorway
| | | | - Howard I. Browman
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | - Anne Berit Skiftesvik
- Institute of Marine Research, Austevoll Research Station, Ecosystem Acoustics GroupTromsøNorway
| | | | - Erik Selander
- Department of Marine SciencesUniversity of GothenburgGothenburgSweden
| | - Samantha Bui
- Institute of Marine Research, Matre Research StationMatredalNorway
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5
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What Can Genetics Do for the Control of Infectious Diseases in Aquaculture? Animals (Basel) 2022; 12:ani12172176. [PMID: 36077896 PMCID: PMC9454762 DOI: 10.3390/ani12172176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/02/2022] [Accepted: 08/22/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Infectious diseases place an economic burden on aquaculture and a limitation to its growth. This state-of-the-art review describes the application of genetics and genomics as novel tools to control infectious disease in aquaculture. Abstract Infectious diseases place an economic burden on aquaculture and a limitation to its growth. An innovative approach to mitigate their impact on production is breeding for disease resistance: selection for domestication, family-based selection, marker-assisted selection, and more recently, genomic selection. Advances in genetics and genomics approaches to the control of infectious diseases are key to increasing aquaculture efficiency, profitability, and sustainability and to reducing its environmental footprint. Interaction and co-evolution between a host and pathogen can, however, turn breeding to boost infectious disease resistance into a potential driver of pathogenic change. Parallel molecular characterization of the pathogen and its virulence and antimicrobial resistance genes is therefore essential to understand pathogen evolution over time in response to host immunity, and to apply appropriate mitigation strategies.
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Thaijongrak P, Chotwiwatthanakun C, Laphyai P, Prachumwat A, Kruangkum T, Sobhon P, Vanichviriyakit R. Molecular characterization and expression profiling of transformer 2 and fruitless-like homologs in the black tiger shrimp, Penaeus monodon. PeerJ 2022; 10:e12980. [PMID: 35194532 PMCID: PMC8858584 DOI: 10.7717/peerj.12980] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 01/31/2022] [Indexed: 01/11/2023] Open
Abstract
Transformer 2 (tra 2) and fruitless (fru) genes have been proven to play a key role in sex determination pathways in many Arthropods, including insects and crustaceans. In this study, a paralog of P. monodon tra 2 (Pmtra 2), P. monodon ovarian associated transformer 2 (PmOvtra 2) and 2 isoforms of P. monodon fruitless-like gene (Pmfru-1 and Pmfru-2) were identified and characterized. The full cDNA sequence of PmOvtra 2 consisted of 1,774 bp with the longest open reading frame (ORF) of 744 bp encoding for 247 amino acids. The PmOvtra 2 exhibited a predicted RNA-recognition motif (RRM) domain and two arginine-serine (RS) regions, suggesting its function in RNA splicing. The full cDNA sequence of Pmfru-1 consisted of 1,306 bp with 1,182 bp ORF encoding for 393 amino acids, whereas the full cDNA sequence of Pmfru-2 consisted of 1,858 bp with 1,437 bp ORF encoding 478 amino acids. The deduced amino acid sequences of Pmfru-1 and Pmfru-2 exhibited highly conserved domains of Fru proteins, including Broad-complex, Tramtrack and Bric-a-brac (BTB), and zinc finger (ZF) domains. In addition, Pmfru-1 and Pmfru-2 were suggestively originated from the same single genomic locus by genomic sequence analysis. Specifically, Pmfru pre-mRNA was alternatively spliced for Pmfru-1 and Pmfru-2 to include mutually exclusive exon 7 and exon 6, respectively. Temporal and spatial expression of PmOvtra 2, Pmfru-1, and Pmfru-2 were also investigated by qPCR. The results showed that all were expressed in early developmental stages with undifferentiated gonads starting from nauplius until postlarvae. The expression of PmOvtra 2 started at nauplius stage and gradually increased from mysis to postlarvae (PL) 1. However, the expression of Pmfru-1 was low at the nauplii stage and slightly increased from protozoea to PL5, whereas the expression of Pmfru-2 maintained a low level from nauplius to mysis and then gradually increased at the PL stages. Expressions of PmOvtra 2, Pmfru-1, and Pmfru-2 were detected in various tissues including nervous tissue, gill, heart, hepatopancreas, gut, and gonads. Interestingly, the sexually dimorphic expression of PmOvtra 2, Pmfru-1, and Pmfru-2 was demonstrated in fully developed gonads in which the ovary showed significantly higher expressions than the testis. The great difference in the expression pattern of PmOvtra 2, Pmfru-1, and Pmfru-2 in the ovary and testis suggested their roles in the female sex determination in P. monodon.
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Affiliation(s)
- Prawporn Thaijongrak
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Charoonroj Chotwiwatthanakun
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Nakhonsawan Campus, Mahidol University, Nakhonsawan, Thailand
| | - Phaivit Laphyai
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Anuphap Prachumwat
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Thanapong Kruangkum
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Prasert Sobhon
- Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Rapeepun Vanichviriyakit
- Center of Excellence for Shrimp Molecular Biology and Biotechnology, Faculty of Science, Mahidol University, Bangkok, Thailand,Department of Anatomy, Faculty of Science, Mahidol University, Bangkok, Thailand
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Zhang Y, Zhang C, Yao N, Huang J, Sun X, Zhao B, Li H. Construction of a high-density linkage map and detection of sex-specific markers in Penaeus japonicus. PeerJ 2021; 9:e12390. [PMID: 34760384 PMCID: PMC8559604 DOI: 10.7717/peerj.12390] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/05/2021] [Indexed: 12/13/2022] Open
Abstract
Penaeus japonicus is one of the most important farmed shrimp species in many countries. Sexual dimorphism is observed in P. japonicus, in which females grow faster and larger than males; therefore, a unisexual female culture of P. japonicus could improve the efficiency of productivity. However, the genetic mechanisms underlying sex determination in P. japonicus are unclear. In this study, we constructed a high-density genetic linkage map of P. japonicus using genotyping-by-sequencing (GBS) technology in a full-sib family. The final map was 3,481.98 cM in length and contained 29,757 single nucleotide polymorphisms (SNPs). These SNPs were distributed on 41 sex-averaged linkage groups, with an average inter-marker distance of 0.123 cM. One haplotype, harboring five sex-specific SNPs, was detected in linkage group 1 (LG1), and its corresponding confidence interval ranged from 211.840 to 212.592 cM. Therefore, this high-density genetic linkage map will be informative for genome assembly and marker-assisted breeding, and the sex-linked SNPs will be helpful for further studies on molecular mechanisms of sex determination and unisexual culture of P. japonicus in the future.
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Affiliation(s)
- Yaqun Zhang
- Chinese Academy of Fishery Sciences, Beijing, China
| | - Chuantao Zhang
- Xiaying Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Weifang, Shandong, China
| | - Na Yao
- Chinese Academy of Fishery Sciences, Beijing, China
| | - Jingxian Huang
- Xiaying Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Weifang, Shandong, China
| | - Xiangshan Sun
- Xiaying Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Weifang, Shandong, China
| | - Bingran Zhao
- Xiaying Enhancement and Experiment Station, Chinese Academy of Fishery Sciences, Weifang, Shandong, China
| | - Hengde Li
- Chinese Academy of Fishery Sciences, Beijing, China
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Pooljun C, Jariyapong P, Direkbusarakom S, Saeng-Ngern S, Sakamoto T, Wuthisuthimethavee S. Association between ALFPm3 single nucleotide polymorphism and white spot syndrome virus resistance in black tiger shrimp Penaeus monodon. DISEASES OF AQUATIC ORGANISMS 2020; 142:213-224. [PMID: 33331289 DOI: 10.3354/dao03538] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Here single nucleotide polymorphisms (SNPs) were associated with white spot syndrome virus (WSSV) resistance in black tiger shrimp Penaeus monodon. SNPs were identified by single-strand conformation polymorphism (SSCP) screening and DNA sequencing of shrimp sampled from 3 families (100 shrimp per family) challenged with WSSV. Shrimp that died over the 14 d challenge trial were designated susceptible, with those remaining alive on Day 14 designated resistant. To compare SNPs, 10 samples from the susceptible and resistant groups, each comprising DNA pooled from 3 shrimp, were amplified by polymerase chain reaction (PCR) using primers to 12 selected genes and screened by SSCP. SNPs were only identified in the anti-lipopolysaccharide factor 3 (ALFPm3) gene product. Analysis of complete ALFPm3 gene sequences confirmed the existence of 3 SNPs (g.934C>G, g.1186A>G, and g.1898C>G) that were polymorphic between the susceptible and resistant groups. Further analyses using specific tetra-primer amplification refractory mutation system PCR primer sets associated these 3 SNPS, and particularly the g.1186A>G SNP, with WSSV resistance. This SNP thus has potential for use as a DNA marker to select for WSSV resistance in P. monodon breeding programs.
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Affiliation(s)
- Chettupon Pooljun
- Center of Excellence for Shrimp, School of Agricultural Technology, Walailak University, Nakhon Si Thammarat 80160, Thailand
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Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test. Sci Rep 2020; 10:20571. [PMID: 33239674 PMCID: PMC7688931 DOI: 10.1038/s41598-020-77580-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Accepted: 11/12/2020] [Indexed: 01/09/2023] Open
Abstract
White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine the power and accuracy of genomic selection to improve WSSV resistance in Litopenaeus vannamei. Shrimp were experimentally challenged with WSSV and resistance was evaluated as dead or alive (DOA) 23 days after infestation. All shrimp in the challenge test were genotyped for 18,643 single nucleotide polymorphisms. Breeding candidates (G0) were ranked on genomic breeding values for WSSV resistance. Two G1 populations were produced, one from G0 breeders with high and the other with low estimated breeding values. A third population was produced from “random” mating of parent stock. The average survival was 25% in the low, 38% in the random and 51% in the high-genomic breeding value groups. Genomic heritability for DOA (0.41 in G1) was high for this type of trait. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection.
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10
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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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11
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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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12
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Wang Y, Yu Y, Li S, Zhang X, Xiang J, Li F. Sex-Specific Transcriptome Sequencing of Zoea I Larvae and Identification of Sex-Linked Genes Using Bulked Segregant Analysis in Pacific White Shrimp Litopenaeus vannamei. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:423-432. [PMID: 32281012 DOI: 10.1007/s10126-020-09962-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Accepted: 02/27/2020] [Indexed: 06/11/2023]
Abstract
In order to learn the sex determination and differentiation process in shrimp, we performed sex-specific transcriptome sequencing of the Zoea I larvae in Litopenaeus vannamei (L. vannamei) using a DNA/RNA co-extraction method. The sex-specific genes and the sex-linked SNPs were identified. De novo assembly of all the clean reads generated 41,270 unigenes with an average length of 1026 bp and an N50 of 1922 bp. A total of 60 differentially expressed genes (DEGs) between females and males at Zoea I stage were obtained, in which 41 unigenes had annotations. DEGs that might be related to sex development in L. vannamei were analyzed. Besides, paralogous genes of some known sex-related genes in model organisms such as sex-lethal (Sxl) showed no sex-biased difference, which indicated they may not play roles in sex development at Zoea I stage. Candidate sex-linked SNPs were validated in six populations of L. vannamei, and SNPs in Unigene0020898 and Unigene0020336 were fully linked to genders, suggesting the two genes located in the sex-determining region of L. vannamei. Our report provided the sex-specific gene expression in early developmental stage of L. vannamei, and found some sex-biased genes that may participate in the sex development process. We also detected two sex-linked genes which may be located in the sex determination region of L. vannamei through bulked segregant analysis, and the SNPs on these genes also provided a method for genetic sex identification at transcriptional level. Our findings will facilitate further researches on molecular mechanism of sex determination and differentiation in shrimps.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266000, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, 266071, China.
- The Innovation of Seed Design, Chinese Academy of Sciences, Wuhan, People's Republic of China.
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13
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Wang J, Li M, Qin Z, Li J, Li J. Validation of growth-related quantitative trait loci markers in different Exopalaemon carinicauda families for marker-assisted selection. Anim Genet 2020; 51:324-329. [PMID: 31981462 DOI: 10.1111/age.12914] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2020] [Indexed: 01/08/2023]
Abstract
We detected growth-related QTL and associated markers from the backcross population of Exopalaemon carinicauda in the previous study. Based on our previous study, the 47 SNP markers associated with candidate growth trait QTL were selected to analyze the association between these markers and body weight (BW), body length and abdominal segment length traits in four different populations including wild population, a full-sib family, a half-sib family and a backcross population for evaluating their potential application of marker-assisted selection in E. carinicauda. The general linear model (GLM) and mixed linear model were applied and the associations between SNP loci and three growth-related traits verified. The results showed that the Marker79268 and Marker100644 were significantly associated with the BW trait in more than three populations by the GLM method. The Marker100644 was significantly associated with BW in the full-sib family, half-sib family and backcross populations by the GLM and mixed linear model methods. Our findings will provide useful SNP markers to go forward to improve growth performance through more refined marker-assisted selection in E. carinicauda.
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Affiliation(s)
- J Wang
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - M Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,College of Fishery and Life Sciences, Shanghai Ocean University, Shanghai, 201306, China
| | - Z Qin
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - J Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
| | - J Li
- Key Laboratory for Sustainable Utilization of Marine Fisheries Resources, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, 266071, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, 266071, China
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14
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Rise ML, Martyniuk CJ, Chen M. Comparative physiology and aquaculture: Toward Omics-enabled improvement of aquatic animal health and sustainable production. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2019; 31:100603. [PMID: 31260856 DOI: 10.1016/j.cbd.2019.100603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Omics-technologies have revolutionized biomedical research over the past two decades, and are now poised to play a transformative role in aquaculture. This article serves as an introduction to a Virtual Special Issue of Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics (CBPD), with the objective to showcase the state-of-the-science for Omics in aquaculture. In this editorial, we describe the role that Omics can play in aquaculture, and provide a synopsis for each of the Special Issue articles that use these technologies to improve aquaculture practices. Current genomic resources available for some aquaculture species are also described. The number of datasets is impressive for species such as Atlantic salmon and rainbow trout, totaling in the thousands (NCBI Gene Expression Omnibus and Sequence Read Archive). We present a conceptual framework that describes how Omics can be leveraged to understand complex responses of aquatic animals in culture for relevant physiological outcomes, such as fecundity, growth, and immunity. Lastly, knowledge gaps and new directions are identified to address current obstacles in aquaculture. Articles in this Special Issue on aquaculture in CBPD highlight the diversity and scope of Omics in aquaculture. As the technology becomes more cost-effective, it is anticipated that genomics, transcriptomics, proteomics, metabolomics and lipidomics will play increasingly important roles in stock diagnostics (e.g. genetics, health, performance). The timing is right, as global concerns are reaching critical levels over food availability/security and water restrictions for humankind.
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Affiliation(s)
- Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada
| | - Christopher J Martyniuk
- Department of Physiological Sciences and Center for Environmental and Human Toxicology, University of Florida Genetics Institute, Interdisciplinary Program in Biomedical Sciences Neuroscience, College of Veterinary Medicine, University of Florida, Gainesville, FL 32611, USA.
| | - Muyan Chen
- College of Fisheries, Ocean University of China, Qingdao 266003, China
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15
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Galindo-Torres P, Ventura-López C, Llera-Herrera R, Ibarra AM. A natural antisense transcript of the fem-1 gene was found expressed in female gonads during the characterization, expression profile, and cellular localization of the fem-1 gene in Pacific white shrimp Penaeus vannamei. Gene 2019; 706:19-31. [PMID: 31028869 DOI: 10.1016/j.gene.2019.04.066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 03/29/2019] [Accepted: 04/23/2019] [Indexed: 12/19/2022]
Abstract
The fem-1 gene in Caenorhabditis elegans is involved in sex differentiation; it is specifically required for all aspects of male development. In this study, the full-length cDNA of the fem-1 (Pvfem-1) gene was isolated from the Pacific whiteleg shrimp Penaeus vannamei. The Pvfem-1 transcript is 3778 nt long and encodes a putative protein (PvFEM-1) of 638 amino acids that presented eight ankyrin repeats. The translated protein showed a significant (P < 0.05) structural similitude by superposition with C. elegans FEM-1 protein. Pvfem-1 expression was evaluated by qPCR and in situ hybridization (ISH) during embryogenesis, larval development, and gonads of both genders in subadult and adult life stages. Pvfem-1 was found expressed in brain, intestine, hepatopancreas, and in the gonads of both genders in subadults and adults when quantified by RT-qPCR. A significant finding was the discovery of a natural antisense transcript (NAT) of Pvfem-1 by ISH. It was present in the oocyte nucleus of subadult female shrimp gonads but was not seen within oocytes from adult females, although it was detected in follicular cells, suggesting a possible post-transcriptional regulation of Pvfem-1 in female gonad. Conversely, in males, no NAT was observed, and Pvfem-1 was found expressed in spermatogonia of both, subadult and adult shrimps indicating a function in male sexual differentiation and gametes generation. This study represents the first step for future functional analysis that is expected to contribute to clarifying the role of Pvfem-1 in sex differentiation and determination.
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Affiliation(s)
- Pavel Galindo-Torres
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico.
| | - Claudia Ventura-López
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico
| | - Raúl Llera-Herrera
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico
| | - Ana M Ibarra
- Centro de Investigaciones Biológicas del Noroeste (CIBNOR), Aquaculture Genetics and Breeding Laboratory, Ave. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, 23096 La Paz, Baja California Sur, Mexico.
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16
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Guo L, Xu YH, Zhang N, Zhou FL, Huang JH, Liu BS, Jiang SG, Zhang DC. A High-Density Genetic Linkage Map and QTL Mapping for Sex in Black Tiger Shrimp ( Penaeus monodon). Front Genet 2019; 10:326. [PMID: 31024632 PMCID: PMC6465554 DOI: 10.3389/fgene.2019.00326] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/26/2019] [Indexed: 12/20/2022] Open
Abstract
The black tiger shrimp, Penaeus monodon, is important in both fishery and aquaculture and is the second-most widely cultured shrimp species in the world. However, the current strains cannot meet the market needs in various cultural environments, and the genome resources for P. monodon are still lacking. Restriction-site associated DNA sequencing (RADseq) has been widely used in genetic linkage map construction and in quantitative trait loci (QTL) mapping. We constructed a high-density genetic linkage map with RADseq in a full-sib family. This map contained 6524 single nucleotide polymorphisms (SNPs) and 2208 unique loci. The total length was 3275.4 cM, and the genetic distance was estimated to be 1.1 Mb/cM. The sex trait is a dichotomous phenotype, and the same interval was detected as a QTL using QTL mapping and genome-wide association analysis. The most significant locus explained 77.4% of the phenotype variance. The sex locus was speculated to be the same in this species based on the sequence alignments in Mozambique, India, and Hawaii populations. The constructed genetic linkage map provided a valuable resource for QTL mapping, genome assembly, and genome comparison for shrimp. The demonstrated common sex locus is a step closer to locating the underlying gene.
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Affiliation(s)
- Liang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Yu-Hui Xu
- Biomarker Technologies Corporation, Beijing, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Fa-Lin Zhou
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Jian-Hua Huang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
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17
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Zhao M, Wang W, Chen W, Ma C, Zhang F, Jiang K, Liu J, Diao L, Qian H, Zhao J, Wang T, Ma L. Genome survey, high-resolution genetic linkage map construction, growth-related quantitative trait locus (QTL) identification and gene location in Scylla paramamosain. Sci Rep 2019; 9:2910. [PMID: 30814536 PMCID: PMC6393678 DOI: 10.1038/s41598-019-39070-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 01/11/2019] [Indexed: 11/09/2022] Open
Abstract
Scylla paramamosain is one of the most economically important crabs in China. In this study, the first genome survey sequencing of this crab was performed, and the results revealed that the estimated genome size was 1.21 Gb with high heterozygosity (1.3%). Then, RAD technology was used to construct a high-resolution linkage map for this species. A total of 24,444 single nucleotide polymorphism (SNP) makers were grouped into 47 linkage groups. The total length of the linkage groups was 3087.53 cM with a markers interval of 0.92 cM. With the aid of transcriptome and genome scaffold data, 4,271 markers were linked to genes, including several important growth-related genes such as transforming growth factor-beta regulator I, immune related-gene C-type lectin and ecdysone pathway gene broad-complex-like protein. Further, 442 markers, representing 279 QTLs, associated with 24 traits were identified, and of these markers, 78 were linked to genes. Some interesting genes, such as dedicator of cytokinesis protein 3, tenascin-X and DNA helicase MCM8, were believed to have important relationship with specific traits and merit further exploration. The results of this study will accelerate the genetic improvement and genome sequencing analysis of the mud crab.
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Affiliation(s)
- Ming Zhao
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Wei Wang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Wei Chen
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Chunyan Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Fengying Zhang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Keji Jiang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Junguo Liu
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Le Diao
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Heng Qian
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Junxia Zhao
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Tian Wang
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China
| | - Lingbo Ma
- East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, 300 Jungong Road, Shanghai, 200090, China.
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18
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Perez-Enriquez R, Robledo D, Houston RD, Llera-Herrera R. SNP markers for the genetic characterization of Mexican shrimp broodstocks. Genomics 2018; 110:423-429. [PMID: 30308223 DOI: 10.1016/j.ygeno.2018.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 09/20/2018] [Accepted: 10/03/2018] [Indexed: 12/21/2022]
Abstract
Selective breeding of shrimp has major potential to enhance production traits, including growth and disease resistance. Genetic characterization of broodstock populations is a key element of breeding programs, as it enables decisions on inbreeding restrictions, family structure, and the potential use of genomic selection. Single Nucleotide Polymorphisms (SNPs) are suitable genetic markers for this purpose. A set of SNPs was developed to characterize commercial breeding stocks in Mexico. Individuals from local and imported lines were selected for sequencing using the nextRAD technique, resulting in the identification of 2619 SNPs. Genetic structure analysis showed three to five genetic groups of Ecuadorian and Mexican origins. A subset of 1231 SNPs has potential for stock identification and management. Further, three SNPs were identified as candidate sex-linked markers. The role of SNPs possibly associated with genes related to traits of importance to shrimp farming, such as growth and immune response, should be further investigated.
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Affiliation(s)
- Ricardo Perez-Enriquez
- Aquaculture Genetics & Breeding Lab, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, Baja California Sur 23096, Mexico.
| | - Diego Robledo
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UK
| | - Ross D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian EH25 9RG, UK
| | - Raúl Llera-Herrera
- CONACyT - Centro de Investigaciones en Alimentación y Desarrollo A.C. Sábalo-Cerritos s.n. Mazatlán, Sinaloa 82112, Mexico; Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, PO Box 811, CP 82040 Mazatlán, Sinaloa, Mexico.
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19
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Lv J, Sun D, Huan P, Song L, Liu P, Li J. QTL Mapping and Marker Identification for Sex-Determining: Indicating XY Sex Determination System in the Swimming Crab ( Portunus trituberculatus). Front Genet 2018; 9:337. [PMID: 30210528 PMCID: PMC6119780 DOI: 10.3389/fgene.2018.00337] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/07/2018] [Indexed: 12/23/2022] Open
Abstract
Sex determination is an important area of research, which has always had an intriguing aspect in evolutionary and developmental biology. Quantitative trait locus (QTL) mapping for sex will be helpful in clarifying the sex determination system. In this study, the sex QTL mapping of the swimming crab (Portunus trituberculatus) was performed based on a high-density linkage map, and a highly significant QTL specifically mapped on a single linkage group (LG) was firstly identified (LG24, LOD > 14). Twenty markers in the QTL region showed significant associations with sex by association analysis, of which heterogametic genotypes in males supported the XY sex determination mechanism. Two sex-specific markers at the family level were identified via segregation distortion analysis, which were known to be the most closely linked to the sex of P. trituberculatus. Based on sex marker sequences (Marker3840, Marker20320, and Marker10494), three potential sex-related genes were identified, and the quantitative real-time PCR results suggested that these genes were important in spermatogenesis or sex characteristics in males. Our results will contribute to the fine-mapping of sex-determining genes and clarify the sex determination mechanism of P. trituberculatus.
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Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dongfang Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Pengpeng Huan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Liu Song
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Laboratory for Marine Fisheries and Aquaculture, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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20
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Guppy JL, Jones DB, Jerry DR, Wade NM, Raadsma HW, Huerlimann R, Zenger KR. The State of " Omics" Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization. Front Genet 2018; 9:282. [PMID: 30123237 PMCID: PMC6085479 DOI: 10.3389/fgene.2018.00282] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Accepted: 07/09/2018] [Indexed: 12/19/2022] Open
Abstract
Elucidating the underlying genetic drivers of production traits in agricultural and aquaculture species is critical to efforts to maximize farming efficiency. "Omics" based methods (i.e., transcriptomics, genomics, proteomics, and metabolomics) are increasingly being applied to gain unprecedented insight into the biology of many aquaculture species. While the culture of penaeid shrimp has increased markedly, the industry continues to be impeded in many regards by disease, reproductive dysfunction, and a poor understanding of production traits. Extensive effort has been, and continues to be, applied to develop critical genomic resources for many commercially important penaeids. However, the industry application of these genomic resources, and the translation of the knowledge derived from "omics" studies has not yet been completely realized. Integration between the multiple "omics" resources now available (i.e., genome assemblies, transcriptomes, linkage maps, optical maps, and proteomes) will prove critical to unlocking the full utility of these otherwise independently developed and isolated resources. Furthermore, emerging "omics" based techniques are now available to address longstanding issues with completing keystone genome assemblies (e.g., through long-read sequencing), and can provide cost-effective industrial scale genotyping tools (e.g., through low density SNP chips and genotype-by-sequencing) to undertake advanced selective breeding programs (i.e., genomic selection) and powerful genome-wide association studies. In particular, this review highlights the status, utility and suggested path forward for continued development, and improved use of "omics" resources in penaeid aquaculture.
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Affiliation(s)
- Jarrod L. Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - David B. Jones
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Dean R. Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Nicholas M. Wade
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Aquaculture Program, CSIRO Agriculture & Food, Queensland Bioscience Precinct, St Lucia, QLD, Australia
| | - Herman W. Raadsma
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- Faculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, Australia
| | - Roger Huerlimann
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
| | - Kyall R. Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
- College of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, Australia
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21
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Christie AE, Pascual MG, Yu A. Peptidergic signaling in the tadpole shrimp Triops newberryi: A potential model for investigating the roles played by peptide paracrines/hormones in adaptation to environmental change. Mar Genomics 2018. [DOI: 10.1016/j.margen.2018.01.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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22
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López-Cuadros I, García-Gasca A, Gomez-Anduro G, Escobedo-Fregoso C, Llera-Herrera RA, Ibarra AM. Isolation of the sex-determining gene Sex-lethal (Sxl) in Penaeus (Litopenaeus) vannamei (Boone, 1931) and characterization of its embryogenic, gametogenic, and tissue-specific expression. Gene 2018; 668:33-47. [PMID: 29758296 DOI: 10.1016/j.gene.2018.05.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Revised: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 12/11/2022]
Abstract
The Pacific white shrimp Penaeus vannamei is the most cultured shrimp species around the world. Because females grow larger than males, the culture of 'only females' is of great interest, but knowledge on sex determination and differentiation is required for producing only females. In an effort to obtain information associated with reproduction in P. vannamei, transcriptomic data from female gonads was generated, and partial sequences of a transcript were identified as Sex-lethal (Sxl). Its characterization indicated that, differently from other penaeids in which this gene has been isolated, there are six isoforms of the Sxl transcript in P. vannamei (PvanSxl 1-6). These isoforms result from alternative splicing at three splice sites (SS1, SS2, SS3). The first splice-site is unique to P. vannamei, as it has not been reported for other Arthropod species; the second splice-site (SS2) is common among crustaceans, and the third splice-site (SS3) is also unique to P. vannamei and when spliced-out, it is always together with SS2. All isoforms are expressed during embryogenesis as well as gametogenesis of both genders. The two shorter isoforms, PvanSxl-5 and PvanSxl-6, which result from the splicing of SS2 and SS3, were found mostly expressed in adult testis, but PvanSxl-6 was also expressed in oocytes during gametogenesis. During oogenesis, the second largest isoform, PvanSxl-2, which splices-out only SS1, and PvanSxl-4 that splices-out SS1 and SS2 were highly expressed. These two isoforms were also highly expressed during embryonic development. In situ hybridization allowed pinpointing more specifically the cells where the PvanSxl transcripts were expressed. During embryogenesis, hybridization was observed from the one-cell stage embryo to late gastrula. In the female gonad in previtellogenesis, hybridization occurred in the nucleus of oocytes, whereas in secondary vitellogenesis the transcript also hybridized cytoplasmic granules and cortical crypts. Finally, in situ hybridization corroborated the expression of PvanSxl also in the male gonad during spermatogenesis, mostly occurring in the cytoplasm from spermatogonia and spermatocytes.
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Affiliation(s)
- Itzia López-Cuadros
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico
| | - Alejandra García-Gasca
- Centro de Investigación en Alimentación y Desarrollo A.C., (CIAD) Unidad Mazatlán, Av. Sábalo-Cerritos S/N. Col. Estero del Yugo, C.P. 82000 Mazatlán, Sinaloa, Mexico
| | - Gracia Gomez-Anduro
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico
| | - Cristina Escobedo-Fregoso
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico; CONACYT, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de México 03940, Mexico
| | - Raúl A Llera-Herrera
- Centro de Investigación en Alimentación y Desarrollo A.C., (CIAD) Unidad Mazatlán, Av. Sábalo-Cerritos S/N. Col. Estero del Yugo, C.P. 82000 Mazatlán, Sinaloa, Mexico; CONACYT, Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Ciudad de México 03940, Mexico
| | - Ana M Ibarra
- Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR). Programa de Acuacultura, Av. Instituto Politécnico Nacional No. 195, Col. Playa Palo de Santa Rita, La Paz, Baja California Sur C.P. 23096, Mexico.
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23
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Christie AE. Neuropeptide discovery in Proasellus cavaticus: Prediction of the first large-scale peptidome for a member of the Isopoda using a publicly accessible transcriptome. Peptides 2017; 97:29-45. [PMID: 28893643 DOI: 10.1016/j.peptides.2017.09.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Revised: 09/01/2017] [Accepted: 09/03/2017] [Indexed: 11/29/2022]
Abstract
In silico transcriptome mining is one of the most effective methods for neuropeptide discovery in crustaceans, particularly for species that are small, rare or from geographically inaccessible habitats that make obtaining the large pools of tissue needed for other peptide discovery platforms impractical. Via this approach, large peptidomes have recently been described for members of many of the higher crustacean taxa, one notable exception being the Isopoda; no peptidome has been predicted for any member of this malacostracan order. Using a publicly accessible transcriptome for the isopod Proasellus cavaticus, a subcentimeter subterranean ground water dweller, the first in silico-predicted peptidome for a member of the Isopoda is presented here. BLAST searches employing known arthropod neuropeptide pre/preprohormone queries identified 49 transcripts as encoding putative homologs within the P. cavaticus transcriptome. The proteins deduced from these transcripts allowed for the prediction of 171 distinct mature neuropeptides. The P. cavaticus peptidome includes members of the adipokinetic hormone-corazonin-like peptide, allatostatin A, allatostatin B, allatostatin C, allatotropin, bursicon α, bursicon β, CCHamide, crustacean cardioactive peptide, crustacean hyperglycemic hormone/molt-inhibiting hormone, diuretic hormone 31, eclosion hormone, elevenin, FMRFamide-like peptide, glycoprotein hormone α2, leucokinin, myosuppressin, neuroparsin, neuropeptide F, pigment dispersing hormone, pyrokinin, red pigment concentrating hormone, RYamide, short neuropeptide F, sulfakinin, tachykinin-related peptide and trissin families, as well as many linker/precursor-related sequences that may or may not represent additional bioactive molecules. Interestingly, many of the predicted P. cavaticus neuropeptides possess structures identical (or nearly so) to those previously described from members of several other malacostracan orders, i.e., the Decapoda, Amphipoda and Euphausiacea, a finding that suggests broad phylogenetic conservation of bioactive peptide structures, and possibly functions, may exist within the Malacostraca.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822 USA, USA.
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24
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Christie AE, Yu A, Pascual MG. Circadian signaling in the Northern krill Meganyctiphanes norvegica: In silico prediction of the protein components of a putative clock system using a publicly accessible transcriptome. Mar Genomics 2017; 37:97-113. [PMID: 28964713 DOI: 10.1016/j.margen.2017.09.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 09/01/2017] [Accepted: 09/02/2017] [Indexed: 11/25/2022]
Abstract
The Northern krill Meganyctiphanes norvegica is a significant component of the zooplankton community in many regions of the North Atlantic Ocean. In the areas it inhabits, M. norvegica is of great importance ecologically, as it is both a major consumer of phytoplankton/small zooplankton and is a primary food source for higher-level consumers. One behavior of significance for both feeding and predator avoidance in Meganyctiphanes is diel vertical migration (DVM), i.e., a rising from depth at dusk and a return to depth at dawn. In this and other euphausiids, an endogenous circadian pacemaker is thought, at least in part, to control DVM. Currently, there is no information concerning the identity of the genes/proteins that comprise the M. norvegica circadian system. In fact, there is little information concerning the molecular underpinnings of circadian rhythmicity in crustaceans generally. Here, a publicly accessible transcriptome was used to identify the molecular components of a putative Meganyctiphanes circadian system. A complete set of core clock proteins was deduced from the M. norvegica transcriptome (clock, cryptochrome 2, cycle, period and timeless), as was a large suite of proteins that likely function as modulators of the core clock (e.g., doubletime), or serves as inputs to it (cryptochrome 1) or outputs from it (pigment dispersing hormone). This is the first description of a "complete" (core clock through putative output pathway signals) euphausiid clock system, and as such, provides a foundation for initiating molecular investigations of circadian signaling in M. norvegica and other krill species, including how clock systems may regulate DVM and other behaviors.
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Affiliation(s)
- Andrew E Christie
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA.
| | - Andy Yu
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
| | - Micah G Pascual
- Békésy Laboratory of Neurobiology, Pacific Biosciences Research Center, School of Ocean and Earth Science and Technology, University of Hawaii at Manoa, 1993 East-West Road, Honolulu, HI 96822, USA
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25
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Budd AM, Hinton TM, Tonks M, Cheers S, Wade NM. Rapid expansion of pigmentation genes in penaeid shrimp with absolute preservation of function. ACTA ACUST UNITED AC 2017; 220:4109-4118. [PMID: 28851818 DOI: 10.1242/jeb.164988] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 08/23/2017] [Indexed: 12/25/2022]
Abstract
Crustaceans form their distinct patterns and colours through the interaction of the carotenoid astaxanthin with a protein called crustacyanin (CRCN). Presently, the expression of just two CRCN genes is thought to provide the protein subunits that combine to form the crustacyanin complex and associated carotenoid colour change from red to blue. This study aimed to explore the genetic complexity underlying the production of pigmentation and camouflage in penaeid shrimp. We isolated 35 new CRCN genes from 12 species, and their sequence analysis indicated that this gene family has undergone significant expansion and diversification in this lineage. Despite this duplication and sequence divergence, the structure of the CRCN proteins and their functional role in shrimp colour production has been strictly conserved. Using CRCN isoforms from Penaeus monodon as an example, we showed that isoforms were differentially expressed, and that subtle phenotypes were produced by the specific downregulation of individual isoforms. These findings demonstrate that our knowledge of the molecular basis of pigmentation in shrimp was overly simplistic, and suggests that multiple copies of the CRCN genes within species may be advantageous for colour production. This result is of interest for the origin and evolution of pigmentation in crustaceans, and the mechanisms by which gene function is maintained, diversified or sub-functionalized.
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Affiliation(s)
- Alyssa M Budd
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, St Lucia, Queensland 4067, Australia
| | - Tracey M Hinton
- CSIRO Health and Biosecurity, Australian Animal Health Laboratories, Geelong, Victoria 3220, Australia
| | - Mark Tonks
- CSIRO Oceans and Atmosphere, Ecosciences Precinct, Dutton Park, Queensland 4102, Australia
| | - Sue Cheers
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, St Lucia, Queensland 4067, Australia
| | - Nicholas M Wade
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, St Lucia, Queensland 4067, Australia .,ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, Queensland 4811, Australia
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26
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Yu Y, Zhang X, Yuan J, Wang Q, Li S, Huang H, Li F, Xiang J. Identification of Sex-determining Loci in Pacific White Shrimp Litopeneaus vannamei Using Linkage and Association Analysis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2017; 19:277-286. [PMID: 28508952 DOI: 10.1007/s10126-017-9749-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 04/19/2017] [Indexed: 06/07/2023]
Abstract
The Pacific white shrimp Litopenaeus vannamei is a predominant aquaculture shrimp species in the world. Like other animals, the L. vannamei exhibited sexual dimorphism in growth trait. Mapping of the sex-determining locus will be very helpful to clarify the sex determination system and further benefit the shrimp aquaculture industry towards the production of mono-sex stocks. Based on the data used for high-density linkage map construction, linkage-mapping analysis was conducted. The sex determination region was mapped in linkage group (LG) 18. A large region from 0 to 21.205 cM in LG18 showed significant association with sex. However, none of the markers in this region showed complete association with sex in the other populations. So an association analysis was designed using the female parent, pool of female progenies, male parent, and pool of male progenies. Markers were de novo developed and those showing significant differences between female and male pools were identified. Among them, three sex-associated markers including one fully associated marker were identified. Integration of linkage and association analysis showed that the sex determination region was fine-mapped in a small region along LG18. The identified sex-associated marker can be used for the sex detection of this species at genetic level. The fine-mapped sex-determining region will contribute to the mapping of sex-determining gene and help to clarify sex determination system for L. vannamei.
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Affiliation(s)
- Yang Yu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Xiaojun Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Jianbo Yuan
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Quanchao Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Shihao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Hao Huang
- Hainan Guangtai Ocean Breeding Co., Ltd., Wenchang, 571300, China
| | - Fuhua Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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27
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Abdelrahman H, ElHady M, Alcivar-Warren A, Allen S, Al-Tobasei R, Bao L, Beck B, Blackburn H, Bosworth B, Buchanan J, Chappell J, Daniels W, Dong S, Dunham R, Durland E, Elaswad A, Gomez-Chiarri M, Gosh K, Guo X, Hackett P, Hanson T, Hedgecock D, Howard T, Holland L, Jackson M, Jin Y, Khalil K, Kocher T, Leeds T, Li N, Lindsey L, Liu S, Liu Z, Martin K, Novriadi R, Odin R, Palti Y, Peatman E, Proestou D, Qin G, Reading B, Rexroad C, Roberts S, Salem M, Severin A, Shi H, Shoemaker C, Stiles S, Tan S, Tang KFJ, Thongda W, Tiersch T, Tomasso J, Prabowo WT, Vallejo R, van der Steen H, Vo K, Waldbieser G, Wang H, Wang X, Xiang J, Yang Y, Yant R, Yuan Z, Zeng Q, Zhou T. Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research. BMC Genomics 2017; 18:191. [PMID: 28219347 PMCID: PMC5319170 DOI: 10.1186/s12864-017-3557-1] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 02/06/2017] [Indexed: 12/31/2022] Open
Abstract
Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.
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Affiliation(s)
- Hisham Abdelrahman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Mohamed ElHady
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | | | - Standish Allen
- Aquaculture Genetics & Breeding Technology Center, Virginia Institute of Marine Science, Gloucester Point, VA, 23062, USA
| | - Rafet Al-Tobasei
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Lisui Bao
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ben Beck
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Harvey Blackburn
- USDA-ARS-NL Wheat & Corn Collections at a Glance GRP, National Animal Germplasm Program, 1111 S. Mason St., Fort Collins, CO, 80521-4500, USA
| | - Brian Bosworth
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - John Buchanan
- Center for Aquaculture Technologies, 8395 Camino Santa Fe, Suite E, San Diego, CA, 92121, USA
| | - Jesse Chappell
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - William Daniels
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Sheng Dong
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Rex Dunham
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Evan Durland
- Department of Fisheries and Wildlife, Oregon State University, Corvallis, OR, 97331, USA
| | - Ahmed Elaswad
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Marta Gomez-Chiarri
- Department of Fisheries, Animal & Veterinary Science, 134 Woodward Hall, 9 East Alumni Avenue, Kingston, RI, 02881, USA
| | - Kamal Gosh
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ximing Guo
- Haskin Shellfish Research Laboratory, Department of Marine and Coastal Sciences, Rutgers University, 6959 Miller Avenue, Port Norris, NJ, 08349, USA
| | - Perry Hackett
- Department of Genetics, Cell Biology and Development, 5-108 MCB, 420 Washington Avenue SE, Minneapolis, MN, 55455, USA
| | - Terry Hanson
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dennis Hedgecock
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-0371, USA
| | - Tiffany Howard
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Leigh Holland
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Molly Jackson
- Taylor Shellfish Farms, 130 SE Lynch RD, Shelton, WA, 98584, USA
| | - Yulin Jin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Karim Khalil
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Thomas Kocher
- Department of Biology, University of Maryland, 2132 Biosciences Research Building, College Park, MD, 20742, USA
| | - Tim Leeds
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Ning Li
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Lauren Lindsey
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Shikai Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Zhanjiang Liu
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA.
| | - Kyle Martin
- Troutlodge, 27090 Us Highway 12, Naches, WA, 98937, USA
| | - Romi Novriadi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Ramjie Odin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | - Eric Peatman
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Dina Proestou
- USDA ARS NEA NCWMAC Shellfish Genetics at the University Rhode Island, 469 CBLS, 120 Flagg Road, Kingston, RI, 02881, USA
| | - Guyu Qin
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Benjamin Reading
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, 27695-7617, USA
| | - Caird Rexroad
- USDA ARS Office of National Programs, George Washington Carver Center Room 4-2106, 5601 Sunnyside Avenue, Beltsville, MD, 20705, USA
| | - Steven Roberts
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, 98105, USA
| | - Mohamed Salem
- Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA
| | - Andrew Severin
- Genome Informatics Facility, Office of Biotechnology, Iowa State University, Ames, IA, 50011, USA
| | - Huitong Shi
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Craig Shoemaker
- Aquatic Animal Health Research Unit, USDA-ARS, 990 Wire Road, Auburn, AL, 36832, USA
| | - Sheila Stiles
- USDOC/NOAA, National Marine Fisheries Service, NEFSC, Milford Laboratory, Milford, Connectcut, 06460, USA
| | - Suxu Tan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Kathy F J Tang
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, 85721, USA
| | - Wilawan Thongda
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Terrence Tiersch
- Aquatic Germplasm and Genetic Resources Center, School of Renewable Natural Resources, Louisiana State University Agricultural Center, Baton Rouge, LA, 70820, USA
| | - Joseph Tomasso
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Wendy Tri Prabowo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Vallejo
- National Center for Cool and Cold Water Aquaculture, Agricultural Research Service, United States Department of Agriculture, Kearneysville, WV, 25430, USA
| | | | - Khoi Vo
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Geoff Waldbieser
- USDA-ARS/CGRU, 141 Experimental Station Road, Stoneville, MS, 38701, USA
| | - Hanping Wang
- Aquaculture Genetics and Breeding Laboratory, The Ohio State University South Centers, Piketon, OH, 45661, USA
| | - Xiaozhu Wang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Jianhai Xiang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, 266071, China
| | - Yujia Yang
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Roger Yant
- Hybrid Catfish Company, 1233 Montgomery Drive, Inverness, MS, 38753, USA
| | - Zihao Yuan
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Qifan Zeng
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Tao Zhou
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL, 36849, USA
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Chandler JC, Aizen J, Fitzgibbon QP, Elizur A, Ventura T. Applying the Power of Transcriptomics: Understanding Male Sexual Development in Decapod Crustacea. Integr Comp Biol 2016; 56:1144-1156. [PMID: 27252217 DOI: 10.1093/icb/icw007] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The decapod Crustacea are the most species-rich order of the Crustacea and include some of the most charismatic and highly valued commercial species. Thus the decapods draw a significant research interest in relation to aquaculture, as well as gaining a broader understanding of these species' biology. However, the diverse physiology of the group considered with the lack of a model species have presented an obstacle for comparative analyses. In reflection of this, the recent integration of comparative transcriptomics has rapidly advanced our understanding of key regulatory pathways and developmental phenomena, an example being our understanding of sexual development. We discuss our work in the Eastern spiny lobster, Sagmariasus verreauxi, in the context of what is currently known about male sexual development in the decapods, highlighting the importance of transcriptomic techniques in achieving our recent advancements. We describe the progression made in our understanding of male sexual differentiation and maturation, as mediated by the insulin-like androgenic gland hormone (IAG), integrating the role of regulatory binding proteins (IGFBPs), a tyrosine kinase insulin receptor (TKIR), as well as the upstream effect of neuroendocrine hormones (GIH and MIH). We then consider the less well understood mechanism of male sex determination, with an emphasis on what we believe to be the key regulatory factors, the Dsx- and mab-3-related transcription factors (Dmrts). Finally, we discuss the function of the antennal gland (AnG) in sexual development, relating to the emergence of male-biased upregulation in the AnG in later sexual maturation and the sexually dimorphic expression of two key genes Sv-TKIR and Sv-Dmrt1 We then present the AnG as a case study to illustrate how comparative transcriptomic techniques can be applied to guide preliminary analyses, like the hypothesis that the AnG may function in pheromone biosynthesis. In summary, we describe the power of transcriptomics in facilitating the progress made in our understanding of male sexual development, as illustrated by the commercial decapod species, S. verreauxi Considering future directions, we suggest that the integration of multiple omics-based techniques offers the most powerful tool to ensure we continue to piece together the biology of the important group of decapod Crustacea.
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Affiliation(s)
- Jennifer C Chandler
- *Faculty of Science, Health, Education and Engineering, GeneCology Research Centre, University of the Sunshine Coast (USC), 4 Locked Bag, Maroochydore, Queensland 4558, Australia
| | - Joseph Aizen
- *Faculty of Science, Health, Education and Engineering, GeneCology Research Centre, University of the Sunshine Coast (USC), 4 Locked Bag, Maroochydore, Queensland 4558, Australia
| | - Quinn P Fitzgibbon
- Fisheries and Aquaculture Centre, Institute for Marine and Antarctic Studies (IMAS), University of Tasmania, Private Bag 49, Hobart, Tasmania 7001, Australia
| | - Abigail Elizur
- *Faculty of Science, Health, Education and Engineering, GeneCology Research Centre, University of the Sunshine Coast (USC), 4 Locked Bag, Maroochydore, Queensland 4558, Australia
| | - Tomer Ventura
- *Faculty of Science, Health, Education and Engineering, GeneCology Research Centre, University of the Sunshine Coast (USC), 4 Locked Bag, Maroochydore, Queensland 4558, Australia
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Powell D, Knibb W, Nguyen NH, Elizur A. Transcriptional Profiling of Banana Shrimp Fenneropenaeus merguiensis with Differing Levels of Viral Load. Integr Comp Biol 2016; 56:1131-1143. [PMID: 27252205 DOI: 10.1093/icb/icw029] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Viral pathogens are of serious concern to the culture of penaeid shrimps worldwide. However, little is known about the molecular response of shrimp to viral infection. Selective breeding has been suggested as an effective long-term strategy to manage viral disease, though more information on gene function is needed to help inform breeding programs. The study of cultured banana shrimp (Fenneropenaeus merguiensis) infected with hepatopancreatic parvo-like virus (HPV) provides a unique opportunity to explore the host response to viral infection independent of challenge testing. To gain insight into the genetic mechanisms underlying resistance to high levels of HPV, we examined hepatopancreas tissue from six full-sib groups of banana shrimp with differing levels of HPV infection for differences in gene expression. A total of 404 differentially expressed genes were identified with 180 being over-expressed and 224 under-expressed among high-HPV full-sib groups. Based on homology analysis, a large proportion of these genes were associated with processes reported to be involved in the immune response of crustaceans, including pattern recognition proteins, antimicrobial peptides, components of the prophenoloxidase system, and antiviral activity. The results indicate shrimp from high-HPV full-sib groups appear to have a lower presence of important immune response elements, yet possess upregulated putative antiviral pathways. Within the differentially expressed genes, over 4000 sequence variants were identified to be exclusive to either the high- or low-HPV full-sib groups. To our knowledge, this is the first report of differential expression analysis using RNA-Seq to explore differences in viral load among high- and low-HPV full-sib groups of cultured shrimp. This research has provided additional insight into our understanding of the mechanisms involved in the response of this shrimp species to a naturally occurring viral pathogen. Sequence variants identified in this study offer an exceptional resource for mining gene-associated markers of HPV resistance.
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Affiliation(s)
- Daniel Powell
- Faculty of Science, Health, Education and Engineering, Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Wayne Knibb
- Faculty of Science, Health, Education and Engineering, Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Nguyen Hong Nguyen
- Faculty of Science, Health, Education and Engineering, Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
| | - Abigail Elizur
- Faculty of Science, Health, Education and Engineering, Genecology Research Centre, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia
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Molecular characterization and expression profile of three Fem-1 genes in Eriocheir sinensis provide a new insight into crab sex-determining mechanism. Comp Biochem Physiol B Biochem Mol Biol 2015; 189:6-14. [PMID: 26188322 DOI: 10.1016/j.cbpb.2015.07.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2015] [Revised: 06/25/2015] [Accepted: 07/07/2015] [Indexed: 02/02/2023]
Abstract
The FEM-1 protein of Caenorhabditis elegans plays a crucial role in the nematode sex-determination pathway. Here, we reported the characterization of three members of Fem-1 gene family in Eriocheir sinensis (designated EsFem-1a, EsFem-1b, and EsFem-1c), which were homologs of the nematode FEM-1 protein. The amino acid sequences of EsFem-1a, EsFem-1b, and EsFem-1c contained eight, nine, and eight ankyrin repeats, respectively. None of the ankyrin repeats had its own specific signature, and the evolution of ankyrin repeat was not completely independent. The predicted three-dimensional structure of EsFem-1 proteins exhibited highly similar superhelical conformation, especially the N-terminal six contiguous ankyrin repeats, which provided a binding surface for the protein-protein interaction. Phylogenetic tree based on the amino acid sequences revealed that EsFem-1a, EsFem-1b, and EsFem-1c were divided into three obvious separated clades. EsFem-1 genes were highly expressed in fertilized egg, 2-4 cell and blastula stage comparing with larval stage (P<0.01), which suggested they might be maternal genes. They also showed a certain degree of sexually dimorphic expression in some tissues. Notably, the highest expression of EsFem-1a was in the hepatopancreas, with EsFem-1b in testes and EsFem-1c in muscle (P<0.05), which indicated their potential role in a broad array of tissues. In addition, the genes initially involved in sex differentiation were not limited to those specifically expressed in the developing gonad. Taken together, these results suggested that EsFem-1 might function in crab early sex determination and late gonad development. The identification of Fem-1 gene family in E. sinensis provides a new insight into crab sex-determination mechanism.
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High-density linkage mapping aided by transcriptomics documents ZW sex determination system in the Chinese mitten crab Eriocheir sinensis. Heredity (Edinb) 2015; 115:206-15. [PMID: 25873149 DOI: 10.1038/hdy.2015.26] [Citation(s) in RCA: 76] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 01/21/2015] [Accepted: 02/23/2015] [Indexed: 01/20/2023] Open
Abstract
The sex determination system in crabs is believed to be XY-XX from karyotypy, but centromeres could not be identified in some chromosomes and their morphology is not completely clear. Using quantitative trait locus mapping of the gender phenotype, we revealed a ZW-ZZ sex determination system in Eriocheir sinensis and presented a high-density linkage map covering ~98.5% of the genome, with 73 linkage groups corresponding to the haploid chromosome number. All sex-linked markers in the family we used were located on a single linkage group, LG60, and sex linkage was confirmed by genome-wide association studies (GWAS). Forty-six markers detected by GWAS were heterozygous and segregated only in the female parent. The female LG60 was thus the putative W chromosome, with the homologous male LG60 as the Z chromosome. The putative Z and W sex chromosomes were identical in size and carried many homologous loci. Sex ratio (5:1) skewing towards females in induced triploids using unrelated animals also supported a ZW-ZZ system. Transcriptome data were used to search for candidate sex-determining loci, but only one LG60 gene was identified as an ankyrin-2 gene. Double sex- and mab3-related transcription factor 1 (Dmrt1), a Z-linked gene in birds, was located on a putative autosome. With complete genome sequencing and transcriptomic data, more genes on putative sex chromosomes will be characterised, thus leading towards a comprehensive understanding of the sex determination and differentiation mechanisms of E. sinensis, and decapod crustaceans in general.
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