Comparative physiology and aquaculture: Toward Omics-enabled improvement of aquatic animal health and sustainable production

Matthew L. Rise1, Christopher J. Martyniuk2, Muyan Chen3
1Department of Ocean Sciences, Memorial University of Newfoundland, 1 Marine Lab Road, St. John's, NL A1C 5S7, Canada
2Department 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
3College of Fisheries, Ocean University of China, Qingdao 266003, China

Tài liệu tham khảo

Abdelrahman, 2017, Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research, BMC Genomics, 18, 191, 10.1186/s12864-017-3557-1 Adamovsky, 2018, The gut microbiome and aquatic toxicology: An emerging concept for environmental health, Environ. Toxicol. Chem., 37, 2758, 10.1002/etc.4249 Andersson, 2015, Coordinated international action to accelerate genome-to-phenome with FAANG, the functional annotation of animal genomes project, Genome Biol., 16, 57, 10.1186/s13059-015-0622-4 Aslam, 2018, Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing, BMC Genet., 19, 43, 10.1186/s12863-018-0631-x Baranski, 2014, The development of a high density linkage map for black tiger shrimp (Penaeus monodon) based on cSNPs, PLoS One, 9, 10.1371/journal.pone.0085413 Berthelot, 2014, The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates, Nat. Commun., 5, 3657, 10.1038/ncomms4657 BOF:Bureau of Fisheries, 2017 Brawand, 2014, vol. 513, 375 Caballero-Solares, 2018, Changes in the liver transcriptome of farmed Atlantic salmon (Salmo salar) fed experimental diets based on terrestrial alternatives to fish meal and fish oil, BMC Genomics, 19, 796, 10.1186/s12864-018-5188-6 Casu, 2019, Investigation of graded-level soybean meal diets in red drum (Sciaenops ocellatus) using NMR-based metabolomics analysis, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 173, 10.1016/j.cbd.2018.11.009 Cerda, 2013, Advances in genomics for flatfish aquaculture, Genes Nutr., 8, 5, 10.1007/s12263-012-0312-8 Debnath, 2016, Review of the history, status and prospects of the black tiger shrimp (Penaeus monodon) hatchery sector in Bangladesh, Rev. Aquac., 8, 301, 10.1111/raq.12094 Détrée, 2019, Transcriptome mining of apoptotic mechanisms in response to density and functional diets in Oncorhynchus mykiss and role in homeostatic regulation, Comp. Biochem. Physiol. Part D Genomics Proteomics, 31, 100595, 10.1016/j.cbd.2019.100595 Du, 2012, Transcriptome sequencing and characterization for the sea cucumber Apostichopus japonicus (Selenka, 1867), PLoS One, 7, 10.1371/journal.pone.0033311 Dunham, 2014, Development of strategies for integrated breeding, genetics and applied genomics for genetic improvement of aquatic organisms, Aquaculture, S121, 10.1016/j.aquaculture.2013.10.020 Fan, 2019, Genome-wide identification and characterization of glucose transporter (glut) genes in spotted sea bass (Lateolabrax maculatus) and their regulated hepatic expression during short-term starvation, Comp. Biochem. Physiol. Part D Genomics Proteomics, 30, 217, 10.1016/j.cbd.2019.03.007 FAO, 2017 FAO, 2018 Froehlich, 2018, Comparative terrestrial feed and land use of an aquaculture-dominant world, Proc. Natl. Acad. Sci., 115, 5295, 10.1073/pnas.1801692115 Fu, 2018, LC-MS/MS-based metabolome analysis of biochemical pathways altered by food limitation in larvae of ivory shell, Babylonia areolata, Mar. Biotechnol. (New York, N.Y.), 20, 451, 10.1007/s10126-018-9808-6 Fu, 2019, Comparative transcriptology reveals effects of circadian rhythm in the nervous system on precocious puberty of the female Chinese mitten crab, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 67, 10.1016/j.cbd.2018.11.004 Gomez-Chiarri, 2015, The use of-omic tools in the study of disease processes in marine bivalve mollusks, J. Invertebr. Pathol., 131, 137, 10.1016/j.jip.2015.05.007 Guan, 2018, Is the nutritional value of fish fillet related to fish maturation or fish age? Integrated analysis of transcriptomics and metabolomics in blunt snout bream (Megalobrama amblycephala), Cell. Physiol. Biochem., 49, 17, 10.1159/000492837 Guo, 2012, Genetic mapping and QTL analysis of growth-related traits in the Pacific oyster, Mar. Biotechnol., 14, 218, 10.1007/s10126-011-9405-4 Guppy, 2018, The state of “omics” research for farmed penaeids: advances in research and impediments to industry utilization, Front. Genet., 9, 10.3389/fgene.2018.00282 Gutierrez, 2017, Development of a medium density combined-species SNP array for pacific and european oysters (Crassostrea gigas and Ostrea edulis), G3: Genes, Genomes, Genetics, 7, 2209, 10.1534/g3.117.041780 Gutierrez, 2018, Genomic selection for growth traits in Pacific oyster (Crassostrea gigas): potential of low-density marker panels for breeding value prediction, Front. Genet., 9, 10.3389/fgene.2018.00391 Hedgecock, 2015, Second-generation linkage maps for the pacific oyster Crassostrea gigas reveal errors in assembly of genome scaffolds, G3: Genes, genomes, genetics, 5, 2007, 10.1534/g3.115.019570 Hollenbeck, 2018, Genomic Tools and Selective Breeding in Molluscs, Front. Genet., 9, 10.3389/fgene.2018.00253 Houston, 2018, Atlantic salmon (Salmo salar L.) genetics in the 21st century: taking leaps forward in aquaculture and biological understanding, Front. Genet., 50, 3 Jones, 2017, A comparative integrated gene-based linkage and locus ordering by linkage disequilibrium map for the Pacific white shrimp, Litopenaeus vannamei, Sci. Rep., 7, 10360, 10.1038/s41598-017-10515-7 Katan, 2019, Effect of plant-based diets with varying ratios of Ω6 to Ω3 fatty acids on growth performance, tissue composition, fatty acid biosynthesis and lipid-related gene expression in Atlantic salmon (Salmo salar), Comp. Biochem. Physiol. Part D Genomics Proteomics, 30, 290, 10.1016/j.cbd.2019.03.004 Khatkar, 2017, Quantitative genomic analyses in the pacific whiteleg shrimp Litopenaeus vannamei, Proc. Assoc. Advmt. Anim. Breed. Genet., 121 Kim, 2003, A double-screening method to identify reliable candidate non-synonymous SNPs from chicken EST data, Anim. Genet., 249, 10.1046/j.1365-2052.2003.01003.x Li, 2009, A genetic linkage map of the sea cucumber, Apostichopus japonicus (Selenka), based on AFLP and microsatellite markers, Anim. Genet., 40, 678, 10.1111/j.1365-2052.2009.01900.x Li, 2011, Comparative genomics identifies candidate genes for infectious salmon anemia (ISA) resistance in Atlantic salmon (Salmo salar), Mar. Biotechnol., 13, 232, 10.1007/s10126-010-9284-0 Li, 2019, Comparative transcriptional analysis and RNA interference reveal immunoregulatory pathways involved in growth of the oriental river prawn Macrobranchium nipponense, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 24, 10.1016/j.cbd.2018.10.008 Li, 2019, Metabolic response of longitudinal muscles to acute hypoxia in sea cucumber Apostichopus japonicus (Selenka): a metabolome integrated analysis, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 235, 10.1016/j.cbd.2018.12.007 Lien, 2016, The Atlantic salmon genome provides insights into rediploidization, Nature, 533, 200, 10.1038/nature17164 Liu, 2016, The channel catfish genome sequence provides insights into the evolution of scale formation in teleosts, Nat. Commun., 7, 11757, 10.1038/ncomms11757 Liu, 2019, Genome-wide identification and expression profiling of the Wnt gene family in three bivalve molluscs, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 299, 10.1016/j.cbd.2019.01.008 Liu, 2019, Global metabolic responses of the lenok (Brachymystax lenok) to thermal stress, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 308, 10.1016/j.cbd.2019.01.006 Llewellyn, 2014, Teleost microbiomes: the state of the art in their characterization, manipulation and importance in aquaculture and fisheries, Front. Microbiol., 5, 207, 10.3389/fmicb.2014.00207 Lu, 2016, High-resolution genetic linkage mapping, high-temperature tolerance and growth-related quantitative trait locus (QTL) identification in Marsupenaeus japonicus, Mol. Genetics Genomics, 291, 1391, 10.1007/s00438-016-1192-1 Lu, 2019, Comparative analysis of growth performance and liver transcriptome response of juvenile Ancherythroculter nigrocauda fed diets with different protein levels, Comp. Biochem. Physiol. Part D Genomics Proteomics, 31, 100592, 10.1016/j.cbd.2019.05.002 Lund, 2019, A time-course study of gene expression and antibody repertoire at early time post vaccination of Atlantic salmon, Mol. Immunol., 106, 99, 10.1016/j.molimm.2018.12.018 Mackay, 2009, The genetics of quantitative traits: challenges and prospects, Nat. Rev. Genet., 10, 565, 10.1038/nrg2612 Macqueen, 2017, Functional Annotation of All Salmonid Genomes (FAASG): an international initiative supporting future salmonid research, conservation and aquaculture, BMC Genomics, 18, 484, 10.1186/s12864-017-3862-8 Martin, 2017, Nutrigenomics and immune function in fish: new insights from omics technologies, Dev. Comp. Immunol., 75, 86, 10.1016/j.dci.2017.02.024 Mekuchi, 2017, Trans-omics approaches used to characterise fish nutritional biorhythms in leopard coral grouper Plectropomus leopardus)., Sci. Rep., 7, 9372, 10.1038/s41598-017-09531-4 Mun, 2017, The Whole-Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum), Genome Biol. Evol., 9, 1487, 10.1093/gbe/evx096 Olsvik, 2019, Transcriptional effects of dietary chlorpyrifosmethyl exposure in Atlantic salmon (Salmo salar) brain and liver, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 43, 10.1016/j.cbd.2018.11.003 Pérez-Sánchez, 2014, Probiotics in aquaculture: a current assessment, Rev. Aquac., 6, 133, 10.1111/raq.12033 Powell, 2018, The genome of the oyster Saccostreaoffers insight into the environmental resilience of bivalves, DNA Res., 25, 655, 10.1093/dnares/dsy032 Qi, 2017, Construction and evaluation of a high-density SNP array for the Pacific oyster (Crassostrea gigas), PLoS One, 12, 10.1371/journal.pone.0174007 Quilang, 2007, Generation and analysis of ESTs from the eastern oyster, Crassostrea virginica Gmelin and identification of microsatellite and SNP markers, BMC Genomics, 8, 157, 10.1186/1471-2164-8-157 Rise, 2004, Microarray analyses identify molecular biomarkers of Atlantic salmon macrophage and hematopoietic kidney response to Piscirickettsia salmonis infection, Physiol. Genomics, 20, 21, 10.1152/physiolgenomics.00036.2004 Rise, 2004, Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics, Genome Res., 14, 478, 10.1101/gr.1687304 Robalino, 2007, Insights into the immune transcriptome of the shrimp Litopenaeus vannamei: tissue-specific expression profiles and transcriptomic responses to immune challenge, Physiol. Genomics, 29, 44, 10.1152/physiolgenomics.00165.2006 Robinson, 2014, QTL for white spot syndrome virus resistance and the sex-determining locus in the Indian black tiger shrimp (Penaeus monodon), BMC Genomics, 15, 731, 10.1186/1471-2164-15-731 Sapkota, 2019, Water Reuse, Food Production and Public Health: Adopting Transdisciplinary, Systems-Based Approaches to Achieve Water and Food Security in a Changing Climate, Environ. Res., 171, 576, 10.1016/j.envres.2018.11.003 Sarropoulou, 2005, Gene expression profiling of gilthead sea bream during early development and detection of stress related genes by the application of cDNA microarray technology, Physiol. Genomics, 23, 182, 10.1152/physiolgenomics.00139.2005 Sauvage, 2007, Single nucleotide polymorphisms and their relationship to codon usage bias in the Pacific oyster Crassostrea gigas, Gene, 406, 13, 10.1016/j.gene.2007.05.011 Sauvage, 2010, QTL for resistance to summer mortality and OsHV-1 load in the Pacific oyster (Crassostrea gigas), Anim. Genet., 41, 390 Schock, 2012, An NMR-based metabolomic assessment of cultured cobia health in response to dietary manipulation, Food Chem., 133, 90, 10.1016/j.foodchem.2011.12.077 Shen, 2019, Hemolymph and transcriptome analysis to understand innate immune responses to hypoxia in Pacific abalone, Comp. Biochem. Physiol. Part D Genomics Proteomics, 30, 102, 10.1016/j.cbd.2019.02.001 Solbakken, 2019, Whole transcriptome analysis of the Atlantic cod vaccine response reveals subtle changes in adaptive immunity, Comp. Biochem. Physiol. Part D Genomics Proteomics, 31, 10.1016/j.cbd.2019.100597 Spencer, 2019, Pacific geoduck (Panopea generosa) resilience to natural pH variation, Comp. Biochem. Physiol. Part D Genomics Proteomics, 30, 91, 10.1016/j.cbd.2019.01.010 Star, 2011, The genome sequence of Atlantic cod reveals a unique immune system, Nature, 477, 207, 10.1038/nature10342 Stead, 2019, Using systems thinking and open innovation to strengthen aquaculture policy for the United Nations Sustainable Development Goals, J. Fish Biol., 94, 837 Sun, 2010, Characterization of thirteen single nucleotide polymorphism markers in the sea cucumber (Apostichopus japonicus), Conserv. Genet. Resour., 2, 141, 10.1007/s12686-010-9270-x Sun, 2019, Liver transcriptome analysis and de novo annotation of the orange-spotted groupers (Epinephelus coioides) under cold stress, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 264, 10.1016/j.cbd.2018.12.008 Suweis, 2015, Resilience and reactivity of global food security, Proc. Natl. Acad. Sci. U. S. A., 112, 6902, 10.1073/pnas.1507366112 Tamea, 2016, Global effects of local food-production crises: a virtual water perspective, Sci. Rep., 6, 18803, 10.1038/srep18803 Tian, 2015, Construction of a high-density genetic map and quantitative trait locus mapping in the sea cucumber Apostichopus japonicus, Sci. Rep., 5, 14852, 10.1038/srep14852 Tian, 2019, Dietary arachidonic acid decreases the expression of transcripts related to adipocyte development and chronic inflammation in the adipose tissue of juvenile grass carp, Ctenopharyngodon idella, Comp. Biochem. Physiol. Part D Genomics Proteomics, 30, 122, 10.1016/j.cbd.2019.02.006 Tong, 2016, Climate change, food, water and population health in China, Bull. World Health Organ., 94, 759, 10.2471/BLT.15.167031 Tørresen, 2016, An improved version of the Atlantic cod genome and advancements in functional genomics: implications for the future of cod farming, Genomics in Aquaculture, 45, 10.1016/B978-0-12-801418-9.00003-2 Troost, 2010, Causes and effects of a highly successful marine invasion: case-study of the introduced Pacific oyster Crassostrea gigas in continental NW European estuaries, J. Sea Res., 64, 145, 10.1016/j.seares.2010.02.004 Wang, 2015, Discovery and validation of genic single nucleotide polymorphisms in the Pacific oysterCrassostrea gig, Mol. Ecol. Resour., 15, 123, 10.1111/1755-0998.12278 Watson, 2019, Investigation of graded levels of soybean meal diets for red drum, Sciaenops ocellatus, using quantitative PCR derived biomarkers, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 274, 10.1016/j.cbd.2019.01.002 Xing, 2018, De novo assembly and comparative transcriptome analyses of purple and green morphs of Apostichopus japonicus during body wall pigmentation process, Comp. Biochem. Physiol. Part D Genomics Proteomics, 28, 151, 10.1016/j.cbd.2018.09.001 Xu, 2019, Hepatic transcriptome of the euryhaline teleost Japanese seabass (Lateolabrax japonicus) fed diets characterized by alpha-linolenic acid or linoleic acid, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 106, 10.1016/j.cbd.2018.11.005 Yan, 2013, A genetic linkage map of the sea cucumber (Apostichopus japonicus) based on microsatellites and SNPs, Aquaculture, 404, 1, 10.1016/j.aquaculture.2013.04.011 Yang, 2012, Characterization of fifteen SNP markers by mining EST in sea cucumber Apostichopus japonicus, J. Genet., 1 Yang, 2019, Effect of Temperature on the Microflora Community Composition in the Digestive Tract of the Veined Rapa Whelk (Rapanavenosa) Revealed by 16S rRNA Gene Sequencing, vol. 29, 145 Ye, 2018, Applications of transcriptomics and proteomics in understanding fish immunity, Fish Shellfish Immunol.,, 77, 319, 10.1016/j.fsi.2018.03.046 Yu, 2015, Genome survey and high-density genetic map construction provide genomic and genetic resources for the Pacific white shrimpLitopenaeus vanname, Sci. Rep., 5, 15612, 10.1038/srep15612 Zhan, 2019, Comparative transcriptome analysis identifies genes associated with papilla development in the sea cucumber Apostichopus japonicus, Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 255, 10.1016/j.cbd.2018.12.009 Zhang, 2010, Development and validation of single nucleotide polymorphism markers in the eastern oyster Crassostrea virginica Gmelin by mining ESTs and resequencing, Aquaculture, 302, 124, 10.1016/j.aquaculture.2010.02.012 Zhang, 2012, The oyster genome reveals stress adaptation and complexity of shell formation, Nature, 490, 49, 10.1038/nature11413 Zhang, 2017, The sea cucumber genome provides insights into morphological evolution and visceral regeneration, PLoS Biol., 15, 10.1371/journal.pbio.2003790 Zhang, 2018, Identification of a gene encoding microphthalmia-associated transcription factor and its association with shell color in the clam Meretrix petechialis, Comp. Biochem. Physiol. Part B Biochem. Mol. Biol., 225, 75, 10.1016/j.cbpb.2018.04.007 Zhang, 2019, Penaeid shrimp genome provides insights into benthic adaptation and frequent molting, Nat. Commun., 10, 356, 10.1038/s41467-018-08197-4 Zhong, 2014, QTL mapping for glycogen content and shell pigmentation in the Pacific oyster Crassostrea gigas using microsatellites and SNPs, Aquac. Int., 22, 1877, 10.1007/s10499-014-9789-z Zhou, 2014, Transcriptome sequencing of sea cucumber (Apostichopus japonicus) and the identification of gene-associated markers, Mol. Ecol. Resour., 14, 127, 10.1111/1755-0998.12147 Zhou, 2019 Zhou, 2019, Brain and intestine transcriptome analyses and identification of genes involved in feed conversion efficiency of Yellow River carp (Cyprinus carpio haematopterus), Comp. Biochem. Physiol. Part D Genomics Proteomics, 29, 221, 10.1016/j.cbd.2018.12.004