The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization
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 in...
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Frontiers Media S.A.
2018-08-01
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Series: | Frontiers in Genetics |
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Online Access: | https://www.frontiersin.org/article/10.3389/fgene.2018.00282/full |
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doaj-0e5f5a34d2a6461f89a96ba810a4e029 |
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Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jarrod L. Guppy Jarrod L. Guppy David B. Jones David B. Jones Dean R. Jerry Dean R. Jerry Nicholas M. Wade Nicholas M. Wade Herman W. Raadsma Herman W. Raadsma Roger Huerlimann Roger Huerlimann Kyall R. Zenger Kyall R. Zenger |
spellingShingle |
Jarrod L. Guppy Jarrod L. Guppy David B. Jones David B. Jones Dean R. Jerry Dean R. Jerry Nicholas M. Wade Nicholas M. Wade Herman W. Raadsma Herman W. Raadsma Roger Huerlimann Roger Huerlimann Kyall R. Zenger Kyall R. Zenger The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization Frontiers in Genetics penaeid shrimps omics advanced breeding aquaculture genome assembly linkage mapping |
author_facet |
Jarrod L. Guppy Jarrod L. Guppy David B. Jones David B. Jones Dean R. Jerry Dean R. Jerry Nicholas M. Wade Nicholas M. Wade Herman W. Raadsma Herman W. Raadsma Roger Huerlimann Roger Huerlimann Kyall R. Zenger Kyall R. Zenger |
author_sort |
Jarrod L. Guppy |
title |
The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization |
title_short |
The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization |
title_full |
The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization |
title_fullStr |
The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization |
title_full_unstemmed |
The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry Utilization |
title_sort |
state of “omics” research for farmed penaeids: advances in research and impediments to industry utilization |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2018-08-01 |
description |
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. |
topic |
penaeid shrimps omics advanced breeding aquaculture genome assembly linkage mapping |
url |
https://www.frontiersin.org/article/10.3389/fgene.2018.00282/full |
work_keys_str_mv |
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doaj-0e5f5a34d2a6461f89a96ba810a4e0292020-11-25T02:28:07ZengFrontiers Media S.A.Frontiers in Genetics1664-80212018-08-01910.3389/fgene.2018.00282396422The State of “Omics” Research for Farmed Penaeids: Advances in Research and Impediments to Industry UtilizationJarrod L. Guppy0Jarrod L. Guppy1David B. Jones2David B. Jones3Dean R. Jerry4Dean R. Jerry5Nicholas M. Wade6Nicholas M. Wade7Herman W. Raadsma8Herman W. Raadsma9Roger Huerlimann10Roger Huerlimann11Kyall R. Zenger12Kyall R. Zenger13Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, AustraliaCollege of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, AustraliaAustralian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, AustraliaCollege of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, AustraliaAustralian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, AustraliaCollege of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, AustraliaAustralian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, AustraliaAquaculture Program, CSIRO Agriculture & Food, Queensland Bioscience Precinct, St Lucia, QLD, AustraliaAustralian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, AustraliaFaculty of Science, Sydney School of Veterinary Science, The University of Sydney, Camden, NSW, AustraliaAustralian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, AustraliaCollege of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, AustraliaAustralian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, AustraliaCollege of Science and Engineering and Centre for Sustainable Tropical Fisheries and Aquaculture, James Cook University, Townsville, QLD, AustraliaElucidating 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.https://www.frontiersin.org/article/10.3389/fgene.2018.00282/fullpenaeid shrimpsomicsadvanced breedingaquaculturegenome assemblylinkage mapping |