Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Abdelrahman et al. BMC Genomics (2017) 18:191 DOI 10.1186/s12864-017-3557-1 COMMENTARY Open Access Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research The Aquaculture Genomics, Genetics and Breeding Workshop, Hisham Abdelrahman1, Mohamed ElHady2, Acacia Alcivar-Warren3, Standish Allen4, Rafet Al-Tobasei5, Lisui Bao1, Ben Beck6, Harvey Blackburn7, Brian Bosworth8, John Buchanan9, Jesse Chappell1, William Daniels1, Sheng Dong1, Rex Dunham1, Evan Durland10, Ahmed Elaswad1, Marta Gomez-Chiarri11, Kamal Gosh1, Ximing Guo12, Perry Hackett13, Terry Hanson1, Dennis Hedgecock14, Tiffany Howard1, Leigh Holland1, Molly Jackson15, Yulin Jin1, Karim Khalil1, Thomas Kocher16, Tim Leeds17, Ning Li1, Lauren Lindsey1, Shikai Liu1, Zhanjiang Liu1*, Kyle Martin18, Romi Novriadi1, Ramjie Odin1, Yniv Palti17, Eric Peatman1, Dina Proestou19, Guyu Qin1, Benjamin Reading20, Caird Rexroad21, Steven Roberts22, Mohamed Salem5, Andrew Severin23, Huitong Shi1, Craig Shoemaker6, Sheila Stiles24, Suxu Tan1, Kathy F. J. Tang25, Wilawan Thongda1, Terrence Tiersch26, Joseph Tomasso1, Wendy Tri Prabowo1, Roger Vallejo17, Hein van der Steen27, Khoi Vo1, Geoff Waldbieser8, Hanping Wang28, Xiaozhu Wang1, Jianhai Xiang29, Yujia Yang1, Roger Yant30, Zihao Yuan1, Qifan Zeng1 and Tao Zhou1 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, highdensity 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. (Continued on next page) * Correspondence: 1 School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA Full list of author information is available at the end of the article © The Author(s). 2017 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Abdelrahman et al. BMC Genomics (2017) 18:191 Page 2 of 23 (Continued from previous page) 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. Keywords: Aquaculture, Genetic resources, Genome, Transcriptome, QTL, RNA-Seq, SNP, Fish, Shellfish Background The major goals of research programs having components related to aquaculture genomics, genetics and breeding are to enhance aquaculture production efficiency, sustainability, product quality and profitability in support of the commercial sector and for the benefit of U.S. consumers. Progress towards achieving these goals includes genetic improvement of production, performance and animal welfare/ fitness traits, and this progress is predicated upon the access and utilization of an array of genetic resources within each species group. To this end, various genetic stock enhancement approaches are currently being studied by the aquaculture research community, and major progress has been made since the start of aquaculture genomics research 20 years ago [1]. Such progress includes advances in traditional selection, intraspecific crossbreeding, interspecific hybridization, genome-enabled selection (e.g., marker/causal mutation-assisted selection and/or genomic selection), polypoidy, sex reversal and breeding, xenogenesis, gene transfer, and genome editing. Some of the most important traits studied for genetic improvement in U.S. aquaculture species include disease resistance, feed conversion efficiency, growth rate, behaviour, processing yield, reproductive characteristics and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salini (...truncated)