From FAANG to fork: application of highly annotated genomes to improve farmed animal production
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From FAANG to fork: application of highly annotated genomes to improve farmed animal production Emily L. Clark1* , Alan L. Archibald1, Hans D. Daetwyler2,3, Martien A. M. Groenen4, Peter W. Harrison5, Ross D. Houston1, Christa Kühn6,7, Sigbjørn Lien8, Daniel J. Macqueen1, James M. Reecy9, Diego Robledo1, Mick Watson1, Christopher K. Tuggle9 and Elisabetta Giuffra10
* Correspondence: emily.clark@ roslin.ed.ac.uk 1 The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Edinburgh EH25 9RG, UK Full list of author information is available at the end of the article
Introduction The Food and Agriculture Organisation of the United Nations (FAO) reports that by the year 2050 the global human population is likely to reach 9.7 billion, rising to 11.2 billion by 2100 (https://population.un.org/wpp/Publications/Files/Key_Findings_ WPP_2015.pdf). This population growth poses several challenges to the global food system, which will need to produce more healthy food using fewer natural resources, reducing the environmental impact, conserving biodiversity and flexibly adjusting to changing societal expectations. Meeting this demand requires environmentally sustainable improvements to farmed animal health and welfare, and of efficiency and diversification (e.g. to include a broader range of locally adapted species) [1]. The changes in breeding strategies and management practises required to meet these goals will need to build on an improved ability to accurately use genotype to predict phenotype in the world’s farmed animal species, both terrestrial and aquatic (Fig. 1). Here we describe a set of research priorities to meet such present and future challenges that build on progress, successes and resources from the Functional Annotation of ANimal Genomes (FAANG) project [2]. The first stages of FAANG focused on foundational data generation to characterise expressed and regulatory genomic regions, curation and provision of annotated farmed animal genomes [2, 3]. These were largely based on individual level, high depth approaches [3]. The primary challenge facing this community now is harnessing these resources to link genotype, phenotype and genetic merit in order to translate this research out of the laboratory and into industry application in the field. To achieve this effectively, we will need to generate functional genomic information for large populations of animals, rather than relying on a small number of deeply annotated individuals. Furthermore, to date, most of the datasets are from tissues consisting of heterogeneous cell populations, hindering the resolution of © The Author(s). 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other thi
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