Genome to Phenome: Improving Animal Health, Production, and Well-Being - A New USDA Blueprint for Animal Genome Research 2018-2027

Abstract

In 2008, a consortium led by the Agricultural Research Service (ARS) and the National Institute for Food and Agriculture (NIFA) published the "Blueprint for USDA Efforts in Agricultural Animal Genomics 2008-2017," which served as a guiding document for research and funding in animal genomics. In the decade that followed, many of the goals set forth in the blueprint were accomplished. However, several other goals require further research. In addition, new topics not covered in the original blueprint, which are the result of emerging technologies, require exploration. To develop a new, updated blueprint, ARS and NIFA, along with scientists in the animal genomics field, convened a workshop titled "Genome to Phenome: A USDA Blueprint for Improving Animal Production" in November 2017, and these discussions were used to develop new goals for the next decade. Like the previous blueprint, these goals are grouped into the broad categories "Science to Practice," "Discovery Science," and "Infrastructure." New goals for characterizing the microbiome, enhancing the use of gene editing and other biotechnologies, and preserving genetic diversity are included in the new blueprint, along with updated goals within many genome research topics described in the previous blueprint. The updated blueprint that follows describes the vision, current state of the art, the research needed to advance the field, expected deliverables, and partnerships needed for each animal genomics research topic. Accomplishment of the goals described in the blueprint will significantly increase the ability to meet the demands for animal products by an increasing world population within the next decade.

Keywords: animal; biotechnology; discovery; genomics; health; infrastructure; phenotype; production.

FIGURE 1

Locations of 1,136,252 genotyped Holsteins. Figure provided by Troy Rowan using zip code data contributed by George Wiggans.

FIGURE 2

Average genetic value for net merit of artificial insemination bulls by year of entry into artificial insemination. The acceleration of genetic gain for net merit by incorporating genomic selection is illustrated by comparing rates of genetic gain across three time periods. Net merit is an index of traits designed to optimize productivity and profitability of daughters in a dairy herd. Genomic information from high-density genotyping was introduced in 2009. Reproduced from Wiggans and Cole (2017) which is not subject to copyright protection.

FIGURE 3

Reduction in the age of parents for selection in dairy cattle using genomic analysis. The generation interval has reduced to nearly one-third of that required without genomic selection. Reprinted from Wiggans and Cole (2017) which is not subject to copyright protection.

FIGURE 4

Locations of 521,645 genotyped animals. Figure provided by of Dan Moser, American Angus Association.

FIGURE 5

The Porcine Genetic Improvement in US Dollars index shows the genetic gain achieved in the nucleus hers of the Pig Improvement Company (PIC). The index shows the genetic gain achieved in the porcine nucleus herds of PIC, the world’s largest porcine breeding company. It measures the marginal economic value of improvement in customer profitability. A greater increase (>35% long term) in the rate of change in genetic gain as a direct result of implementing genomic selection has been achieved. Reproduced as a courtesy from Ernst Van Orsouw from the Genus Annual Report 2015 (p. 16, https://www.genusplc.com/investors/results-reports-and-presentations/).

FIGURE 6

Genetic improvement in a nucleus herd translates into visible gains on commercial farms. Reproduced as a courtesy from Ernst Van Orsouw from the Genus 2018 investor presentation (https://www.genusplc.com/media/1460/genus-interim-results-presentation-28feb2018.pdf).

FIGURE 7

U.S. poultry companies export genome-selected poultry breeding stock to 110 countries (http://www.hyline.com/UserDocs/Pages/INNO_ISSUE_15_ENG.pdf).

FIGURE 8

Genomic selection in rainbow trout doubles selection accuracy in a single generation compared with traditional pedigree-based predictions. This figure is reproduced and modified from Additional file 2 of Figure S1 in Vallejo and Leeds (2017).

FIGURE 9

Publication dates for initial draft genome assemblies of major agricultural animals.

FIGURE 10

Efficient isolation of pluripotent embryonic stem cells (ESCs) from cattle embryos allows the development of in vitro breeding schemes based on an embryo-stem cell-gamete cycle, including an intermediate genomic selection to provide directional selection of genetic progress. If such a scheme could be accomplished, it would significantly decrease the generation interval and allow for increased selection intensity leading to accelerated genetic progress. IVF, in vitro fertilization; ET, Embryo transfer. Image from Van Eenennaam (2018). Reproduced with permission from the author’s entry in the Encyclopedia of Food Security and Sustainability, Ferranti et al., (2018).