A National Food Genome Program

A National Food Genome Program
January, 1998
Overview
The long-range scientific goal of the National Food Genome Program (NFGP) should be to identify, map, and understand the function and control of the genes responsible for economically important traits in the major agriculturally important species of animals, microbes, and plants. Achieving this goal will permit the development of new genetic technologies for improvement in yield, composition, and quality of the domestic agricultural output. The desired practical outcomes of the NFGP will be a safe and abundant food supply that meets consumer demands for quality and an increase in agricultural exports to meet the needs of the growing world population while ensuring U.S. competitiveness in agriculture and agricultural research.

Animal Genome Program
The pathway by which the important genes of animals can be identified has been clearly established. At this time, animal genome research is being conducted primarily by scientists in USDA's Agricultural Research Service and the State Agricultural Experiment Stations. These programs are highly collaborative and fully complementary. The scientific thrust of the NFGP must address the core obstacles limiting the development and implementation of gene-based approaches for animal improvement. The most fundamental tool required for identifying agriculturally useful genes is a high-resolution genomic map of genes. Comparative maps result from mapping the same genes in several species and identifying regions of conserved gene order among species. Comparative mapping will allow discoveries in one species to be transferred to other species and will utilize the results of federally funded efforts of human and mouse mapping for agriculture. Increasing interest in non-major agriculture (e.g., sheep, goat, horse) and aquaculture (e.g., catfish, trout, salmon) species can benefit from comparative map information even if major efforts are focused on cattle, pig, and poultry genomes. Focusing on comparative map developing and sequencing and mapping of important genes will be a rapid and cost-effective means for achieving the primary aims of the NFGP. Using well-designed resource populations, performance data, and densely saturated marker linkage maps (e.g., microsatellites), the chromosomal regions in which quantitative trait locus (QTL) reside can be localized. This provides a focus for identification of multiple genes controlling single traits.
A three-pronged strategy will be employed to meet the objectives of the animal genome program. There will be competitive grants for consortia (or teams) of laboratories (agricultural experiment stations and Agricultural Research Service, with industry if appropriate) for mapping. Functional genomics and computational biology will be the province of individual investigator (single or teams) initiated proposals submitted to a competitive grant program. Development of shared resources is required, such as radiation hybrid panels for comparative mapping, oligonucleotide arrays for "DNA-chip" based expression studies and genotyping, large insert DNA libraries for gene identification and databases for genomic information. Shared resources should be funded on a competitive contract basis, with all public and private institutions eligible for participation in the program. Such resources will be made available to all domestic investigators, with appropriate mechanisms to ensure the federal government's return on investment.
In summary, the primary scientific objective of the NFGP during the first five years will be to map and characterize genes with potentially large effects on animal health, production, food safety, and product quality in major agriculturally important species of animals.
Objectives

1. To develop high resolution genetic maps focusing on cattle, pigs, and chickens (mapping)

[This will utilize comparative mapping strategies to align mapping of agricultural species with those of human, mouse, and each other. Marker density of existing linkage maps will be increased to 0.2 cm to enhance their utility in QTL mapping. Linkage maps will be integrated with complete physical maps of chromosomes. Ordered physical maps will be created from large-insert DNA libraries (e.g., yeast or bacterial artificial chromosomes-YAC and BAC).]

2. To determine the sequence and function of structural genes in food animal species (functional genomics)

[This will include sequence data on structural genes including regulatory elements. In one strategy, the sequence of expressed sequence tags (ESTs) will be first established. In addition, the function of the gene product will be determined as will how variation in the gene product or expression level influences the gene's biological impact.]

3. To create the computational biology necessary for the unique population structure of agricultural species (informatics and statistical design)

[This will include developing the new statistical designs to allow efficient determination of quantitative trait loci (using also molecular population data) with high power and accuracy.]

4. To provide and maintain a repository for shared resources including database (infrastructure)

[This will include: a) centralized database(s) staffed by skilled technicians and well-qualified editors; b) technology centers where sophisticated technologies exist (e.g., high throughput genotyping and DNA chip technology); c) repositories of DNA [YAC, BAC libraries and DNA for mapping from reference and resource families together with accompanying performance data]; and d) animal resource population.]

Budget
To ensure the U.S. food animal industries remain competitive in both U.S. and world markets, it is essential to have: 1) increased USDA funding to provide a minimum of $30 million per year in USDA competitive grants focused specifically for animal genome research, and 2) increased USDA funding for a long-term sustained effort by USDA's Agricultural Research Service. This increased federal funding should be coupled with increased funding by the State Agricultural Experiment Stations, and an industry level commitment of resources at least equivalent to public sector funding.
Conceptually, the $30 million could include funds for:

Program support for mapping to consortia of large and small laboratories from land grant universities and Agricultural Research Service, with industry partners, if appropriate.
Investigator-initiated projects (functional genomics; informatics and statistical design)
Shared resources including database
Technology transfer
$12M/year for mapping each of cattle, pig, and chicken
$2.5M/year for mapping other food animal species
$8M/year for functional genomics
$2M/year for computational biology
$5.5M/year for shared resources

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1.	To develop high resolution genetic maps focusing on cattle, pigs, and chickens (mapping) [This will utilize comparative mapping strategies to align mapping of agricultural species with those of human, mouse, and each other. Marker density of existing linkage maps will be increased to 0.2 cm to enhance their utility in QTL mapping. Linkage maps will be integrated with complete physical maps of chromosomes. Ordered physical maps will be created from large-insert DNA libraries (e.g., yeast or bacterial artificial chromosomes-YAC and BAC).]
2.	To determine the sequence and function of structural genes in food animal species (functional genomics) [This will include sequence data on structural genes including regulatory elements. In one strategy, the sequence of expressed sequence tags (ESTs) will be first established. In addition, the function of the gene product will be determined as will how variation in the gene product or expression level influences the gene's biological impact.]
3.	To create the computational biology necessary for the unique population structure of agricultural species (informatics and statistical design) [This will include developing the new statistical designs to allow efficient determination of quantitative trait loci (using also molecular population data) with high power and accuracy.]
4.	To provide and maintain a repository for shared resources including database (infrastructure) [This will include: a) centralized database(s) staffed by skilled technicians and well-qualified editors; b) technology centers where sophisticated technologies exist (e.g., high throughput genotyping and DNA chip technology); c) repositories of DNA [YAC, BAC libraries and DNA for mapping from reference and resource families together with accompanying performance data]; and d) animal resource population.]