“Identifying the Future Needs for Long-Term USDA Efforts in Agricultural Animal Genomics”
Green RD, et. al., “Identifying Future Needs for Long-Term USDA Efforts in Agricultural Animal Genomics,” International Journal of Biological Sciences, 3, 185-191, (2007).
The purpose of this article was to summarize the conclusions and recommendations made at the USDA workshop held in Washington, D.C. in September 2004 titled “Chartering the Road Map for Long Term USDA Efforts in Agricultural Animal Genomics.” This workshop was organized to determine the direction of further research into agricultural animal genomics, with an emphasis on downstream applications that will lead to animal improvements that will benefit producers, consumers and researchers.
BAC bacterial artificial chromosome – a plasmid cloning vector derived from the F plasmid, which can accept very large clones of DNA. It is often used in genome-sequencing project to create DNA libraries [Snyder].
cDNA complementary DNA – DNA that has been synthesized from mRNA through the action of a reverse transcriptase. It is often used to clone genes and create DNA libraries in genome-sequencing projects [Snyder].
EST expressed sequence tag – a short sequence of cDNA, which is often used to identify gene transcripts and to determine gene sequence [Snyder].
genome annotation assigning biological information to a sequence of a genome [Snyder].
in silico performed on a computer or via a computer simulation [Wikipedia.org].
linkage maps map of a species genome, showing the position of known genes and gene markers relative to one another, as determined by recombination frequencies [Snyder].
QTL (see Figure 1) quantitative trait locus – sequences of DNA that are closely related to a specific, measurable phenotype [Snyder].
radiation hybrid mapping a technique for determining the order of genetic loci along chromosomes, which involves fusing irradiated donor cells with host cells from another species. This allows fragments of DNA from the irradiated cells to become integrated into the chromosome of the host cells. Molecular probing of the DNA from the fused cells can then be used to determine whether two or more genetic loci are located within the same fragment of donor DNA [Snyder].
RNAi RNA interference – a cellular mechanism which controls gene expression through the action of two types of RNA molecules – microRNA and small interfering RNA – which can bind to mRNA to promote or hinder its translation [Snyder].
SNP single nucleotide polymorphism – a variation of a single nucleotide in a DNA sequence that occurs between members of the same species [Snyder].
Snyder, L, Champness, W, (2007). Molecular Genetics of Bacteria. Washington, D.C.: ASM Press.
Molecular biology has positively impacted agricultural animal research, allowing for the development of more accurate and rapid animal improvements. In September 2004, a USDA workshop was held in Washington, D.C. to determine how continued research in agricultural animal genomics should be organized, funded and directed. An emphasis was placed on the downstream applications of animal genomics research, including applications in metabolomics. The ultimate goal of this research is to understand the biological mechanisms behind economically favorable phenotypes in livestock, using an integrated biological systems approach.
The first session of the workshop addressed the priorities for structural genomics in animal genomics research. The linkage and comparative maps, SNP maps and fine QTL maps (see figure 1) being created through animal genomics research projects will allow researchers to evaluate the genetic diversity of each animal species and to develop DNA-based animal identification systems. A general consensus was reached that all genome-sequencing data should be organized into public databases to facilitate these research efforts. The workshop attendees outlined several goals for future research towards structural genomics. They recommended that: 1) the swine genome be sequenced next, 2) BAC maps and 2-fold sequence coverage be obtained, 3) cDNA libraries be developed to allow functional annotation and complete integration of genetic linkage, radiation hybrid and physical maps for horse, turkey, goat, catfish , salmon and trout genomes, 4) SNP markers be discovered and validated and haplotype maps be developed for all species to allow for fine mapping of QTL, 5) standardized population and phenotype resources for each species be developed.
The second session of the workshop focused on the priorities for functional genomics in animal genomics research. Emphasis was placed on support for downstream applications in the areas of proteomics, metabolomics and metagenomics. Research in these areas will fully capitalize on the structural genomics infrastructure and will increase knowledge of the biology underlying economically desirable phenotypes in livestock. Metabolomics will allow for the genomic characterization of systems of proteins, leading to applications in animal health and nutrition. The attendees recommended that: 1) downstream research be made a high priority, 2) standardized methods for defining phenotypes be developed, 3) bioinformatics capacity be enhanced to handle the increased complexity and volume of the resulting data, 4) an integrative systems biology perspective be taken, and 5) a long-term strategic plan for USDA animal genomics research be developed and integrated.
The third and final session of the workshop addressed the priorities for bioinformatics in animal genomics research. The databases and bioinformatics tools required to manage the vast amounts of data being accrued in this research is already available. However, these systems are spread out amongst many different agencies and there is a widespread lack of the specially trained personnel required to utilize them. The attendees recommended that 1) the resources available at the various agencies be integrated, 2) special programs be developed to train researchers to use these tools, 3) standard descriptions of phenotypes be developed, and 4) USDA resources be dedicated to develop new bioinformatics tools specific to agricultural animal research.
The full benefits of the research being conducted in agricultural animal genomics will be reaped in its downstream applications in structural and functional genomics. An integrated approach which includes proteomics, metabolomics and metagenomics will lead to an understanding of how genome sequences relate to economically important phenotypes in livestock, such as phenotypes involving disease resistance, behavior, growth, product quality and reproductive ability. The USDA workshop has provided recommendations for the organization and direction of further research in agricultural animal genomics that emphasize such an integrated biological systems approach.
Figure 1. An example of a QTL scan [Wikipedia Commons].