<i>Medicago truncatula</i> functional genomics: an invaluable resource for studies on agriculture sustainability

Legume functional genomics has moved many steps forward in the last two decades thanks to the improvement of genomics technologies and to the efforts of the research community. Tools for functional genomics studies are now available in Lotus japonicus, Medicago truncatula and soybean. In this chapter we focus on M.truncatula, as a model species for forage legumes, on the main achievements obtained due to the reported resources and on the future perspectives for the study of gene function in this species

Development of FuGO: An ontology for functional genomics investigations

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans

Expression profiles of genes regulating dairy cow fertility: recent findings, ongoing activities and future possibilities

Subfertility has negative effects for dairy farm profitability, animal welfare and sustainability of animal production. Increasing herd sizes and economic pressures restrict the amount of time that farmers can spend on counteractive management Genetic improvement will become increasingly important to restore reproductive performance. Complementary to traditional breeding value estimation procedures, genomic selection based on genome-wide information will become more widely applied. Functional genomics, including transcriptomics (gene expression profiling), produces the information to understand the consequences of selection as it helps to unravel physiological mechanisms underlying female fertility traits. Insight into the latter is needed to develop new effective management strategies to combat subfertility. Here, the importance of functional genomics for dairy cow reproduction so far and in the near future is evaluated. Recent gene profiling studies in the field of dairy cow fertility are reviewed and new data are presented on genes that are expressed in the brains of dairy cows and that are involved in dairy cow oestrus (behaviour). Fast-developing new research areas in the field of functional genomics, such as epigenetics, RNA interference, variable copy numbers and nutrigenomics are discussed including their promising future value for dairy cow fertility

Clinical Functional Genomics

Functional genomics is the study of how the genome and its products, including RNA and proteins, function and interact to affect different biological processes. The field of functional genomics includes transcriptomics, proteomics, metabolomics and epigenomics, as these all relate to controlling the genome leading to expression of particular phenotypes. By studying whole genomes—clinical genomics, transcriptomes and epigenomes—functional genomics allows the exploration of the diverse relationship between genotype and phenotype, not only for humans as a species but also in individuals, allowing an understanding and evaluation of how the functional genome ‘contributes’ to different diseases. Functional variation in disease can help us better understand that disease, although it is currently limited in terms of ethnic diversity, and will ultimately give way to more personalized treatment plans

Integrative functional genomics

A report on the Keystone Symposium 'Biological Discovery Using Diverse High-Throughput Data', Steamboat Springs, USA, 30 March-4 April 2004

Improved Reference Genome Sequence of Coccidioides immitis Strain WA_211, Isolated in Washington State.

Coccidioides fungi are widely distributed in the American continents, with an expanding western range documented by a recently discovered cryptic population of Coccidioides immitis in Washington State. The assembled and annotated reference genome sequence of the soil-derived C. immitis strain WA_211 will support population and functional genomics studies