Functional Genomics of Natural Populations
The Earth is a complex web of diverse ecological communities that are controlled by numerous organisms and their interactions. Utah State University researchers are among the first to study how genes in naturally existing populations influence the way these organisms adapt to changes in their environment. This research is opening doors to improving the diversity and strength of aquatic, animal, and plant communities and will ultimately contribute to understanding how such organisms, including humans, will cope with long-term environmental change.
Why this research is important
Perhaps the most daunting challenges of the genomics era are to understand how genes in individual organisms function and interact in diverse environmental settings, and how genetically-based traits influence the survival of individuals, populations, species, and ecosystems. Armed with greater genetic knowledge than ever before, Utah State University researchers are working to understand these processes in a wide variety of natural populations, with direct application towards human health and environmental welfare.
Understanding these genomic processes is critical to our ability to effectively manage and manipulate plant and animal populations. Applications of this work include healthier and more efficient agricultural practices, improved water resource management and an understanding of how living beings are affected by UV sunlight.
What is functional genomics in natural populations?
Utah State University has expanded the study of genomics into studying how genes function in naturally existing populations. The initial focus in this emerging field has been the function of targeted genes in species that are conducive to controlled study and rapid results. Furthermore, our scientists are leveraging the use of the newest genomic tools?high through-put sequencing and gene expression studies?to continue learning how we can understand the complex interactions between the numerous organisms that make up the world.
Scientific Perspective
Investigators at USU are applying a synthetic, multidisciplinary approach to the study of functional genomics, combining molecular and quantitative genetic techniques with the direct assessment of gene expression patterns in natural populations. Understanding of the relationship between gene function and organismal response to environmental change is directly linked to 1) our ability to detect, predict, and manage adaptive responses in natural populations, and 2) our ability to develop and maintain cultivars with economically important genetic traits. Their goal is to develop robust methodologies for assessing adaptive genetic variation in natural populations that will be directly applicable in non-model systems (aquatic, terrestrial, plant, and animal). From this information, they can assess detrimental impacts of environmental change and develop rational ecosystem management strategies that maximize species diversity and ecosystem function.
Topical Overview
Rangeland and Agriculture Improvement
Researchers at USU are using DNA fingerprinting, highdensity genetic maps, and microarray analysis of gene expression to modify and manipulate genes that control functionally important traits. Their practical objective is to improve seed production, plant establishment, and forage production in rangelands and cultivated fields or pastures, and to identify and select appropriate seed sources of native plant species used for large-scale revegetation including fire rehabilitation. The genes identified in these studies are also likely to have significant importance in "grass" field crops such as wheat, barley, oats, rye, maize, and rice.
UV Radiation and DNA repair
The global increase in the levels of UV radiation is a growing concern for human health and natural populations. The genetic response of organisms to the mutagenic effects of UV exposure is being examined in microorganisms, plants and aquatic invertebrates. Researchers at USU are identifying the genes responsible for detecting DNA damage and enabling DNA repair. This research is especially relevant to understanding how populations will cope with long-term changes in the environment.
Environmental Genomics in Daphnia
Daphnia, a small freshwater crustacean, is an ecologically important sentinel organism inhabiting virtually every freshwater ecosystem in North America. Researchers at USU are studying changes in gene expression in response to harsh environments, UV radiation and pollutants to understand how natural populations respond to environmental change. Recent efforts have lead to the development of a diverse array of genetic tools, including a cooperative effort with the DOE to decipher the complete genome sequence.
Gene Flow, Diversity, and Divergence in Natural Populations
Focusing on Great Basin and Great Salt Lake Basin vertebrates and invertebrates, scientists at USU are studying the distribution of functionally important genes in natural populations. These studies will facilitate watershed management and contribute to maintaining healthy ecosystem function in these critical basins.
Invasive and Pest Species
Outbreaks of insect pest species cause yearly loss of economically important crops and forests throughout the intermountain west. Using an interdisciplinary strategy, scientists at USU and the USFS are developing evolutionary and demographic models of population dynamics, assessing genetic diversity and structure, and examining the genetic basis of diapause. This multilevel approach will contribute to predictive models for managing pest species and minimizing their economic impacts.
Resistance to Toxic Compounds in the Environment
The ability of populations to persist when challenged with long-term chronic exposure to toxic compounds in the environment depends on the evolution of resistance. USU researchers are using garter snakes as a model system for studying the evolution of resistance in natural populations by examining the molecular basis of resistance to tetrodotoxin and functional changes in sodium channel genes. This research has direct bearing on the ubiquitous problem of development of resistance to pesticides and herbicides in pest species.