PIs: Katrien M. Devos (University of Georgia) and Elizabeth A. Kellogg (University of Missouri - Saint Louis)
CoPI: Jeffrey Bennetzen (University of Georgia)
Setaria viridis or green foxtail is a ubiquitous weed that was introduced from Eurasia during the past 500 years. It is often found in and around cultivated fields and the extensive herbicide pressure imposed by agricultural weed control has led to the development of herbicide resistant genotypes. Resistance to four different types of herbicides has been identified in S. viridis. Under continued herbicide application, the genome region that carries the resistance will be under strong selection and this is expected to lead to reduced variation at the herbicide resistance locus and surrounding genome region. The project aims to compare the genetic variation at the whole genome level with the variation present in and around three herbicide resistance genes. To achieve this objective, S. viridis accessions will be collected from North America and Canada, where herbicide resistance has previously been observed. S. viridis accessions from around the world will be obtained from national and international germplasm repositories. The plants will be tested for herbicide resistance. Cutting edge molecular techniques, including high-throughput sequencing, will be used to analyze the genetic variation. The project will provide new insights into the diversity of green foxtail worldwide, the history and origin of green foxtail introductions into North America, the nature of the mutations that give rise to herbicide resistance, how the resistance spreads through populations and the effects of intense directional selection on genome evolution.
The project provides a vehicle for training students at the undergraduate, graduate and post-doctoral level in independent research. In addition, the project data will be used as hands-on teaching materials in graduate courses taught by the PIs. The project also aims to provide a link between weed scientists, germplasm curators and geneticists with an interest in green foxtail. To raise awareness of the research interests of the different groups and to facilitate collaborations, the project will organize a workshop to discuss available green foxtail collections, maintenance of those stocks, genomic tools and common goals. All sequence data produced by this project will be made publicly available through GenBank. Germplasm can be obtained from the University of Georgia and the USDA-ARS Germplasm Resources Information Network (GRIN) (www.ars-grin.gov).
US agriculture faces challenges such as drought, heat, and changes in insect pests as the climate continues to warm. The country needs to be sure that the crops that we plant are bred with these challenges in mind to be sure that appropriate seed stocks are available for specific climatic challenges. However, in many cases it is difficult to do the necessary experiments in the crops themselves because they are often large plants (e.g. corn, sorghum), and/or can up to a year to mature (e.g. switchgrass). Therefore it is common to use a closely related plant as a model. Just as an architectural model is smaller and easier to manipulate than a full-sized building, a crop model is also far more amenable to experimentation than the crop itself. The recently completed project focused on the model plant green millet, Setaria viridis (Fig. 1), which is closely related to switchgrass, corn, and sorghum, and is used for the study of photosynthesis, drought, and pest resistance. To make full use of green millet, it was important to have a) a sequence of the genome, b) a large set of wild-grown plants collected from throughout its range, c) an understanding of how those plants are related to each other, and d) detailed information on how green millet is distinguished from other species with which it might be confused. This set of tools is central to allow future researchers to correlate variation in genes with variation in the environment, a process known as Genome-Wide Association Studies (GWAS). Identifying a critical gene in green millet will then allow the comparable gene in corn or switchgrass to be targeted. The project produced a sequence of the genome of foxtail millet, the domesticated form of green millet, and sequences of the genomes of many accessions of green millet. Many of the green millet sequences were produced via collaboration with the Department of Energy's Joint Genome Institute (JGI). The paper describing the foxtail millet genome was published in Nature Biotechnology and the one describing the green millet genome is currently being written. In addition, the project has produced hundreds of wild-collected plants from all over the world; many of these have been deposited at the USDA Germplasm Resource Information Network for free distribution to anyone who asks. In addition, the JGI has sequenced many of the genomes of the wild accessions, which creates a tremendous public resource for discovering genes and their functions. These genome sequences are being deposited in GenBank where any researcher anywhere in the world can access them. Using the genetic and genomic sequences plus the wild-collected plants described in the previous paragraph, it was possible to determine how the plants were related to each other. The data show that green millet is divided into three distinct genetic groups, one of which is similar to plants from Europe, one group from western Asia, and one group similar to cultivated plants from China. These data were published in the journal Molecular Ecology. Green millet has been introduced into North America several times but the three groups can still be distinguished genetically. Having identified the three subsets of green millet, it was then possible to look closely at the plants and to find subtle differences in plant form and physiology that correlate with their place of origin. Also in follow-up research after the grant ended, GWAS studies have found genes that affect size of the inflorescence (flower stalk) and structure of the seed. As a final contribution to development of green millet as a model, a detailed morphological and genomic study compared green millet with closely related species. This study was published in the American Journal of Botany. This information allows other researchers to locate additional wild populations of green millet and points out the necessary characteristics for correct identification. This part of the study also used DNA sequences to find species with duplicated genomes (polyploids) for which green millet was one ancestor. Thus green millet genomes are present in other weedy millets, Setaria faberi and S. verticillata. In summary, the funding for this project provided the necessary infrastructure to develop the model system green millet (Setaria viridis). It led to several publications and formed the foundation for several more in progress. It supported acquisition of a remarkable set of germplasm that is now available to the entire plant science community. It also provided the basis for sequencing the genomes of the wild accessions, again providing a rich public resource. This model system is now useful for the rest of the plant science community wanting to use it as a tool for study of crop response to the environment.
