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ARS Home » Midwest Area » Columbia, Missouri » Plant Genetics Research » Research » Publications at this Location » Publication #308575
Title: Population genetics of Setaria viridis, a new model system

Author
item HUANG, PU - Danforth Plant Science Center
item FELDMAN, MAXIMILIAN - Danforth Plant Science Center
item SCHRODER, STEPHAN - University Of Georgia
item BAHRI, BOCHRA - University Of Georgia
item DIAO, XIANMIN - Chinese Academy Of Agricultural Sciences
item ZHI, HUI - Chinese Academy Of Agricultural Sciences
item ESTEP, MATT - Appalachian State University
item Baxter, Ivan
item DEVOS, KATRIEN - University Of Georgia
item KELLOGG, ELIZABETH - Danforth Plant Science Center

Submitted to: Molecular Ecology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/29/2014
Publication Date: 10/1/2014
Publication URL: http://handle.nal.usda.gov/10113/61179
Citation: Huang, P., Feldman, M., Schroder, S., Bahri, B.A., Diao, X., Zhi, H., Estep, M., Baxter, I.R., Devos, K.M., Kellogg, E.A. 2014. Population genetics of Setaria viridis, a new model system. Molecular Ecology. 23(20):4912-4925.

Interpretive Summary: Model plants are extremely useful for research because they are smaller and easier to manipulate than many crop and wild plants. Recently green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has become a model for a group of plants that include corn, sorghum and several biofuel grasses that perform a particular form of photosythesis. To survey the diversity of the species, we conducted low pass sequencing of 200 accessions including new collections from the western United States. We identified three distinct groups of lines and found associations between the genetic variation and geographical location of the accession and climate variables. These results together provide an in-depth understanding of the pattern of genetic diversity of this new model species on a broad geographic scale. They also provide key guidelines for on-going and future work.

Technical Abstract: An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new model system for C4 grasses and bioenergy crops, due to its rapid life cycle, large amount of seed production, and small diploid genome, among other characters. However, remarkably little is known about the genetic diversity in natural populations of this species. In this study, we survey the genetic diversity of a world-wide sample of more than 200 S. viridis accessions, using the genotyping by sequencing technique. Two distinct genetic groups in S. viridis and a third group resembling S. italica were identified, with considerable admixture among the three groups. We find the genetic variation of North American S. viridis correlates with both geography and climate, and is representative of the total genetic diversity in this species. This pattern may reflect several introduction/dispersal events of S. viridis into North America. We also modeled demographic history and show signal of recent population decline in one subgroup. Finally we show linkage disequilibrium decay is rapid (less then 45kb) in our total sample and slow in genetic subgroups. These results together provide an in-depth understanding of the pattern of genetic diversity of this new model species on a broad geographic scale. They also provide key guidelines for on-going and future work including germplasm preservation, local adaptation, crossing designs and genome-wide association studies.