Skip to main content
SpringerLink
Log in

Genetic Diversity and Geographic Distribution of North American Setaria viridis Populations

  • Chapter
  • First Online:
Genetics and Genomics of Setaria

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 19))

Abstract

Setaria viridis is an emerging model system that is used to study C4 photosynthesis and many other traits relating to agricultural productivity of panicoid grain crops and bioenergy grasses. Originally from China, naturalized populations of S. viridis are widely distributed in North America and contain a high degree of genetic and phenotypic diversity. In this chapter, we estimate the distribution range of S. viridis in North America using a climate-based species distribution model. We then summarize some recent advances in understanding the genetic diversity, population structure, linkage disequilibrium, and biogeography of North American S. viridis populations. We further expound upon the necessity of expanding germplasm collections of S. viridis, our own ongoing collection efforts, and some of the sequence and germplasm resources currently being generated. Finally, we discuss utilizing these tools as a means for genetic dissection of complex traits, potential opportunities for gene discovery, and how our understanding of the natural variation in S. viridis populations will make agriculture a more productive and sustainable industry.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Barton L, Newsome SD, Chen F-H, Wang H, Guilderson TP, Bettinger RL. Agricultural origins and the isotopic identity of domestication in northern China. Proc Natl Acad Sci. 2009;106(14):5523–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beissinger TM, Hirsch CN, Sekhon RS, Foerster JM, Johnson JM, Muttoni G, et al. Marker density and read depth for genotyping populations using genotyping-by-sequencing. Genetics. 2013;193(4):1073–81.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, et al. Reference genome sequence of the model plant Setaria. Nat Biotechnol. 2012;30(6):555–61.

    Article  CAS  PubMed  Google Scholar 

  • Bergelson J, Roux F. Towards identifying genes underlying ecologically relevant traits in Arabidopsis thaliana. Nat Rev Genet. 2010;11(12):867–79.

    Article  CAS  PubMed  Google Scholar 

  • Brachi B, Morris GP, Borevitz JO. Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol. 2011;12(10):232.

    Article  PubMed  PubMed Central  Google Scholar 

  • Brutnell TP, Wang L, Swartwood K, Goldschmidt A, Jackson D, Zhu X-G, et al. Setaria viridis: a model for C4 photosynthesis. Plant Cell. 2010;22(8):2537–44.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Brutnell TP, Bennetzen JL, Vogel JP. Brachypodium distachyon and Setaria viridis: model genetic systems for the grasses. Annu Rev Plant Biol. 2015;66:465–85.

    Article  CAS  PubMed  Google Scholar 

  • Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, et al. The genetic architecture of maize flowering time. Science. 2009;325(5941):714–8.

    Article  CAS  PubMed  Google Scholar 

  • Dekker J. The foxtail (Setaria) species-group. Weed Sci. 2003;51(5):641–56.

    Article  CAS  Google Scholar 

  • Délye C, Wang T, Darmency H. An isoleucine-leucine substitution in chloroplastic acetyl-CoA carboxylase from green foxtail (Setaria viridis L. Beauv.) is responsible for resistance to the cyclohexanedione herbicide sethoxydim. Planta. 2002;214(3):421–7.

    Article  PubMed  Google Scholar 

  • Doust AN, Kellogg EA. Effect of genotype and environment on branching in weedy green millet (Setaria viridis) and domesticated foxtail millet (Setaria italica) (Poaceae). Mol Ecol. 2006;15(5):1335–49.

    Article  CAS  PubMed  Google Scholar 

  • Doust AN, Devos KM, Gadberry MD, Gale MD, Kellogg EA. Genetic control of branching in foxtail millet. Proc Natl Acad Sci U S A. 2004;101(24):9045–50.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Doust AN, Devos KM, Gadberry MD, Gale MD, Kellogg EA. The genetic basis for inflorescence variation between foxtail and green millet (Poaceae). Genetics. 2005;169(3):1659–72.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Doust AN, Kellogg EA, Devos KM, Bennetzen JL. Foxtail millet: a sequence-driven grass model system. Plant Physiol. 2009;149(1):137–41.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Elith J, Leathwick JR. Species distribution models: ecological explanation and prediction across space and time. Annu Rev Ecol Evol Syst. 2009;40(1):677.

    Article  Google Scholar 

  • Evans LM, Slavov GT, Rodgers-Melnick E, Martin J, Ranjan P, Muchero W, et al. Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations. Nat Genet. 2014;46(10):1089–96.

    Article  CAS  PubMed  Google Scholar 

  • Fournier-Level A, Korte A, Cooper MD, Nordborg M, Schmitt J, Wilczek AM. A map of local adaptation in Arabidopsis thaliana. Science. 2011;334(6052):86–9.

    Article  CAS  PubMed  Google Scholar 

  • Gore MA, Chia J-M, Elshire RJ, Sun Q, Ersoz ES, Hurwitz BL, et al. A first-generation haplotype map of maize. Science. 2009;326(5956):1115–7.

    Article  CAS  PubMed  Google Scholar 

  • Hancock AM, Brachi B, Faure N, Horton MW, Jarymowycz LB, Sperone FG, et al. Adaptation to climate across the Arabidopsis thaliana genome. Science. 2011;334(6052):83–6.

    Article  CAS  PubMed  Google Scholar 

  • Hijmans RJ, Cameron SE, Parra JL, Jones PG, Jarvis A. Very high resolution interpolated climate surfaces for global land areas. Int J Climatol. 2005;25(15):1965–78.

    Article  Google Scholar 

  • Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, et al. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010;42(11):961–7.

    Article  CAS  PubMed  Google Scholar 

  • Huang P, Molina J, Flowers JM, Rubinstein S, Jackson SA, Purugganan MD, et al. Phylogeography of Asian wild rice, Oryza rufipogon: a genome-wide view. Mol Ecol. 2012a;21(18):4593–604.

    Article  PubMed  Google Scholar 

  • Huang X, Zhao Y, Wei X, Li C, Wang A, Zhao Q, et al. Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm. Nat Genet. 2012b;44(1):32–9.

    Article  Google Scholar 

  • Huang P, Feldman M, Schroder S, Bahri BA, Diao X, Zhi H, et al. Population genetics of Setaria viridis, a new model system. Mol Ecol. 2014;23(20):4912–25.

    Article  CAS  PubMed  Google Scholar 

  • Jia G, Shi S, Wang C, Niu Z, Chai Y, Zhi H, et al. Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis. J Exp Bot. 2013a;64(12):3645–56.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Jia G, Huang X, Zhi H, Zhao Y, Zhao Q, Li W, et al. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet. 2013b;45(8):957–61.

    Article  CAS  PubMed  Google Scholar 

  • Jiang H, Barbier H, Brutnell T. Methods for performing crosses in Setaria viridis, a new model system for the grasses. J Vis Exp. 2013;80:e50527.

    Google Scholar 

  • Long Q, Rabanal FA, Meng D, Huber CD, Farlow A, Platzer A, et al. Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden. Nat Genet. 2013;45(8):884–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mauro-Herrera M, Wang X, Barbier H, Brutnell TP, Devos KM, Doust AN. Genetic control and comparative genomic analysis of flowering time in Setaria (Poaceae). G3 Genes Genom Genet. 2013;3(2):283–95.

    Google Scholar 

  • McMullen MD, Kresovich S, Villeda HS, Bradbury P, Li H, Sun Q, et al. Genetic properties of the maize nested association mapping population. Science. 2009;325(5941):737–40.

    Article  CAS  PubMed  Google Scholar 

  • Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, et al. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci. 2013;110(2):453–8.

    Article  CAS  PubMed  Google Scholar 

  • Petti C, Shearer A, Tateno M, Ruwaya M, Nokes S, Brutnell T, et al. Comparative feedstock analysis in Setaria viridis L. as a model for C4 bioenergy grasses and Panicoid crop species. Front Plant Sci. 2013;4:181.

    Article  PubMed  PubMed Central  Google Scholar 

  • Phillips SJ, Dudík M. Modeling of species distributions with Maxent: new extensions and a comprehensive evaluation. Ecography. 2008;31(2):161–75.

    Article  Google Scholar 

  • Rominger JM. Taxonomy of Setaria (Gramineae) in North America. Illinois Biol Monogr. 1962;29:1–132.

    Google Scholar 

  • Sebastian J, Wong MK, Tang E, Dinneny JR. Methods to promote germination of dormant Setaria viridis seeds. PLoS One. 2014;9(4):e95109.

    Article  PubMed  PubMed Central  Google Scholar 

  • Takagi H, Tamiru M, Abe A, Yoshida K, Uemura A, Yaegashi H, et al. MutMap accelerates breeding of a salt-tolerant rice cultivar. Nat Biotechnol. 2015;33(5):445–9.

    CAS  PubMed  Google Scholar 

  • Wang R, Wendel JF, Dekker JH. Weedy adaptation in Setaria spp. I. Isozyme analysis of genetic diversity and population genetic structure in Setaria viridis. Am J Bot. 1995;82:308–17.

    Article  Google Scholar 

  • Wang C, Chen J, Zhi H, Yang L, Li W, Wang Y, et al. Population genetics of foxtail millet and its wild ancestor. BMC Genet. 2010;11(1):90.

    Article  PubMed  PubMed Central  Google Scholar 

  • Watterson G. On the number of segregating sites in genetical models without recombination. Theor Popul Biol. 1975;7(2):256–76.

    Article  CAS  PubMed  Google Scholar 

  • Wilson P, Streich J, Borevitz J. In: Genomic diversity and climate adaptation in Brachypodium. New York: Springer; 2015. p. 1–21. doi:10.1007/7397_2015_18.

  • Wright SI, Bi IV, Schroeder SG, Yamasaki M, Doebley JF, McMullen MD, et al. The effects of artificial selection on the maize genome. Science. 2005;308(5726):1310–4.

    Article  CAS  PubMed  Google Scholar 

  • Yuan Y-W, Sagawa JM, Di Stilio VS, Bradshaw HD. Bulk segregant analysis of an induced floral mutant identifies a MIXTA-like R2R3 MYB controlling nectar guide formation in Mimulus lewisii. Genetics. 2013;194(2):523–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgment

Pu Huang is funded by United States National Science Foundation, Award number IOS-1127017 and United States Department of Energy, Award number DE-SC0008769. Max Feldman is funded by United States Department of Energy’s Biological and Environmental Research Program Grant number ER65472. The authors thank Dr. Thomas Brutnell from Donald Danforth Plant Science Center for helpful comments on the manuscript.

Author information

Authors and Affiliations

  1. Donald Danforth Plant Science Center, 975 North Warson Rd., St. Louis, MO, 63132, USA

    Pu Huang & Maximillian Feldman

Authors
  1. Pu Huang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Maximillian Feldman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Pu Huang .

Editor information

Editors and Affiliations

  1. Department of Plant Biology, Ecology, and Evolution, Oklahoma State University, Stillwater, Oklahoma, USA

    Andrew Doust

  2. Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China

    Xianmin Diao

Rights and permissions

Reprints and permissions

Copyright information

© 2017 Springer International Publishing Switzerland

About this chapter

Cite this chapter

Huang, P., Feldman, M. (2017). Genetic Diversity and Geographic Distribution of North American Setaria viridis Populations. In: Doust, A., Diao, X. (eds) Genetics and Genomics of Setaria. Plant Genetics and Genomics: Crops and Models, vol 19. Springer, Cham. https://doi.org/10.1007/978-3-319-45105-3_3

Download citation

Publish with us

Policies and ethics

Search

Navigation