Advertisement

Population Genetics and Genome-Wide Association Mapping of Chinese Populations of Foxtail Millet and Green Foxtail

  • Guanqing JiaEmail author
Chapter
Part of the Plant Genetics and Genomics: Crops and Models book series (PGG, volume 19)

Abstract

Green foxtail (Setaria viridis) and foxtail millet (Setaria italica) are new biological and genomic models for investigation of the biology of C4 photosynthesis and grass evolution. Green foxtail is the ancestor of foxtail millet, an ancient cereal of great importance in arid and semi-arid regions of the world, especially in China and India. To date, China has been recognized as the center of origin and improvement of foxtail millet, and over 80 % of the world’s Setaria accessions are conserved in the National Gene Bank of China. Assessment of germplasm samples collected in China can help to reveal the domestication history and potential for improvement of cultivated foxtail millet. Recently, the molecular diversity, genetic structure, eco-geographical distribution and selection history of foxtail millet cultivars has been revealed through large scale germplasm characterization, genomic analysis, and genome-wide association mapping of QTLs controlling agronomic traits. These achievements have laid the foundation for further exploration of functional genes controlling vital characters in Setaria and will be powerful tools for improved marker-assisted breeding of foxtail millet cultivars. In this chapter, recent studies on the Chinese Setaria gene pool will be discussed, as well as their potential for benefiting future genetic investigations in Setaria.

Keywords

Setaria Germplasm Diversity Structure Domestication Breeding Genome-wide association studies (GWAS) Quantitative trait loci (QTL) 

References

  1. Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J, Pontaroli AC, Estep M, Feng L, Vaughn JN, Grimwood J, Jenkins J, Barry K, Lindquist E, Hellsten U, Deshpande S, Wang X, Wu X, Mitros T, Triplett J, Yang X, Ye C, Mauro-Herrera M, Wang L, Li P, Sharma M, Sharma R, Ronald PC, Panaud O, Kellogg EA, Brutnell TP, Doust AN, Tuskan GA, Rokhsar D, Devos KM. Reference genome sequence of the model plant Setaria. Nat Biotechnol. 2012;30:556–61.CrossRefGoogle Scholar
  2. Brutnell TP, Wang L, Swartwood K, Goldschmidt A, Jackson D, Zhu X-G, Kellogg E, Eck JV. Setaria viridis: a model for C4 photosynthesis. Plant Cell. 2010;22:2537–44.CrossRefPubMedPubMedCentralGoogle Scholar
  3. Caemmerer SV, Quick WP, Furbank RT. The development of C4 rice: current progress and future challenges. Science. 2012;336:1671–2.CrossRefGoogle Scholar
  4. Cao NG. Selection and breeding of cereals, fruit trees and husbandry animals in ancient China. In: Guo WT, Cao NG, Song ZQ, Ma XQ, editors. Traditional agriculture and modern agriculture in China. Beijing: Agricultural Scientech Publishing House; 1986. p. 169–201.Google Scholar
  5. Diao X, Schnable J, Bennetzen JL, Li J. Initiation of Setaria as a model plant. Front Agric Sci Eng. 2014;1(1):16–20.CrossRefGoogle Scholar
  6. Doust AN, Devos KM, Gadberry M, Gale MD, Kellogg EA. Genetic control of branching in the foxtail millet. Proc Natl Acad Sci U S A. 2004;101:9045–50.CrossRefPubMedPubMedCentralGoogle Scholar
  7. Doust AN, Devos KM, Gadberry M, Gale MD, Kellogg EA. The genetic basis for inflorescence variation between foxtail and green millet (Poaceae). Genetics. 2005;169:1659–72.CrossRefPubMedPubMedCentralGoogle Scholar
  8. Doust AN, Kellogg EA, Devos KM, Bennetzen JL. Foxtail millet: a sequence-driven grass model system. Plant Physiol. 2009;149:137–41.CrossRefPubMedPubMedCentralGoogle Scholar
  9. Doust AN, Lukens L, Olsen KM, Mauro-Herrera M, Meyer A, Rogers K. Beyond the single gene: how epistasis and gene-by-environment effects influence crop domestication. Proc Natl Acad Sci U S A. 2014;111:6178–83.CrossRefPubMedPubMedCentralGoogle Scholar
  10. Gale MD, Devos KM. Comparative genetics in the grasses. Proc Natl Acad Sci U S A. 1998;95:1971–4.CrossRefPubMedPubMedCentralGoogle Scholar
  11. Gupta S, Kumari K, Sahu PP, Vidapu S, Prasad M. Sequence-based novel genomic microsatellite markers for robust genotyping purposes in foxtail millet [Setaria italica (L.) Beauv]. Plant Cell Rep. 2012;31:323–37.CrossRefPubMedGoogle Scholar
  12. Gupta S, Kumari K, Muthamilarasan M, Parida SK, Prasad M. Population structure and association mapping of yield contributing agronomic traits in foxtail millet. Plant Cell Rep. 2014;33:881–93.CrossRefPubMedGoogle Scholar
  13. Hirano R, Naito K, Fukunaga K, Watanabe KN, Ohsawa R, Kawase M. Genetic structure of landraces in foxtail millet (Setaria italica (L.) P. Beauv.) revealed with transposon display and interpretation to crop evolution of foxtail millet. Genome. 2011;54:498–506.CrossRefPubMedGoogle Scholar
  14. Huang X, Han B. Natural variations and genome-wide association studies in crop plants. Annu Rev Plant Biol. 2014;65:531–51.CrossRefPubMedGoogle Scholar
  15. Huang X, Wei X, Sang T, Zhao Q, Feng Q, Zhao Y, Li C, Zhu C, Lu T, Zhang Z, Li M, Fan D, Guo Y, Wang A, Wang L, Deng L, Li W, Lu Y, Weng Q, Liu K, Huang T, Zhou T, Jing Y, Li W, Lin Z, Buckler ES, Qian Q, Zhang Q, Li J, Han B. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet. 2010;42:961–7.CrossRefPubMedGoogle Scholar
  16. Huang X, Kurata N, Wei X, Wang Z, Wang A, Zhao Q, Zhao Y, Liu K, Lu H, Li W, Guo Y, Lu Y, Zhou C, Fan D, Weng Q, Zhu C, Huang T, Zhang L, Wang Y, Feng L, Furuumi H, Kubo T, Miyabayashi T, Yuan X, Xu Q, Dong G, Zhan Q, Li C, Fujiyama A, Toyoda A, Lu T, Feng Q, Qian Q, Li J, Han B. A map of rice genome variation reveals the origin of cultivated rice. Nature. 2012;490:497–501.CrossRefPubMedGoogle Scholar
  17. Huang P, Feldman M, Schroder S, Bahri B, Diao X, Zhi H, Estep M, Baxter I, Devos KM, Kellogg EA. Population genetics of Setaria viridis, a new model system. Mol Ecol. 2014;23:4912–25.CrossRefPubMedGoogle Scholar
  18. Jia X, Zhang Z, Liu Y, Zhang C, Shi Y, Song Y, Wang T. Development and genetic mapping of SSR markers in foxtail millet [Setaria italica (L.) P. Beauv.]. Theor Appl Genet. 2009;118:821–9.CrossRefPubMedGoogle Scholar
  19. Jia G, Huang X, Zhi H, Zhao Y, Zhao Q, Li W, Chai Y, Yang L, Liu K, Lu H, Zhu C, Lu Y, Zhou C, Fan D, Weng Q, Guo Y, Huang T, Zhang L, Lu T, Feng Q, Hao H, Liu H, Lu P, Zhang N, Li Y, Guo E, Wang S, Wang S, Liu J, Zhang W, Chen G, Zhang B, Li W, Wang Y, Li H, Zhao B, Li J, Diao X, Han B. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat Genet. 2013a;45:957–61.CrossRefPubMedGoogle Scholar
  20. Jia G, Shi S, Wang C, Niu Z, Chai Y, Zhi H, Diao X. Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis. J Exp Bot. 2013b;64:3645–55.CrossRefPubMedPubMedCentralGoogle Scholar
  21. Jia G, Liu X, James CS, Niu Z, Wang C, Li Y, Wang S, Wang S, Liu J, Guo E, Zhi H, Diao X. Microsatellite variations of elite Setaria varieties released during last six decades in China. PLoS One. 2015;10(5):e0125688.CrossRefPubMedPubMedCentralGoogle Scholar
  22. Jusuf M, Pernes J. Genetic variability of foxtail millet (Setaria italica P. Beauv.). Theor Appl Genet. 1985;63:117–9.Google Scholar
  23. Le Thierry d’Ennequin M, Panaud O, Toupance B, Sarr A. Assessment of genetic relationships between Setaria italica and its wild relative S. viridis using AFLP markers. Theor Appl Genet. 2000;100:1061–6.CrossRefGoogle Scholar
  24. Li P, Brutnell TP. Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses. J Exp Bot. 2011;62:3031–7.CrossRefPubMedGoogle Scholar
  25. Li Y, Wu S. Traditional maintenance and multiplication of foxtail millet (Setaria italica (L.) P. Beauv.) landraces in China. Euphytica. 1996;87:33–8.CrossRefGoogle Scholar
  26. Li C, Pao W, Li H. Interspecific crosses in Setaria. J Hered. 1942;33:351–5.Google Scholar
  27. Li H, Li C, Pao W. Cytogenetical and genetical studies of the interspecific cross between the cultivated foxtail millet, Setaira italica (L.) Beauv. and the green foxtail millet S. viridis L. J Am Soc Agron. 1945;37:32–54.CrossRefGoogle Scholar
  28. Li Y, Wu S, Cao Y. Cluster analysis of an international collection of foxtail millet (Setaria italica (L.) P. Beauv.). Euphytica. 1995;83:79–85.CrossRefGoogle Scholar
  29. Li Y, Jia J, Wang Y, Wu S. Intraspecific and interspecific variation in Setaria revealed by RAPD analysis. Genet Resour Crop Evol. 1998;45:279–85.CrossRefGoogle Scholar
  30. Li W, Zhi H, Wang Y, Li H, Diao X. Assessment of genetic relationship of foxtail millet with its wild ancestor and close relatives by ISSR markers. J Integr Agric. 2012;11(4):556–66.CrossRefGoogle Scholar
  31. Lin Z, Li X, Shannon LM, Yeh C, Wang ML, Bai G, Peng Z, Li J, Trick HN, Clemente TE, Doebley J, Schnable PS, Tuinstra MR, Tesso TT, White F, Yu J. Parallel domestication of the Shattering1 genes in cereals. Nat Genet. 2012;44:720–4.CrossRefPubMedPubMedCentralGoogle Scholar
  32. Lu H, Yang X, Ye M, Liu K, Xia Z, Ren X, Cai L, Wu N, Liu T. Culinary archaeology: millet noodles in late Neolithic China. Nature. 2005;437:967–8.CrossRefPubMedGoogle Scholar
  33. Lu H, Zhang J, Liu KB, Wu N, Li Y, Zhou K, Ye M, Zhang T, Zhang H, Yang X, Shen L, Xu D, Li Q. Earliest domestication of common millet (Panicum miliaceum) in east Asia extended to 10,000 years ago. Proc Natl Acad Sci U S A. 2009;106:7367–72.CrossRefPubMedPubMedCentralGoogle Scholar
  34. Mauro-Herrera M, Doust AN. Development and genetic control of plant architecture and biomass in the panicoid grass, Setaria. PLoS One. 2016;11(3):e0151346.CrossRefPubMedPubMedCentralGoogle Scholar
  35. Mauro-Herrera M, Wang X, Barbier H, Brutnell TP, Devos KM, Doust AN. Genetic control and comparative genomic analysis of flowering tine in Setaria (Poaceae). G3 Genes Genom Genet. 2013;3:283–95.Google Scholar
  36. Morris GP, Ramu P, Deshpande SP, Hash CT, Shah T, Upadhyaya HD, Riera-Lizarazu O, Brown PJ, Acharya CB, Mitchell SE, Harriman J, Glaubitz JC, Buckler ES, Kresovich S. Population genomic and genome-wide association studies of agroclimatic traits in sorghum. Proc Natl Acad Sci U S A. 2013;110:453–8.CrossRefPubMedGoogle Scholar
  37. Muthamilarasan M, Venkata SB, Pandey G, Kumari K, Parida SK, Prasad M. Development of 5123 intron-length polymorphic markers for large-scale genotyping application in foxtail millet. DNA Res. 2014;21:41–52.CrossRefPubMedGoogle Scholar
  38. Pandey G, Misra G, Kumari K, Gupta S, Parida SK, Chattopadhyay D, Prasad M. Genome-wide development and use of microsatellite markers for large-scale genotyping applications in foxtail millet [Setaria italica (L.)]. DNA Res. 2013;20:197–207.CrossRefPubMedPubMedCentralGoogle Scholar
  39. Qie L, Jia G, Zhang W, Schnable J, Shang Z, Li W, Liu B, Li M, Chai Y, Zhi H, Diao X. Mapping of quantitative trait locus (QTLs) that contribute to germination and early seedling drought tolerance in the interspecific cross Setaria italica × Setaria viridis. PLoS One. 2014;9(7):e101868.CrossRefPubMedPubMedCentralGoogle Scholar
  40. Reddy VG, Upadhyaya HD, Gowda CLL. Characterization of world’s foxtail millet germplasm collections for morphological traits. J SAT Agric Res. 2006;2:1–3.Google Scholar
  41. Schontz D, Rether B. Genetic variability in foxtail millet, Setaria italica (L.) P. Beauv.: identification and classification of lines with RAPD markers. Plant Breed. 1999;118:190–2.CrossRefGoogle Scholar
  42. Shi Y, Wang T, Li Y, Darmency H. Impact of transgene inheritance on the mitigation of gene flow between crops and their wild relatives: the example of foxtail millet. Genetics. 2008;180:969–75.CrossRefPubMedPubMedCentralGoogle Scholar
  43. B VS, Muthamilarasan M, Misra G, Prasad M. FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research. PLoS One. 2013;8:e71418.CrossRefPubMedPubMedCentralGoogle Scholar
  44. Van K, Onoda S, Kim MY, Kim KD, Lee SH. Allelic variation of the Waxy gene in foxtail millet [Setaria italica (L.) P. Beauv.] by single nucleotide polymorphisms. Mol Genet Genomics. 2008;279:255–66.CrossRefPubMedGoogle Scholar
  45. Wang ZM, Devos KM, Liu CJ, Wang RQ, Gale MD. Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv. Theor Appl Genet. 1998;96:31–6.CrossRefGoogle Scholar
  46. Wang C, Chen J, Zhi H, Yang L, Li W, Wang Y, Li H, Zhao B, Chen M, Diao X. Population genetics of foxtail millet and its wild ancestor. BMC Genet. 2010;11:90.CrossRefPubMedPubMedCentralGoogle Scholar
  47. Wang C, Jia G, Zhi H, Niu Z, Chai Y, Li W, Wang Y, Li H, Lu P, Zhao B, Diao X. Genetic diversity and population structure of Chinese foxtail millet [Setaria italica (L.) Beauv.] landraces. G3 Genes Genom Genet. 2012;2:769–77.Google Scholar
  48. Xin L, Li X, Zhu H, Tan M. China’s potential of grain production due to changes in agricultural land utilization in recent years. Chin Geogr Sci. 2009;19(2):97–103.CrossRefGoogle Scholar
  49. Yadav CB, Bonthala VS, Muthamilarasan M, Pandey G, Khan Y, Prasad M. Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database. DNA Res. 2015;22:79–90.CrossRefPubMedGoogle Scholar
  50. Yang X, Wan Z, Perry L, Lu H, Wang Q, Zhao C, Li J, Xie F, Yu J, Cui T, Wang T, Li M, Ge Q. Early millet use in northern china. Proc Natl Acad Sci U S A. 2012;109:3726–30.CrossRefPubMedPubMedCentralGoogle Scholar
  51. Zhang S, Tang C, Zhao Q, Li J, Yang L, Qie L, Fan X, Li L, Zhang N, Zhao M, Liu X, Chai Y, Zhang X, Wang H, Li Y, Li W, Zhi H, Jia G, Diao X. Development of highly polymorphic simple sequence repeat markers using genome-wide microsatellite variant analysis in foxtail millet [Setaria italica (L.) P. Beauv]. BMC Genomics. 2014;15:78.CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer International Publishing Switzerland 2017

Authors and Affiliations

  1. 1.Institute of Crop Sciences, Chinese Academy of Agricultural SciencesBeijingPeople’s Republic of China

Personalised recommendations