The family of grasses encompasses the world's most important food, feed, and bioenergy crops, yet we are only now beginning to develop the genetic resources to explore the diversity of form and function that underlies economically important traits. Two emerging model systems, and , promise to greatly accelerate the process of gene discovery in the grasses and to serve as bridges in the exploration of panicoid and pooid grasses, arguably two of the most important clades of plants from a food security perspective. We provide both a historical view of the development of plant model systems and highlight several recent reports that are providing these developing communities with the tools for gene discovery and pathway engineering.


Article metrics loading...

Loading full text...

Full text loading...


Literature Cited

  1. Austin RS, Vidaurre D, Stamatiou G, Breit R, Provart NJ. 1.  et al. 2011. Next-generation mapping of Arabidopsis genes. Plant J. 67:715–25 [Google Scholar]
  2. Bablak P, Draper J, Davey MR, Lynch PT. 2.  1995. Plant regeneration and micropropagation of Brachypodium distachyon. Plant Cell Tissue Organ Cult. 42:97–107 [Google Scholar]
  3. Barton L, Newsome SD, Chen FH, Wang H, Guilderson TP, Bettinger RL. 3.  2009. Agricultural origins and the isotopic identity of domestication in northern China. PNAS 106:5523–28 [Google Scholar]
  4. Beatty PH, Good AG. 4.  2011. Future prospects for cereals that fix nitrogen. Science 333:416–17 [Google Scholar]
  5. Bennetzen JL, Freeling M. 5.  1993. Grasses as a single genetic system: genome composition, collinearity and compatibility. Trends Genet. 9:259–61 [Google Scholar]
  6. Bennetzen JL, Schmutz J, Wang H, Percifield R, Hawkins J. 6.  et al. 2012. Reference genome sequence of the model plant Setaria. Nat. Biotechnol. 30:555–61 [Google Scholar]
  7. Berkman PJ, Skarshewski A, Lorenc MT, Lai K, Duran C. 7.  et al. 2011. Sequencing and assembly of low copy and genic regions of isolated Triticum aestivum chromosome arm 7DS. Plant Biotechnol. J. 9:768–75 [Google Scholar]
  8. Bombarely A, Menda N, Tecle IY, Buels RM, Strickler S. 8.  et al. 2011. The Sol Genomics Network (solgenomics.net): growing tomatoes using Perl. Nucleic Acids Res. 39:D1149–55 [Google Scholar]
  9. Bragg JN, Wu J, Gordon SP, Guttman ME, Thilmony R. 9.  et al. 2012. Generation and characterization of the Western Regional Research Center Brachypodium T-DNA insertional mutant collection. PLOS ONE 7e41916
  10. Brkljacic J, Grotewold E, Scholl R, Mockler TC, Garvin DF. 10.  et al. 2011. Brachypodium as a model for the grasses: today and the future. Plant Physiol. 157:3–13 [Google Scholar]
  11. Brown TB, Cheng R, Sirault XR, Rungrat T, Murray KD. 11.  et al. 2014. TraitCapture: genomic and environment modelling of plant phenomic data. Curr. Opin. Plant Biol. 18:73–79 [Google Scholar]
  12. Brutnell TP, Wang L, Swartwood K, Goldschmidt A, Jackson D. 12.  et al. 2010. Setaria viridis: a model for C4 photosynthesis. Plant Cell 22:2537–44 [Google Scholar]
  13. Burt C, Nicholson P. 13.  2011. Exploiting co-linearity among grass species to map the Aegilops ventricosa-derived Pch1 eyespot resistance in wheat and establish its relationship to Pch2. Theor. Appl. Genet. 123:1387–400 [Google Scholar]
  14. Cao S, Siriwardana CL, Kumimoto RW, Holt BF. 14.  2011. Construction of high quality Gateway™ entry libraries and their application to yeast two-hybrid for the monocot model plant Brachypodium distachyon. BMC Biotechnol. 11:53 [Google Scholar]
  15. Carroll A, Somerville C. 15.  2009. Cellulosic biofuels. Annu. Rev. Plant Biol. 60:165–82 [Google Scholar]
  16. Catalán P, Müller J, Hasterok R, Jenkins G, Mur LAJ. 16.  et al. 2013. Evolution and taxonomic split of the model grass Brachypodium distachyon. Ann. Bot. 109:385 [Google Scholar]
  17. Catalán P, Ying S, Armstrong L, Draper J, Stace CA. 17.  1995. Molecular phylogeny of the grass genus Brachypodium P. Beuav. based on RFLP and RAPD analysis. Bot. J. Linn. Soc. 117:263–80 [Google Scholar]
  18. Chen XP, Cui ZL, Vitousek PM, Cassman KG, Matson PA. 18.  et al. 2011. Integrated soil-crop system management for food security. PNAS 108:6399–404 [Google Scholar]
  19. Choulet F, Wicker T, Rustenholz C, Paux E, Salse J. 19.  et al. 2010. Megabase level sequencing reveals contrasted organization and evolution patterns of the wheat gene and transposable element spaces. Plant Cell 22:1686–701 [Google Scholar]
  20. Cockram J, Jones H, Leigh FJ, O'Sullivan D, Powell W. 20.  et al. 2007. Control of flowering time in temperate cereals: genes, domestication, and sustainable productivity. J. Exp. Bot. 58:1231–44 [Google Scholar]
  21. Coudert Y, Perin C, Courtois B, Khong NG, Gantet P. 21.  2010. Genetic control of root development in rice, the model cereal. Trends Plant Sci. 15:219–26 [Google Scholar]
  22. Cowperthwaite M, Park W, Xu Z, Yan X, Maurais SC, Dooner HK. 22.  2002. Use of the transposon Ac as a gene-searching engine in the maize genome. Plant Cell 14:713–26 [Google Scholar]
  23. Cui Y, Lee MY, Huo N, Bragg J, Yan L. 23.  et al. 2012. Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLOS ONE 7:e38333 [Google Scholar]
  24. Dalmais M, Antelme S, Ho-Yue-Kuang S, Wang Y, Darracq O. 24.  et al. 2013. A TILLING platform for functional genomics in Brachypodium distachyon. PLOS ONE 8:e65503 [Google Scholar]
  25. Doust AN, Kellogg EA, Devos KM, Bennetzen JL. 25.  2009. Foxtail millet: a sequence-driven grass model system. Plant Physiol. 149:137–41 [Google Scholar]
  26. Draper J, Mur LAJ, Jenkins G, Ghosh-Biswas GC, Bablak P. 26.  et al. 2001. Brachypodium distachyon. A new model system for functional genomics in grasses. Plant Physiol. 127:1539–55 [Google Scholar]
  27. Febrer M, Goicoechea JL, Wright J, McKenzie N, Song X. 27.  et al. 2010. An integrated physical, genetic and cytogenetic map of Brachypodium distachyon, a model system for grass research. PLOS ONE 5:e13461 [Google Scholar]
  28. Filiz E, Ozdemir BS, Budak F, Vogel JP, Tuna M, Budak H. 28.  2009. Molecular, morphological, and cytological analysis of diverse Brachypodium distachyon inbred lines. Genome 52:876–90 [Google Scholar]
  29. Fleury D, Luo MC, Dvorak J, Ramsay L, Gill BS. 29.  et al. 2010. Physical mapping of a large plant genome using global high-information-content-fingerprinting: the distal region of the wheat ancestor Aegilops tauschii chromosome 3DS. BMC Genomics 11:382 [Google Scholar]
  30. Furbank RT, Tester M. 30.  2011. Phenomics—technologies to relieve the phenotyping bottleneck. Trends Plant Sci. 16:635–44 [Google Scholar]
  31. Garvin DF. 31.  2012. Garvin lab Brachypodium information Agric. Res. Serv., US Dep. Agric., Peoria, IL. http://www.ars.usda.gov/News/docs.htm?docid=18531
  32. Garvin DF, McKenzie N, Vogel JP, Mockler TC, Blankenheim ZJ. 32.  et al. 2010. An SSR-based genetic linkage map of the model grass Brachypodium distachyon. Genome 53:1–13 [Google Scholar]
  33. Gebbers R, Adamchuk VI. 33.  2010. Precision agriculture and food security. Science 327:828–31 [Google Scholar]
  34. 34. Genomics Gene Discov. Res. Unit 2014. Brachypodium resources West. Reg. Resour. Cent., Agric. Res. Serv., US Dep. Agric., Albany, CA. http://brachypodium.pw.usda.gov
  35. Glover JD, Reganold JP, Bell LW, Borevitz J, Brummer EC. 35.  et al. 2010. Increased food and ecosystem security via perennial grains. Science 328:1638–39 [Google Scholar]
  36. Godfray HC, Beddington JR, Crute IR, Haddad L, Lawrence D. 36.  et al. 2010. Food security: the challenge of feeding 9 billion people. Science 327:812–18 [Google Scholar]
  37. Godfray HC, Pretty J, Thomas SM, Warham EJ, Beddington JR. 37.  2011. Global food supply: linking policy on climate and food. Science 331:1013–14 [Google Scholar]
  38. Goff SA, Ricke D, Lan TH, Presting G, Wang R. 38.  et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92–100 [Google Scholar]
  39. Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M. 39.  et al. 2014. Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J. 79:361–74 [Google Scholar]
  40. Griffiths S, Sharp R, Foote TN, Bertin I, Wanous M. 40.  et al. 2006. Molecular characterization of Ph1 as a major chromosome pairing locus in polyploid wheat. Nature 439:749–52 [Google Scholar]
  41. Han J, Xie H, Sun Q, Wang J, Lu M. 41.  et al. 2014. Bioinformatic identification and experimental validation of miRNAs from foxtail millet (Setaria italica). Gene 546:367–77 [Google Scholar]
  42. Hasterok R, Draper J, Jenkins G. 42.  2004. Laying the cytotaxonomic foundations of a new model grass, Brachypodium distachyon (L.) Beauv. Chromosome Res. 12:397–403 [Google Scholar]
  43. Hayama R, Coupland G. 43.  2004. The molecular basis of diversity in the photoperiodic flowering responses of Arabidopsis and rice. Plant Physiol. 135:677–84 [Google Scholar]
  44. Higgins JA, Bailey PC, Laurie DA. 44.  2010. Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. PLOS ONE 5:e10065 [Google Scholar]
  45. Hirochika H, Guiderdoni E, An G, Hsing YI, Eun MY. 45.  et al. 2004. Rice mutant resources for gene discovery. Plant Mol. Biol. 54:325–34 [Google Scholar]
  46. Huang P, Feldman M, Schroder S, Bahri BA, Diao X. 46.  et al. 2014. Population genetics of Setaria viridis, a new model system. Mol. Ecol. 23:4912–25 [Google Scholar]
  47. Huang X, Wei X, Sang T, Zhao Q, Feng Q. 47.  et al. 2010. Genome-wide association studies of 14 agronomic traits in rice landraces. Nat. Genet. 42:961–67 [Google Scholar]
  48. Huo N, Garvin DF, You FM, McMahon S, Luo MC. 48.  et al. 2011. Comparison of a high-density genetic linkage map to genome features in the model grass Brachypodium distachyon. Theor. Appl. Genet. 123:455–64 [Google Scholar]
  49. Huo N, Gu Y, Lazo G, Vogel JP, Coleman-Derr D. 49.  et al. 2006. Construction and characterization of two BAC libraries from Brachypodium distachyon, a new model for grass genomics. Genome 49:1099–108 [Google Scholar]
  50. Huo N, Lazo GR, Vogel JP, You FM, Ma Y. 50.  et al. 2008. The nuclear genome of Brachypodium distachyon: analysis of BAC end sequences. Funct. Integr. Genomics 8:135–47 [Google Scholar]
  51. Huo N, Vogel JP, Lazo GR, You FM, Ma Y. 51.  et al. 2009. Structural characterization of Brachypodium genome and its syntenic relationship with rice and wheat. Plant Mol. Biol. 70:47–61 [Google Scholar]
  52. Idziak D, Betekhtin A, Wolny E, Lesniewska K, Wright J. 52.  et al. 2011. Painting the chromosomes of Brachypodium—current status and future prospects. Chromosoma 120:469–79 [Google Scholar]
  53. 53. Int. Brachypodium Initiat 2010. Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463:763–68 [Google Scholar]
  54. 54. Int. Wheat Genome Seq. Consort 2014. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 345:1251788 [Google Scholar]
  55. Jenkins G, Hasterok R, Draper J. 55.  2003. Building the molecular cytogenetic infrastructure of a new model grass. Application of Novel Cytogenetic and Molecular Techniques in Genetics and Breeding of the Grasses Z Zwierzykowski, M Surma, P Kachlicki 77–84 Poznan, Pol: Pol. Acad. Sci. [Google Scholar]
  56. Jia G, Huang X, Zhi H, Zhao Y, Zhao Q. 56.  et al. 2013. A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica). Nat. Genet. 45:957–61 [Google Scholar]
  57. Jia G, Shi S, Wang C, Niu Z, Chai Y. 57.  et al. 2013. Molecular diversity and population structure of Chinese green foxtail [Setaria viridis (L.) Beauv.] revealed by microsatellite analysis. J. Exp. Bot. 64:3645–56 [Google Scholar]
  58. Jia J, Zhao S, Kong X, Li Y, Zhao G. 58.  et al. 2013. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature 496:91 [Google Scholar]
  59. Jiang H, Barbier H, Brutnell TP. 59.  2013. Methods for performing crosses in Setaria viridis, a new model system for the grasses. J. Vis. Exp. 80:e50527 [Google Scholar]
  60. 60. Joint Genome Inst 2014. FY 2015 CSP plans. Joint Genome Inst., US Dep. Energy, Washington, DC. http://jgi.doe.gov/our-projects/csp-plans/fy-2015-csp-plans
  61. Khan MA, Stace CA. 61.  1999. Breeding relationships in the genus Brachypodium (Poaceae: Pooideae). Nord. J. Bot. 19:257–69 [Google Scholar]
  62. Kikuchi K, Chesnais C, Regan S, Brutnell TP. 62.  2010. Concepts and strategies for reverse genetics in field, forest and bioenergy crop species. Principles and Practices of Plant Genomics 3 Advanced Genomics C Kole, AG Abbott 354–98 Enfield, NH: Sci. Publ. [Google Scholar]
  63. Krattinger SG, Lagudah ES, Wicker T, Risk JM, Ashton AR. 63.  et al. 2011. Lr34 multi-pathogen resistance ABC transporter: molecular analysis of homoeologous and orthologous genes in hexaploid wheat and other grass species. Plant J. 65:392–403 [Google Scholar]
  64. Laurie DA. 64.  1997. Comparative genetics of flowering time. Plant Mol. Biol. 35:167–77 [Google Scholar]
  65. Li C, Yue J, Wu X, Xu C, Yu J. 65.  2014. An ABA-responsive DRE-binding protein gene from Setaria italica, SiARDP, the target gene of SiAREB, plays a critical role under drought stress. J. Exp. Bot. 65:5415–27 [Google Scholar]
  66. Li HW, Meng CJ, Liu TN. 66.  1935. Problems in the breeding of millet (Setaria italica (L.) Beauv.). Agron. J. 27:963–70 [Google Scholar]
  67. Li P, Brutnell TP. 67.  2011. Setaria viridis and Setaria italica, model genetic systems for the Panicoid grasses. J. Exp. Bot. 62:3031–37 [Google Scholar]
  68. Ling HQ, Wang J, Zhao S, Liu D, Wang J. 68.  et al. 2013. Draft genome of the wheat A-genome progenitor Triticum urartu. Nature 496:87 [Google Scholar]
  69. Lozano-Juste J, Cutler SR. 69.  2014. Plant genome engineering in full bloom. Trends Plant Sci. 19:284 [Google Scholar]
  70. Lucas SJ, Bastas K, Budak H. 70.  2014. Exploring the interaction between small RNAs and R genes during Brachypodium response to Fusarium culmorum infection. Gene 536:254–64 [Google Scholar]
  71. Mayer KFX, Martis M, Hedley PE, Šimková H, Liu H. 71.  et al. 2011. Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–63 [Google Scholar]
  72. McCallum CM, Comai L, Greene EA, Henikoff S. 72.  2000. Targeted screening for induced mutations. Nat. Biotechnol. 18:455–57 [Google Scholar]
  73. McCallum CM, Comai L, Greene EA, Henikoff S. 73.  2000. Targeting induced local lesions in genomes (TILLING) for plant functional genomics. Plant Physiol. 123:439–42 [Google Scholar]
  74. McClintock B. 74.  1929. A cytological and genetical study of triploid maize. Genetics 14:180–222 [Google Scholar]
  75. Mendel JG. 75.  1866. Versuche über Pflanzenhybriden. Verh. Nat. Ver. Brünn 4:3–47 (English translation: Druery CT, Bateson W, transl. 1901. Experiments in plant hybridization J. R. Hort. Soc. 26:1–32) [Google Scholar]
  76. Mertz RA, Brutnell TP. 76.  2014. Bundle sheath suberization in grass leaves: multiple barriers to characterization. J. Exp. Bot. 65:3371–80 [Google Scholar]
  77. Michelmore RW, Paran I, Kesseli RV. 77.  1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. PNAS 88:9828–32 [Google Scholar]
  78. Mishra AK, Muthamilarasan M, Khan Y, Parida SK, Prasad M. 78.  2014. Genome-wide investigation and expression analyses of WD40 protein family in the model plant foxtail millet (Setaria italica L.). PLOS ONE 9:e86852 [Google Scholar]
  79. Deleted in proof
  80. Mochida K, Uehara-Yamaguchi Y, Takahashi F, Yoshida T, Sakurai T, Shinozaki K. 80.  2013. Large-scale collection and analysis of full-length cDNAs from Brachypodium distachyon and integration with Pooideae sequence resources. PLOS ONE 8:e75265 [Google Scholar]
  81. Mur LAJ, Allainguillaume J, Catalán P, Hasterok R, Jenkins G. 81.  et al. 2011. Exploiting the Brachypodium Tool Box in cereal and grass research. New Phytol. 191:334–47 [Google Scholar]
  82. Muthamilarasan M, Khandelwal R, Yadav CB, Bonthala VS, Khan Y, Prasad M. 82.  2014. Identification and molecular characterization of MYB transcription factor superfamily in C4 model plant foxtail millet (Setaria italica L.). PLOS ONE 9:e109920 [Google Scholar]
  83. Mutwil M, Usadel B, Schütte M, Loraine A, Ebenhöh O, Persson S. 83.  2010. Assembly of an interactive correlation network for the Arabidopsis genome using a novel heuristic clustering algorithm. Plant Physiol. 152:29–43 [Google Scholar]
  84. Myers SS, Zanobetti A, Kloog I, Huybers P, Leakey AD. 84.  et al. 2014. Increasing CO2 threatens human nutrition. Nature 510:139–42 [Google Scholar]
  85. 85. Natl. Corn Grow. Assoc 2014. U.S. corn crop value: 1933–2013. http://www.worldofcorn.com/#us-corn-crop-value
  86. 86. Natl. Germplasm Resour. Lab 2014. Taxon: Setaria italica (L.) P. Beauv. subsp. viridis (L.) Thell. Germplasm Resour. Inf. Netw. (GRIN), Natl. Genet. Resour. Program, Agric. Res. Serv., US Dep. Agric., Beltsville, MD. http://www.ars-grin.gov/cgi-bin/npgs/html/taxon.pl?430573
  87. Păcurar DI, Thordal-Christensen H, Nielsen KK, Lenk I. 87.  2008. A high-throughput Agrobacterium-mediated transformation system for the grass model species Brachypodium distachyon L. Transgenic Res. 17:965–75 [Google Scholar]
  88. Pasquet JC, Chaouch S, Macadre C, Balzergue S, Huguet S. 88.  et al. 2014. Differential gene expression and metabolomic analyses of Brachypodium distachyon infected by deoxynivalenol producing and non-producing strains of Fusarium graminearum. BMC Genomics 15:629 [Google Scholar]
  89. Perlack RD, Wright LL, Turhollow AF, Graham RL, Stokes BJ, Erbach DC. 89.  2005. Biomass as a feedstock for a bioenergy and bioproducts industry: the technical feasibility of a billion-ton annual supply. Rep. ORNL/TM-2005/66, Oak Ridge Natl. Lab., Oak Ridge, TN
  90. Petti C, Shearer A, Tateno M, Ruwaya M, Nokes S. 90.  et al. 2013. Comparative feedstock analysis in Setaria viridis L. as a model for C4 bioenergy grasses and Panicoid crop species. Front. Plant Sci. 4:181 [Google Scholar]
  91. Qi L, Friebe B, Wu J, Gu Y, Qian C, Gill BS. 91.  2010. The compact Brachypodium genome conserves centromeric regions of a common ancestor with wheat and rice. Funct. Integr. Genomics 10:477–92 [Google Scholar]
  92. Qin B, Cao A, Wang H, Chen T, You FM. 92.  et al. 2011. Collinearity-based marker mining for the fine mapping of pm6, a powdery mildew resistance gene in wheat. Theor. Appl. Genet. 123:207–18 [Google Scholar]
  93. Redei GP. 93.  1975. Arabidopsis as a genetic tool. Annu. Rev. Genet. 9:111–27 [Google Scholar]
  94. Rhodes MM. 94.  1949. Rollins Adams Emerson: 1873–1947.. Biographical Memoirs 25311–23 Washington, DC: Natl. Acad. Sci. [Google Scholar]
  95. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F. 95.  et al. 2009. The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112–15 [Google Scholar]
  96. Schneeberger K, Weigel D. 96.  2011. Fast-forward genetics enabled by new sequencing technologies. Trends Plant Sci. 16:282–88 [Google Scholar]
  97. Settles AM, Holding DR, Tan BC, Latshaw SP, Liu J. 97.  et al. 2007. Sequence-indexed mutations in maize using the UniformMu transposon-tagging population. BMC Genomics 8:116 [Google Scholar]
  98. Somyong S, Munkvold JD, Tanaka J, Benscher D, Sorrells ME. 98.  2011. Comparative genetic analysis of a wheat seed dormancy QTL with rice and Brachypodium identifies candidate genes for ABA perception and calcium signaling. Funct. Integr. Genomics 3:479–90 [Google Scholar]
  99. Steinwand MA, Young HA, Bragg JN, Tobias CM, Vogel JP. 99.  2013. Brachypodium sylvaticum, a model for perennial grasses: transformation and inbred line development. PLOS ONE 8:e75180 [Google Scholar]
  100. Sturtevant AH. 100.  1959. Thomas Hunt Morgan: 1866–1945. Biographical Memoirs 33283–325 Washington, DC: Natl. Acad. Sci. [Google Scholar]
  101. Thole V, Peraldi A, Worland B, Nicholson P, Doonan JH, Vain P. 101.  2012. T-DNA mutagenesis in Brachypodium distachyon. J. Exp. Bot. 63:567 [Google Scholar]
  102. Tian F, Bradbury PJ, Brown PJ, Hung H, Sun Q. 102.  et al. 2011. Genome-wide association study of leaf architecture in the maize nested association mapping population. Nat. Genet. 43:159–62 [Google Scholar]
  103. Till BJ, Cooper J, Tai TH, Colowit P, Greene EA. 103.  et al. 2007. Discovery of chemically induced mutations in rice by TILLING. BMC Plant Biol. 7:19 [Google Scholar]
  104. Till BJ, Reynolds SH, Weil C, Springer N, Burtner C. 104.  et al. 2004. Discovery of induced point mutations in maize genes by TILLING. BMC Plant Biol. 4:12 [Google Scholar]
  105. Tollenaar M, Lee EA. 105.  2002. Yield potential, yield stability and stress tolerance in maize. Field Crops Res. 75:161–69 [Google Scholar]
  106. Trick M, Adamski NM, Mugford SG, Jiang CC, Febrer M, Uauy C. 106.  2012. Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat. BMC Plant Biol. 12:14 [Google Scholar]
  107. Tsai H, Howell T, Nitcher R, Missirian V, Watson B. 107.  et al. 2011. Discovery of rare mutations in populations: TILLING by sequencing. Plant Physiol. 156:1257–68 [Google Scholar]
  108. Tyler L, Fangel JU, Fagerström AD, Steinwand MA, Raab TK. 108.  et al. 2014. Selection and phenotypic characterization of a core collection of Brachypodium distachyon inbred lines. BMC Plant Biol. 14:25 [Google Scholar]
  109. 109. US Dep. Energy 2006. Breaking the biological barriers to cellulosic ethanol: a joint research agenda. Publ. DOE/SC-0095, Off. Sci. and Off. Energy Effic. Renew. Energy, US Dep. Energy, Washington, DC
  110. Vain P, Worland B, Thole V, McKenzie N, Alves SC. 110.  et al. 2008. Agrobacterium-mediated transformation of the temperate grass Brachypodium distachyon (genotype Bd21) for T-DNA insertional mutagenesis. Plant Biotechnol. J. 6:236–45 [Google Scholar]
  111. Van Eck J, Swartwood K. 111.  2015. Setaria viridis. Methods Mol. Biol. 1223:57–67 [Google Scholar]
  112. Van Tassel DL, DeHaan LR, Cox CS. 112.  2010. Missing domesticated plant forms: Can artificial selection fill the gap?. Evol. Appl. 3:434–52 [Google Scholar]
  113. Vogel JP, Garvin DF, Leong OM, Hayden DM. 113.  2006. Agrobacterium-mediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell Tissue Organ Cult. 85:199–211 [Google Scholar]
  114. Vogel JP, Gu Y, Twigg P, Lazo G, Laudencia-Chingcuanco D. 113a.  et al. 2006. EST sequencing and phylogenetic analysis of the model grass Brachypodium distachyon. Theor. Appl. Genet. 113:186–95 [Google Scholar]
  115. Vogel JP, Hill T. 114.  2008. High-efficiency Agrobacterium-mediated transformation of Brachypodium distachyon inbred line Bd21-3. Plant Cell Rep. 27:471–78 [Google Scholar]
  116. Vogel JP, Tuna M, Budak H, Huo N, Gu YQ, Steinwand MA. 115.  2009. Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biol. 9:88 [Google Scholar]
  117. Vollbrecht E, Duvick J, Schares JP, Ahern KR, Deewatthanawong P. 116.  et al. 2010. Genome-wide distribution of transposed Dissociation elements in maize. Plant Cell 22:1667–85 [Google Scholar]
  118. Wang C, Chen J, Zhi H, Yang L, Li W. 117.  et al. 2010. Population genetics of foxtail millet and its wild ancestor. BMC Genet. 11:90 [Google Scholar]
  119. Wang C, Jia G, Zhi H, Niu Z, Chai Y. 118.  et al. 2012. Genetic diversity and population structure of Chinese foxtail millet [Setaria italica (L.) Beauv.] landraces. G3 2:769–77 [Google Scholar]
  120. Wheeler T, von Braun J. 119.  2013. Climate change impacts on global food security. Science 341:508–13 [Google Scholar]
  121. Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB. 120.  et al. 2010. Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J. 63:167–77 [Google Scholar]
  122. Wolny E, Hasterok R. 121.  2009. Comparative cytogenetic analysis of the genomes of the model grass Brachypodium distachyon and its close relatives. Ann. Bot. 104:873–81 [Google Scholar]
  123. Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W. 122.  et al. 2004. The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303:1640–44 [Google Scholar]
  124. Young ND, Bharti AK. 123.  2012. Genome-enabled insights into legume biology. Annu. Rev. Plant Biol. 63:283–305 [Google Scholar]
  125. Yu J, Hu S, Wang J, Wong GK, Li S. 124.  et al. 2002. A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79–92 [Google Scholar]
  126. Yuan YW, Sagawa JM, Di Stilio VS, Bradshaw HD Jr. 125.  2013. Bulk segregant analysis of an induced floral mutant identifies a MIXTA-like R2R3 MYB controlling nectar guide formation in Mimulus lewisii. Genetics 194:523–28 [Google Scholar]
  127. Zhang G, Liu X, Quan Z, Cheng S, Xu X. 126.  et al. 2012. Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential. Nat. Biotechnol. 30:549–54 [Google Scholar]
  128. Zhang H, Guan H, Li J, Zhu J, Xie C. 127.  et al. 2010. Genetic and comparative genomics mapping reveals that a powdery mildew resistance gene Ml3D232 originating from wild emmer co-segregates with an NBS-LRR analog in common wheat (Triticum aestivum L.). Theor. Appl. Genet. 121:1613–21 [Google Scholar]
  129. Zhang Y, Shan Q, Wang Y, Chen K, Liang Z. 128.  et al. 2013. Rapid and efficient gene modification in rice and Brachypodium using TALENs. Mol. Plant 6:1365–68 [Google Scholar]
  130. Zhang Z, Friesen TL, Xu SS, Shi G, Liu Z. 129.  et al. 2011. Two putatively homoeologous wheat genes mediate recognition of SnTox3 to confer effector-triggered susceptibility to Stagonospora nodorum. Plant J. 65:27–38 [Google Scholar]
  131. Zhu XG, Shan L, Wang Y, Quick WP. 130.  2010. C4 rice—an ideal arena for systems biology research. J. Integr. Plant Biol. 52:762–70 [Google Scholar]

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error