[en] The transition to reproductive development is a crucial step in the plant life cycle, and the timing of this transition is an important factor in crop yields. Here, we report new insights into the genetic control of natural variation in flowering time in Brachypodium distachyon, a nondomesticated pooid grass closely related to cereals such as wheat (Triticum spp.) and barley (Hordeum vulgare L.). A recombinant inbred line population derived from a cross between the rapid-flowering accession Bd21 and the delayed-flowering accession Bd1-1 were grown in a variety of environmental conditions to enable exploration of the genetic architecture of flowering time. A genotyping-by-sequencing approach was used to develop SNP markers for genetic map construction, and quantitative trait loci (QTLs) that control differences in flowering time were identified. Many of the flowering-time QTLs are detected across a range of photoperiod and vernalization conditions, suggesting that the genetic control of flowering within this population is robust. The two major QTLs identified in undomesticated B. distachyon colocalize with VERNALIZATION1/PHYTOCHROME C and VERNALIZATION2, loci identified as flowering regulators in the domesticated crops wheat and barley. This suggests that variation in flowering time is controlled in part by a set of genes broadly conserved within pooid grasses.
R.M.A.’s laboratory was funded by the National Science Foun- dation under grant no. IOS-1258126, and the Great Lakes Bioenergy Research Center (Department of Energy Biological and Environmen- tal Research Office of Science grant no. DE-FCO2-07ER64494); D.P.W. was funded in part by a National Institutes of Health-sponsored pre- doctoral training fellowship to the University of Wisconsin Genetics Training Program; F.B. thanks the Belgian American Educational Foundation (BAEF) for their post-doctoral fellowship; J.P.V. and S.P.G. were funded by the U.S. Department of Energy Joint Genome Institute (a Department of Energy Office of Science User Facility), which is supported under contract no. DE-AC02-05CH11231, with additional funding provided by Office of Biological and Environmen- tal Research, Office of Science, U.S. Department of Energy, under interagency agreement no. DE-SC0006999; and D.F.G. was supported by USDA-ARS CRIS project no. 5062-21000-030-00D.
Abe M, Kobayashi Y, Yamamoto S, Daimon Y, Yamaguchi A, Ikeda Y, Ichinoki H, Notaguchi M, Goto K, Araki T (2005) FD, a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex. Science 309: 1052–1056
Amasino R (2010) Seasonal and developmental timing of flowering. Plant J 61: 1001–1013
Barrero JM, Jacobsen JV, Talbot MJ, White RG, Swain SM, Garvin DF, Gubler F (2012) Grain dormancy and light quality effects on germination in the model grass Brachypodium distachyon. New Phytol 193: 376–386
Bettgenhaeuser J, Corke FM, Opanowicz M, Green P, Hernández-Pinzón I, Doonan JH, Moscou MJ (2016) Natural variation in Brachypodium links vernalization and flowering time loci as major flowering determinants. Plant Physiol 2016 Sep. 20. pii: pp.00813.2016
Brkljacic J, Grotewold E, Scholl R, Mockler T, Garvin DF, Vain P, Brutnell T, Sibout R, Bevan M, Budak H, Caicedo AL, Gao C, et al (2011) Brachypodium as a model for the grasses: today and the future. Plant Physiol 157: 3–13
Broman KW, Wu H, Sen S, Churchill GA (2003) R/qtl: QTL mapping in experimental crosses. Bioinformatics 19: 889–890
Brutnell TP, Bennetzen JL, Vogel JP (2015) Brachypodium distachyon and Setaria viridis: model genetic systems for the grasses. Annu Rev Plant Biol 66: 465–485
Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, et al (2009) The genetic architecture of maize flowering time. Science 325: 714–718
Cass CL, Lavell AA, Santoro N, Foster CE, Karlen SD, Smith RA, Ralph J, Garvin DF, Sedbrook JC (2016) Cell wall composition and biomass recalcitrance differences within a genotypically diverse set of Brachypodium distachyon inbred lines. Front Plant Sci 7: 708
Chen A, Dubcovsky J (2012) Wheat TILLING mutants show that the vernalization gene VRN1 down-regulates the flowering repressor VRN2 in leaves but is not essential for flowering. PLoS Genet 8: e1003134
Chen A, Li C, Hu W, Lau MY, Lin H, Rockwell NC, Martin SS, Jernstedt JA, Lagarias JC, DubcovskyJ (2014) Phytochrome C plays a major role in the acceleration of wheat flowering under long-day photoperiod. Proc Natl Acad Sci USA 111: 10037–10044 10.1073/pnas.1409795111
Chouard P (1960) Vernalization and its relations to dormancy. Annu Rev Plant Physiol 11: 191–238
Colton-Gagnon K, Ali-Benali MA, Mayer BF, Dionne R, Bertrand A, Do Carmo S, Charron J-B (2014) Comparative analysis of the cold acclimation and freezing tolerance capacities of seven diploid Brachypodium distachyon accessions. Ann Bot (Lond) 113: 681–693
Corbesier L, Vincent C, Jang S, Fornara F, Fan Q, Searle I, Giakountis A, Farrona S, Gissot L, Turnbull C, Coupland G (2007) FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316: 1030–1033
Cui Y, Lee MY, Huo N, Bragg J, Yan L, Yuan C, Li C, Holditch SJ, Xie J, Luo M-C, Li D, Yu J, et al (2012) Fine mapping of the Bsr1 barley stripe mosaic virus resistance gene in the model grass Brachypodium distachyon. PLoS One 7: e38333
Des Marais DL, Razzaque S, Hernandez KM, Garvin DF, Juenger TE (2016) Quantitative trait loci associated with natural diversity in wateruse efficiency and response to soil drying in Brachypodium distachyon. Plant Sci 251: 2–11
Distelfeld A, Dubcovsky J (2010) Characterization of the maintained vegetative phase deletions from diploid wheat and their effect on VRN2 and FT transcript levels. Mol Genet Genomics 283: 223–232
Distelfeld A, Li C, Dubcovsky J (2009) Regulation of flowering in temperate cereals. Curr Opin Plant Biol 12: 178–184
Dubcovsky J, Chen C, Yan L (2005) Molecular characterization of the allelic variation at the VRN-H2 vernalization locus in barley. Mol Breed 15: 395–407
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One 6: e19379
Fjellheim S, Boden S, Trevaskis B (2014) The role of seasonal flowering responses in adaptation of grasses to temperate climates. Front Plant Sci 5: 431
Fu D, Szucs P, Yan L, Helguera M, Skinner J, Hayes P, Dubcovsky J (2005) Large deletions in the first intron of the VRN-1 vernalization gene are associated with spring growth habit in barley and polyploid wheat. Mol Genet Genomics 273: 54–65
Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Mitros T, Dirks W, Hellsten U, Putnam N, Rokhsar DS (2012) Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res 40: D1178–D1186
Gordon SP, Priest H, Des Marais DL, Schackwitz W, Figueroa M, Martin J, Bragg JN, Tyler L, Lee CR, Bryant D, Wang W, Messing J, et al (2014) Genome diversity in Brachypodium distachyon: deep sequencing of highly diverse inbred lines. Plant J 79: 361–374
Greenup A, Peacock WJ, Dennis ES, Trevaskis B (2009) The molecular biology of seasonal flowering-responses in Arabidopsis and the cereals. Ann Bot (Lond) 103: 1165–1172
Haley CS, Knott SA (1992) A simple regression method for mapping quantitative trait loci in line crosses using flanking markers. Heredity (Edinb) 69: 315–324
Herten K, Hestand MS, Vermeesch JR, van Houdt JK (2015) GBSX: a toolkit for experimental design and demultiplexing genotyping by sequencing experiments. BMC Bioinformatics 16: 73
Higgins JA, Bailey PC, Laurie DA (2010) Comparative genomics of flowering time pathways using Brachypodium distachyon as a model for the temperate grasses. PLoS One 5: e10065
Hung H-Y, Shannon LM, Tian F, Bradbury PJ, Chen C, Flint-Garcia SA, McMullen MD, Ware D, Buckler ES, Doebley JF, Holland JB (2012) ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize. Proc Natl Acad Sci USA 109: E1913– E1921
International Brachypodium Initiative (2010) Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature 463: 763– 768
Karsai I, Szűcs P, Mészáros K, Filichkina T, Hayes PM, Skinner JS, Láng L, Bedő Z (2005) The Vrn-H2 locus is a major determinant of flowering time in a facultative x winter growth habit barley (Hordeum vulgare L.) mapping population. Theor Appl Genet 110: 1458–1466
Kippes N, Chen A, Zhang X, Lukaszewski AJ, Dubcovsky J (2016) Development and characterization of a spring hexaploid wheat line with no functional VRN2 genes. Theor Appl Genet 129: 1417–1428
Li H, Durbin R (2010) Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics 26: 589–595
Loukoianov A, Yan L, Blechl A, Sanchez A, Dubcovsky J (2005) Regulation of VRN-1 vernalization genes in normal and transgenic polyploid wheat. Plant Physiol 138: 2364–2373
Nishida H, Ishihara D, Ishii M, Kaneko T, Kawahigashi H, Akashi Y, Saisho D, Tanaka K, Handa H, Takeda K, Kato K (2013) PHYTOCHROME C is a key factor controlling long-day flowering in barley. Plant Physiol 163: 804–814
Pankin A, Campoli C, Dong X, Kilian B, Sharma R, Himmelbach A, Saini R, Davis SJ, Stein N, Schneeberger K, von Korff M (2014) Mapping-bysequencing identifies HvPHYTOCHROME C as a candidate gene for the early maturity 5 locus modulating the circadian clock and photoperiodic flowering in barley. Genetics 198: 383–396
Ream TS, Woods DP, Amasino RM (2012) The molecular basis of vernalization in different plant groups. Cold Spring Harb Symp Quant Biol 77: 105–115
Ream TS, Woods DP, Schwartz CJ, Sanabria CP, Mahoy JA, Walters EM, Kaeppler HF, Amasino RM (2014) Interaction of photoperiod and vernalization determines flowering time of Brachypodium distachyon. Plant Physiol 164: 694–709
Saïdou A-A, Clotault J, Couderc M, Mariac C, Devos KM, Thuillet A-C, Amoukou IA, Vigouroux Y (2014) Association mapping, patterns of linkage disequilibrium and selection in the vicinity of the PHYTOCHROME C gene in pearl millet. Theor Appl Genet 127: 19–32
Salomé PA, Bomblies K, Laitinen RAE, Yant L, Mott R, Weigel D (2011) Genetic architecture of flowering-time variation in Arabidopsis thaliana. Genetics 188: 421–433
Sasani S, Hemming MN, Oliver SN, Greenup A, Tavakkol-Afshari R, Mahfoozi S, Poustini K, Sharifi HR, Dennis ES, Peacock WJ, et al (2009) The influence of vernalization and daylength on expression of flowering-time genes in the shoot apex and leaves of barley (Hordeum vulgare). J Exp Bot 60: 2169–2178
Schwartz CJ, Doyle MR, Manzaneda AJ, Rey PJ, Mitchell-Olds T, Amasino RM (2010) Natural variation of flowering time and vernalization responsiveness in Brachypodium distachyon. Bioenerg Res 3: 38–46
Shaw LM, Turner AS, Herry L, Griffiths S, Laurie DA (2013) Mutant alleles of Photoperiod-1 in wheat (Triticum aestivum L.) that confer a late flowering phenotype in long days. PLoS One 8: e79459
Shimada S, Ogawa T, Kitagawa S, Suzuki T, Ikari C, Shitsukawa N, Abe T, Kawahigashi H, Kikuchi R, Handa H, Murai K (2009) A genetic network of flowering-time genes in wheat leaves, in which an APETALA1/FRUITFULLlike gene, VRN1, is upstream of FLOWERING LOCUS T. Plant J 58: 668–681
Song YH, Shim JS, Kinmonth-Schultz HA, Imaizumi T (2015) Photoperiodic flowering: time measurement mechanisms in leaves. Annu Rev Plant Biol 66: 441–464
Trevaskis B, Bagnall DJ, Ellis MH, Peacock WJ, Dennis ES (2003) MADS box genes control vernalization-induced flowering in cereals. Proc Natl Acad Sci USA 100: 13099–13104
Turner A, Beales J, Faure S, Dunford RP, Laurie DA (2005) The pseudoresponse regulator Ppd-H1 provides adaptation to photoperiod in barley. Science 310: 1031–1034
Tyler L, Fangel JU, Fagerström AD, Steinwand MA, Raab TK, Willats WG, Vogel JP (2014) Selection and phenotypic characterization of a core collection of Brachypodium distachyon inbred lines. BMC Plant Biol 14: 25
Tyler L, Lee SJ, Young ND, DeIulio GA, Benavente E, Reagon M, Sysopha J, Baldini RM, Troìa A, Hazen SP, et al (2016) Population structure in the model grass Brachypodium distachyon is highly correlated with flowering differences across broad geographic areas. Plant Genome J 9: 1–20
Vogel JP, Garvin DF, Leong OM, Hayden DM (2006) Agrobacteriummediated transformation and inbred line development in the model grass Brachypodium distachyon. Plant Cell Tissue Organ Cult 84: 199– 211
Vogel JP, Tuna M, Budak H, Huo N, Gu YQ, Steinwand MA (2009) Development of SSR markers and analysis of diversity in Turkish populations of Brachypodium distachyon. BMC Plant Biol 9: 88
von Zitzewitz J, Szűcs P, Dubcovsky J, Yan L, Francia E, Pecchioni N, Casas A, Chen THH, Hayes PM, Skinner JS (2005) Molecular and structural characterization of barley vernalization genes. Plant Mol Biol 59: 449–467
Weigel D, Nordborg M (2015) Population genomics for understanding adaptation in wild plant species. Annu Rev Genet 49: 315–338
Wickham H (2009) ggplot2: Elegant Graphics for Data Analysis. Springer, New York
Wilson P, Streich J, Borevitz J (2015) Genomic diversity and climate adaptation in Brachypodium. In PJ Vogel, ed, Genetics and Genomics of Brachypodium. Springer International Publishing, Basel, Switzerland, pp 107–127
Woods DP, Amasino RM (2015) Dissecting the control of flowering time in grasses using Brachypodium distachyon. In PJ Vogel, ed, Genetics and Genomics of Brachypodium. Springer International Publishing, Basel, Switzerland, pp 259–273
Woods DP, McKeown MA, Dong Y, Preston JC, Amasino RM (2016) Evolution of VRN2/Ghd7-like genes in vernalization-mediated repression of grass flowering. Plant Physiol 170: 2124–2135
Woods DP, Ream TS, Amasino RM (2014a) Memory of the vernalized state in plants including the model grass Brachypodium distachyon. Front Plant Sci 5: 99
Woods DP, Ream TS, Minevich G, Hobert O, Amasino RM (2014b) PHYTOCHROME C is an essential light receptor for photoperiodic flowering in the temperate grass, Brachypodium distachyon. Genetics 198: 397–408
Wu Y, Bhat PR, Close TJ, Lonardi S (2008) Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph. PLoS Genet 4: e1000212
Yan L, Fu D, Li C, Blechl A, Tranquilli G, Bonafede M, Sanchez A, Valarik M, Yasuda S, Dubcovsky J (2006) The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc Natl Acad Sci USA 103: 19581– 19586
Yan L, Loukoianov A, Blechl A, Tranquilli G, Ramakrishna W, SanMiguel P, Bennetzen JL, Echenique V, Dubcovsky J (2004) The wheat VRN2 gene is a flowering repressor down-regulated by vernalization. Science 303: 1640–1644
Yan L, Loukoianov A, Tranquilli G, Helguera M, Fahima T, Dubcovsky J (2003) Positional cloning of the wheat vernalization gene VRN1. Proc Natl Acad Sci USA 100: 6263–6268
Zadoks JC, Chang TT, Konzak CF (1974) Decimal code for growth stages of cereals. Weed Res 14: 415–421
