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Cited by 132Plant Taxonomy and PhylogeneticsPlant Molecular Biology ResearchChromosomal and Genetic Variations

Architectural Evolution and its Implications for Domestication in Grasses

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Doust, A.·2007·Annals of Botany
DOI 10.1093/aob/mcm040PMC PMC2759198
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Abstract

BACKGROUND: The cereal crops domesticated from grasses provide a large percentage of the calories consumed by humans. Domestication and breeding in individual cereals has historically occurred in isolation, although this is rapidly changing with comparative genomics of the sequenced or soon-to-be sequenced genomes of rice, sorghum, maize and Brachypodium. Genetic information transferred through genomic comparisons is helping our understanding of genetically less tractable crops such as the hexaploid wheats and polyploid sugarcane, as well as the approx. 10 000 species of wild grasses. In turn, phylogenetic analysis helps put our knowledge of the morphology of cereal crops into an evolutionary context. GRASS ARCHITECTURE: Domestication often involves a change in the pattern and timing of branching, which affects both vegetative and inflorescence architecture, and ultimately yield. Cereal grasses exhibit two main forms of vegetative architecture: the pooid and erhartoid cereals such as wheat and rice have multiple basal tillers, while panicoid cereals such as maize, sorghum and the millets have few tillers or even only a single main stem. These differences are reflected in the differences between the wild species of pooid and some erhartoid grasses, which emphasize basal branching over axillary branching, and the panicoid grasses, where axillary branching is more frequently found. A combination of phylogenetic and genomic analysis is beginning to reveal the similarities and differences between different cereal crops, and relate these to the diversity of wild grasses to which they are related. Recent work on genes controlling branching emphasizes that developmental genetics needs to be viewed in both an evolutionary and ecological framework, if it is to be useful in understanding how morphology evolves. Increasingly, exploring the phylogenetic context of the crop grasses will suggest new ways to identify and create combinations of morphological traits that will best suit our future needs.

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  • Plants of Ehrhartoideae and Pooideae develop many tillers and no axillary branches while members of Panicoideae produce tillers and initiate axillary meristems that can grow into axillary branches.

    “Plants of the Ehrhartoideae and the Pooideae develop many tillers and no axillary branches while members of the Panicoideae produce tillers and, in addition, initiate axillary meristems that can grow into axillary branches (Doust, 2007).”

    From Shaping plant architecture (2015) · cites this paper as Doust, 2007

    The Branching patterns section describes pooid and ehrhartoid cereal grasses as characteristically having many tillers but no axillary branches. It says panicoid cereal grasses produce tillers and, in most cases, axillary meristems that can grow into branches when space and light are non-limiting. The claim extends these patterns to the subfamilies generally and omits the panicoid qualifications. (LLM, conf=0.86)

    Experimental — accuracy not yet measured

  • Analyses of domestication genes in monocot crops led to the identification of a small set of target genes, each of which profoundly influences plant architecture.

    “Analyses of domestication genes in monocot crops led to the identification of a small set of target genes (Doebley et al., 1997; Doust, 2007; Yu et al., 2007; Tan et al., 2008; Ku et al., 2011; Remigereau et al., 2011), of which each profoundly influences plant architecture.”

    From Shaping plant architecture (2015) · cites this paper as Doust, 2007

    The Vegetative Branching section (page unavailable) identifies genes controlling branching in crop grasses, including Zm-tb1, whose mutant produces many tillers and axillary branches in maize. It does not establish that domestication-gene analyses identified a small set of targets each with a profound architectural effect; it says the related Os-tb1 has less effect in rice. (LLM, conf=0.84)

    Experimental — accuracy not yet measured

  • SL genes have not been a target during monocot domestication, since the architectural trait selected during domestication of crops is low branching.

    “Also, SL genes have not been a target during monocot domestication, since the architectural trait selected during domestication of crops is low branching (Doust, 2007).”

    From Shaping plant architecture (2015) · cites this paper as Doust, 2007

    In ‘Vegetative Branching > Branching patterns’ (page unavailable), Doust says maize and other panicoid crop grasses were selected for decreased tillering and axillary branching. The paper does not say that SL-pathway genes were not domestication targets, and it does not present low branching as a universal crop-domestication trait: it also describes rice breeding for more productive tillers. (LLM, conf=0.88)

    Experimental — accuracy not yet measured

  • Grasses exhibit two types of vegetative branching patterns depending on the position of branch development with respect to the plant main axis.

    “Grasses exhibit two types of vegetative branching patterns (Doust, 2007), depending on the position of branch development with respect to the plant main axis.”

    From Shaping plant architecture (2015) · cites this paper as Doust, 2007

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Research works printed but not linked: 86

  1. AGI Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 2000 408 796 815 11130711
  2. Babb S Muehlbauer GJ Genetic and morphological characterization of the barley uniculm2 (cul2) mutant Theoretical and Applied Genetics 2003 106 846 857 12647059
  3. Bennett T Sieberer T Willett B Booker J Luschnig C Leyser O The Arabidopsis MAX pathway controls shoot branching by regulating auxin transport Current Biology 2006 16 553 563 16546078
  4. Bennetzen JL Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions The Plant Cell 2000 12 1021 1029 10899971 PMC149046
  5. Bennetzen JL Freeling M Grasses as a single genetic system: genome composition, collinearity and compatibility Trends in Genetics 1993 9 259 261 8379002
  6. Bommert P Satoh-Nagasawa N Jackson D Hirano HY Genetics and evolution of inflorescence and flower development in grasses Plant and Cell Physiology 2005 46 69 78 15659432
  7. Booker J Sieberer T Wright W Williamson L Willett B Stirnberg P MAX1 encodes a cytochrome P450 family member that acts downstream of MAX3/4 to produce a carotenoid-derived branch-inhibiting hormone Developmental Cell 2005 8 443 449 15737939
  8. Bortiri E Chuck G Vollbrecht E Rocheford T Martienssen R Hake S ramosa2 encodes a LATERAL ORGAN BOUNDARY domain protein that determines the fate of stem cells in branch meristems of maize The Plant Cell 2006 18 574 585 16399802 PMC1383634
  9. Bowers JE Arias MA Asher R Avise JA Ball RT Brewer GA Comparative physical mapping links conservation of microsynteny to chromosome structure and recombination in grasses 2005 102 Proceedings of the National Academy of Sciences of the USA 13206 13211 PMC1201573 16141333
  10. Bremer K Gondwanan evolution of the grass alliance of families (Poales) Evolution 2002 56 1374 1387 12206239
  11. Brown P Klein P Bortiri E Acharya C Rooney W Kresovich S Inheritance of inflorescence architecture in sorghum Theoretical and Applied Genetics 2006 113 931 942 16847662
  12. Clark RM Wagler TN Quijada P Doebley J A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescence architecture Nature Genetics 2006 38 594 597 16642024
  13. Crepet WL Feldman GD The earliest remains of grasses in the fossil record American Journal of Botany 1991 78 1010 1014
  14. Devos KM Updating the ‘Crop circle Current Opinion in Plant Biology 2005 8 155 162 15752995
  15. Devos KM Gale MD Genome relationships: the grass model in current research The Plant Cell 2000 12 637 646 10810140 PMC139917
  16. Devos KM Beales J Ogihara Y Doust AN Comparative sequence analysis of the Phytochrome C gene and its upstream region in allohexaploid wheat reveals new data on the evolution of its three constituent genomes Plant Molecular Biology 2005 58 625 641 16158239
  17. Dingkuhn M Luquet D Quilot B de Reffye P Environmental and genetic control of morphogenesis in crops: towards models simulating phenotypic plasticity Australian Journal of Agricultural Research 2005 56 1289 1302
  18. Doebley J Stec A Genetic analysis of the morphological differences between maize and teosinte Genetics 1991 129 285 295 1682215 PMC1204577
  19. Doebley J Stec A Hubbard L The evolution of apical dominance in maize Nature 1997 386 485 488 9087405
  20. Doust AN Kellogg EA Inflorescence diversification in the panicoid ‘bristle grass’ clade (Paniceae, Poaceae): evidence from molecular phylogenies and developmental morphology American Journal of Botany 2002 89 1203 1222 21665721
  21. Doust AN Kellogg EA Effect of genotype and environment on branching in weedy green millet (Setaria viridis) and domesticated foxtail millet (Setaria italica) (Poaceae) Molecular Ecology 2006 15 1335 1349 16626457
  22. Doust AN Devos KM Gadberry MD Gale MD Kellogg EA Genetic control of branching in foxtail millet 2004 101 Proceedings of the National Academy of Sciences of the USA 9045 9050 PMC428470 15184666
  23. 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 1659 1672 15654107 PMC1449545
  24. Duggan BL Richards RA van Herwaarden AF Fettell NA Agronomic evaluation of a tiller inhibition gene (tin) in wheat. I. Effect on yield, yield components, and grain protein Australian Journal of Agricultural Research 2005 56 169 178
  25. Gale MD Devos KM Plant comparative genetics after 10 years Science 1998 282 656 659 9784118
  26. Gallavotti A Zhao Q Kyozuka J Meeley RB Ritter MK Doebley JF The role of barren stalk1 in the architecture of maize Nature 2004 432 630 635 15577912
  27. Garg AK Sawers RJH Wang HY Kim JK Walker JM Brutnell TP Light-regulated overexpression of an Arabidopsis phytochrome A gene in rice alters plant architecture and increases grain yield Planta 2006 223 627 636 16136335
  28. Giussani LM Cota-Sanchez JH Zuloaga FO Kellogg EA A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis American Journal of Botany 2001 88 1993 2012 21669633
  29. Goff S Ricke D Lan T Presting G Wang R Dunn M A draft sequence of the rice genome (Oryza sativa L. ssp. japonica) Science 2002 296 92 100 11935018
  30. GPWG Phylogeny and subfamilial classification of the grasses (Poaceae) Annals of the Missouri Botanical Garden 2001 88 373 457
  31. Harlan JR Comparative evolution of cereals Evolution 1973 27 311 325 28564784
  32. Hu FY Tao DY Sacks E Fu BY Xu P Li J Convergent evolution of perenniality in rice and sorghum 2003 100 Proceedings of the National Academy of Sciences of the USA 4050 4054 PMC153046 12642667
  33. Hubbard L McSteen P Doebley J Hake S Expression patterns and mutant phenotype of teosinte branched1 correlate with growth suppression in maize and teosinte Genetics 2002 162 1927 1935 12524360 PMC1462370
  34. IRGS The map-based sequence of the rice genome Nature 2005 436 793 800 16100779
  35. Ishikawa S Maekawa M Arite T Onishi K Takamure I Kyozuka J Suppression of tiller bud activity in tillering dwarf mutants of rice Plant and Cell Physiology 2005 46 79 86 15659436
  36. Kebrom TH Burson BL Finlayson SA Phytochrome B represses Teosinte Branched1 expression and induces sorghum axillary bud outgrowth in response to light signals Plant Physiology 2006 140 1109 1117 16443694 PMC1400571
  37. Kellogg EA The grasses: a case study in macroevolution Annual Review of Ecology and Systematics 2000 31 217 238
  38. Kellogg EA What happens to genes in duplicated genomes 2003 100 Proceedings of the National Academy of Sciences of the USA 4369 4371 PMC153560 12682287
  39. Kellogg EA Progress and challenges in studies of the evolution of development Journal of Experimental Botany 2006 57 b 16990377
  40. Koch M Haubold B Mitchell-Olds T Molecular systematics of the Brassicaceae: evidence from coding plastidic matK and nuclear Chs sequences American Journal of Botany 2001 88 534 544 11250830
  41. Komatsu K Maekawa M Ujiie S Satake Y Furutani I Okamoto H S LAX and SPA: major regulators of shoot branching in rice 2003 100 Proceedings of the National Academy of Sciences of the USA 11765 11770 PMC208832 13130077
  42. Lafarge TA Broad IJ Hammer GL Tillering in grain sorghum over a wide range of population densities: identification of a common hierarchy for tiller emergence, leaf area development and fertility Annals of Botany 2002 90 87 98 12125776 PMC4233856
  43. Laurie DA Pratchett N Devos KM Leitch IJ Gale MD The distribution of RFLP markers on chromosome 2 (2H) of barley in relation to the physical and genetic location of 5S rDNA Theoretical and Applied Genetics 1983 87 177 183 24190210
  44. Leyser O Regulation of shoot branching by auxin Trends in Plant Science 2003 8 541 545 14607099
  45. Leyser O Dynamic integration of auxin transport and signalling Current Biology 2006 16 R424 R433 16753558
  46. Li XY Qian Q Fu ZM Wang YH Xiong GS Zeng DL Control of tillering in rice Nature 2003 422 618 621 12687001
  47. Linder HP Rudall PJ Evolutionary history of Poales Annual Review of Ecology Evolution and Systematics 2005 36 107 124
  48. Londo JP Chiang Y-C Hung K-H Chiang T-Y Schaal BA Phylogeography of Asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa 2006 103 Proceedings of the National Academy of Sciences of the USA 9578 9583 PMC1480449 16766658
  49. Lukens LN Doebley J Epistatic and environmental interactions for quantitative trait loci involved in maize evolution Genetical Research, Cambridge 1999 74 291 302
  50. Luo LJ Li ZK Mei HW Shu QY Tabien R Zhong DB Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components Genetics 2001 158 1755 1771 11514460 PMC1461757
  51. McSteen P Leyser O Shoot branching Annual Review of Plant Biology 2005 56 353 374 15862100
  52. McSteen P Branching out: the ramosa pathway and the evolution of grass inflorescence morphology The Plant Cell 2006 18 518 522 16513602 PMC1383629
  53. Ma JX SanMiguel P Lai JS Messing J Bennetzen JL DNA rearrangement in orthologous Orp regions of the maize, rice and sorghum genomes Genetics 2005 170 1209 1220 15834137 PMC1451190
  54. Malcomber ST Preston JC Reinheimer R Kossuth J Kellogg EA Soltis DE Soltis PS Leebens-Mack J Developmental gene evolution and the origin of grass inflorescence diversity Developmental genetics of the flower. Advances in Botanical Research 2006 44 San Diego & London Academic Press 425 480
  55. Matsuoka Y Vigouroux Y Goodman MM Sanchez GJ Buckler E Doebley J A single domestication for maize shown by multilocus microsatellite genotyping 2002 99 Proceedings of the National Academy of Sciences of the USA 6080 6084 PMC122905 11983901
  56. Messing J Bharti AK Karlowski WM Gundlach H Kim HR Yu Y Sequence composition and genome organization of maize 2004 101 Proceedings of the National Academy of Sciences of the USA 14349 14354 PMC521949 15388850
  57. Michelangeli FA Davis JI Stevenson DW Phylogenetic relationships among Poaceae and related families as inferred from morphology, inversions in the plastid genome, and sequence data from the mitochondrial and plastid genomes American Journal of Botany 2003 90 93 106 21659084
  58. Mitchell PL Sheehy JE Supercharging rice photosynthesis to increase yield New Phytologist 2006 171 688 693 16918541
  59. Moulia B Loup C Chartier M Allirand JM Edelin C Dynamics of architectural development of isolated plants of maize (Zea mays L.), in a non-limiting environment: the branching potential of modern maize Annals of Botany 1999 84 645 656
  60. Neuffer MG Coe EH Wessler SR Mutants of maize 1997 Cold Spring Harbor, NY Cold Spring Harbor Press
  61. Ozkan H Brandolini A Schafer-Pregl R Salamini F AFLP analysis of a collection of tetraploid wheats indicates the origin of emmer and hard wheat domestication in southeast Turkey Molecular Biology and Evolution 2002 19 1797 1801 12270906
  62. Paterson AH Leafing through the genomes of our major crop plants: strategies for capturing unique information Nature Reviews Genetics 2006 7 174 184 16485017
  63. Paterson AH Lin Y-R Li Z Schertz KF Doebley JF Pinson SRM Convergent domestications of cereal crops by independent mutations at corresponding genetic loci Science 1995 269 a 17821643
  64. Paterson AH Schertz KF Lin Y-R Liu S-C Chang Y-L The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halapense (L.) Pers 1995 92 b Proceedings of the National Academy of Sciences of the USA PMC41655 11607551
  65. Paterson AH Bowers JE Chapman BA Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics 2004 101 Proceedings of the National Academy of Sciences of the USA 9903 9908 PMC470771 15161969
  66. Paterson AH Freeling M Sasaki T Grains of knowledge: genomics of model cereals Genome Research 2005 15 1643 1650 16339361
  67. Poncet V Lamy F Devos KM Gale MD Sarr A Robert T Genetic control of domestication traits in pearl millet (Pennisetum glaucum L., Poaceae) Theoretical and Applied Genetics 2000 100 147 159 12582601
  68. Prasad V Stromberg CAE Alimohammadian H Sahni A Dinosaur coprolites and the early evolution of grasses and grazers Science 2005 310 1177 1180 16293759
  69. Sage RF The evolution of C-4 photosynthesis New Phytologist 2004 161 341 370 33873498
  70. Salamin N Hodkinson TR Savolainen V Building supertrees: an empirical assessment using the grass family (Poaceae) Systematic Biology 2002 51 112 126 11943096
  71. SanMiguel P Tikhonov A Jin Y-K Motchoulskaia N Zakharov D Melake-Berhan A Nested retrotransposons in the intergenic regions of the maize genome Science 1996 274 765 768 8864112
  72. Satoh-Nagasawa N Nagasawa N Malcomber S Sakai H Jackson D A trehalose metabolic enzyme controls inflorescence architecture in maize Nature 2006 441 227 230 16688177
  73. Sawers RJH Sheehan MJ Brutnell TP Cereal phytochromes: targets of selection, targets for manipulation? Trends in Plant Science 2005 10 138 143 15749472
  74. Schmitt J Stinchcombe JR Heschel MS Huber H The adaptive evolution of plasticity: phytochrome-mediated shade avoidance responses Integrative and Comparative Biology 2003 43 459 469 21680454
  75. Simons JL Napoli CA Janssen BJ Plummer KM Snowden KC Analysis of the DECREASED APICAL DOMINANCE (DAD) genes of Petunia hybrida in the control of axillary branching Plant Physiology 2006 PMC1803742 17158589
  76. Snowden KC Simkin AJ Janssen BJ Templeton KR Loucas HM Simons JL The Decreased apical dominance 1/petunia hybrida carotenoid cleavage dioxygenase8 gene affects branch production and plays a role in leaf senescence, root growth, and flower development The Plant Cell 2005 17 746 759 15705953 PMC1069696
  77. Stromberg CAE Decoupled taxonomic radiation and ecological expansion of open-habitat grasses in the Cenozoic of North America 2005 102 Proceedings of the National Academy of Sciences of the USA 11980 11984 PMC1189350 16099827
  78. Takeda T Sawa Y Suzuki M Kitano H Ueguchi-Tanaka M Ashikari M Matsuoka M Ueguchi C The OsTB1 gene negatively regulates lateral branching in rice The Plant Journal 2003 33 513 520 12581309
  79. Upadyayula N da Silva H Bohn M Rocheford T Genetic and QTL analysis of maize tassel and ear inflorescence architecture Theoretical and Applied Genetics 2006 112 592 606 16395569
  80. Veit B Stem cell signalling networks in plants Plant Molecular Biology 2006 60 793 810 16724253
  81. Vollbrecht E Springer PS Goh L Buckler IV ES Martienssen R Architecture of floral branch systems in maize and related grasses Nature 2005 436 1119 1126 16041362
  82. Wang H Nussbaum-Wagler T Li B Zhao Q Vigouroux Y Faller M The origin of the naked grains of maize Nature 2005 436 714 719 16079849 PMC1464477
  83. Wang YH Li JY Genes controlling plant architecture Current Opinion in Biotechnology 2006 17 123 129 16504498
  84. Westerbergh A Doebley J Quantitative trait loci controlling phenotypes related to the perennial versus annual habit in wild relatives of maize Theoretical and Applied Genetics 2004 109 1544 1553 15338134
  85. Zachos J Pagani M Sloan L Thomas E Billups K Trends, rhythms, and aberrations in global climate 65 Ma to present Science 2001 292 686 693 11326091
  86. Zou J Chen Z Zhang S Zhang W Jiang G Zhao X Characterizations and fine mapping of a mutant gene for high tillering and dwarf in rice (Oryza sativa L.) Planta 2005 222 604 612 16021500

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Authors
Doust, A.
Affiliations
University of Missouri–St. Louis (US)
Corresponding author
Doust, A.
ORCID
Doust, A.
Venue
Annals of Botany
Publisher
Oxford University Press (OUP)
Published
2007-07-28
Volume
100
Issue
5
Pages
941-950
ISSN
  • 0305-7364 (ISSN-L)
  • 1095-8290
DOI
10.1093/aob/mcm040
PMC
PMC2759198
OpenAlex
W2101472968
Cited by
132
References
5
Citations by year
2026: 4 · 2025: 5 · 2024: 4 · 2023: 6 · 2022: 6 · 2021: 4 · 2020: 9 · 2019: 8 · 2018: 6 · 2017: 4 · 2016: 5 · 2015: 7 · 2014: 12 · 2013: 8 · 2012: 10
FWCI
0.63
Type
journal article
Language
en
Open access
Licence
cc-by-nc
Locations
  • Annals of Botany (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Plant Taxonomy and Phylogenetics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
Keywords
cereals, branching, inflorescence architecture, tillering, phylogenetic analysis, comparative genomics, developmental genetics, wild grass, wheat, rice, maize, sorghum, millet
MeSH terms
Agriculture, Poaceae, Phylogeny, Crops, Agricultural, Flowering Tops

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