Genetic control of root organogenesis in cereals

Methods in Molecular Biology

Volumn 959, Issue , 2013, Pages 69-81

  Marcon, Caroline ^a   Paschold, Anja ^a   Hochholdinger, Frank ^a  

^a NONE

Author keywords

(Lateral) root; Cereal; Maize; Rice

Indexed keywords

ARTICLE; CEREAL; GENE EXPRESSION REGULATION; GENETICS; ORGANOGENESIS; PHYSIOLOGY; PLANT ROOT;

CEREALS; GENE EXPRESSION REGULATION, PLANT; ORGANOGENESIS; PLANT ROOTS;

MLCS; MLOWN;

EID: 84879133963     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-221-6_4     Document Type: Article

References (74)

1. Chandler VL, Brendel V (2002) The maize genome sequencing project. Plant Physiol 130:1594-1597
2. Khush GS (2005) What it will take to feed 5.0 billion rice consumers in 2030. Plant Mol Biol 59:1-6
3. Hochholdinger F, Park WJ, Sauer M, Woll K (2004) From weeds to crops: genetic analysis of root development in cereals. Trends Plant Sci 9:42-48
4. Coudert Y, Perin C, Courtois B, Khong NG, Gantet P (2010) Genetic control of root development in rice, the model cereal. Trends Plant Sci 15:219-226
5. Hochholdinger F (2009) The maize root system: morphology, anatomy and genetics. In: Bennetzen J, Hake S (eds) Handbook of maize. Springer, New York, pp 145-160
6. Moriata S, Nemoto K (1995) Morphology and anatomy of rice roots with special reference to coordination in organo- and histogenesis. In: Baluska T et al (eds) Structure and function of roots. Kluwer academic, Dordrecht
7. Kawata S, Yamazaki K, Ishihara K, Shibayama H, Lai KL (1963) Studies on root system formation in rice plants in a paddy. Proc Crop Sci Soc Japan 32:163
8. Hochholdinger F, Zimmermann R (2009) Molecular and genetic dissection of cereal root system development. In: Beeckman T (ed) Annual plant reviews root development. Wiley, New York, pp 175-191
9. Esau K (1965) Plant anatomy, 2nd edn. Wiley, New York 10. Feldman L (1994) The maize root. In: Freeling M, Walbot V (eds) The maize handbook. Springer, New York, pp 29-37
10. Varney GT, Canny MJ (1993) Rates of water uptake into the mature root system of maize plants. New Phytol 123:775-786
11. Laskowski MJ, Williams ME, Nusbaum HC, Sussex IM (1995) Formation of lateral root meristems is a two-stage process. Development 121:3303-3310
12. Malamy JE, Benfey PN (1997) Organization and cell differentiation in lateral roots of Arabidopsis thaliana. Development 124:33-44
13. Schiefelbein JW, Masucci JD, Wang H (1997) Building a root: the control of patterning and morphogenesis during root development. Plant Cell 9:1089-1098
14. Hochholdinger F, Zimmermann R (2008) Conserved and diverse mechanisms in root development. Curr Opin Plant Biol 11:70-74
15. Ishikawa H, Evans ML (1995) Specialized zones of development in roots. Plant Physiol 109:725-727
16. Jiang K, Meng YL, Feldman LJ (2003) Quiescent center formation in maize roots is associated with an auxin-regulated oxidizing environment. Development 130:1429-1438
17. Feix G, Hochholdinger F, Park WJ (2002) Maize root system and genetic analysis of its formation. In: Waisel Y et al (eds) Plant roots: the hidden half, 4th edn. Marcel Dekker, New York, pp 239-248
18. Gerald JNF, Lehti-Shiu MD, Ingram PA, Deak KI, Biesiada T, Malamy JE (2006) Identi fi cation of quantitative trait loci that regulate Arabidopsis root system size and plasticity. Genetics 172:485-498
19. Trachsel S, Messmer R, Stamp P, Hund A (2009) Mapping of QTLs for lateral and axile root growth of tropical maize. Theor Appl Genet 119:1413-1424
20. Ruta N, Liedgens M, Fracheboud Y, Stamp P, Hund A (2010) QTLs for the elongation of axile and lateral roots of maize in response to low water potential. Theor Appl Genet 120:621-631
21. Landi P, Giuliani S, Salvi S, Ferri M, Tuberosa R, Sanguineti MC (2010) Characterization of root-yield-1.06, a major constitutive QTL for root and agronomic traits in maize across water regimes. J Exp Bot 61:3553-3562
22. Norton GJ, Price AH (2009) Mapping of quantitative trait loci for seminal root morphology and gravitropic response in rice. Euphytica 166:229-237
23. Obara M, Tamura W, Ebitani T, Yano M, Sato T, Yamaya T (2010) Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH 4 + concentrations in hydroponic conditions. Theor Appl Genet 121:535-547
24. Neuffer MG (1994) Mutagenesis. In: Freeling M, Walbot V (eds) The maize handbook, Springer, New York 212-219
25. Walbot V (2000) Saturation mutagenesis using maize transposons. Curr Opin Plant Biol 3:103-107
26. Jeong DH, An S, Park S, Kang HG, Park GG, Kim SR, Sim J, Kim YO, Kim MK, Kim J, Shin M, Jung M, An G (2006) Generation of a fl anking sequence-tag database for activation-tagging lines in japonica rice. Plant J 45:123-132
27. Hetz W, Hochholdinger F, Schwall M, Feix G (1996) Isolation and characterization of rtcs , a maize mutant de fi cient in the formation of nodal roots. Plant J 10:845-857
28. Hochholdinger F, Feix G (1998) Early postembryonic root formation is speci fi cally affected in the maize mutant Irt1 . Plant J 16:247-255
29. Wen TJ, Hochholdinger F, Sauer M, Bruce W, Schnable PS (2005) The roothairless1 gene of maize encodes a homolog of sec3 , which is involved in polar exocytosis. Plant Physiol 138:1637-1643
30. Hochholdinger F, Woll K, Sauer M, Feix G (2005) Functional genomic tools in support of the genetic analysis of root development in maize ( Zea mays L.). Maydica 50:437-442
31. Zhu J, Ingram PA, Benfey PN, Elich T (2011) From lab to fi eld, new approaches to phenotyping root system architecture. Curr Opin Plant Biol 14:1-8
32. Hund A, Trachsel S, Stamp P (2009) Growth of axile and lateral roots of maize: I development of a phenotying platform. Plant Soil 325:335-349
33. Fang SQ, Yan XL, Liao H (2009) 3D reconstruction and dynamic modeling of root architecture in situ and its application to crop phosphorus research. Plant J 60:1096-1108
34. Iyer-Pascuzzi AS, Symonova O, Mileyko Y, Hao YL, Belcher H, Harer J, Weitz JS, Benfey PN (2010) Imaging and analysis platform for automatic phenotyping and trait ranking of plant root systems. Plant Physiol 152: 1148-1157
35. Trachsel S, Kaeppler SM, Brown KM, Lynch JP (2011) Shovelomics: high throughput phenotyping of maize ( Zea mays L.) root architecture in the fi eld. Plant Soil 341:75-87
36. Taramino G, Sauer M, Stauffer JL Jr, Multani D, Niu X, Sakai H, Hochholdinger F (2007) The maize ( Zea mays L.) RTCS gene encodes a LOB domain protein that is a key regulator of embryonic seminal and post-embryonic shootborne root initiation. Plant J 50:649-659
37. Majer C, Hochholdinger F (2011) De fi ning the boundaries: structure and function of LOB domain proteins. Trends Plant Sci 16:47-52
38. Inukai Y, Sakamoto T, Ueguchi-Tanaka M, Shibata Y, Gomi K, Umemura I, Hasegawa Y, Ashikari M, Kitano H, Matsuoka M (2005) Crown rootless1 , which is essential for crown root formation in rice, is a target of an auxin response factor in auxin signaling. Plant Cell 17:1387-1396
39. Liu H, Wang S, Yu X, Yu J, He X, Zhang S, Shou H, Wu P (2005) ARL1, a LOB-domain protein required for adventitious root formation in rice. Plant J 43:47-56
40. Friml J (2003) Auxin transport-shaping the plant. Curr Opin Plant Biol 6:7-12
41. Peret B, De Rybel B, Casimiro I, Benkova E, Swarup R, Laplaze L, Beeckman T, Bennett MJ (2009) Arabidopsis lateral root development: an emerging story. Trends Plant Sci 14:399-408
42. Okushima Y, Fukaki H, Onoda M, Theologis A, Tasaka M (2007) ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. Plant Cell 19:118-130
43. Shuai B, Reynaga-Pena CG, Springer PS (2002) The LATERAL ORGAN BOUNDARIES gene de fi nes a novel, plantspeci fi c gene family. Plant Physiol 129: 747-761
44. Casimiro I, Marchant A, Bhalerao RP, Beeckman T, Dhooge S, Swarup R, Graham N, Inze D, Sandberg G, Casero PJ, Bennett M (2001) Auxin transport promotes Arabidopsis lateral root initiation. Plant Cell 13:843-852
45. Kitomi Y, Ogawa A, Kitano H, Inukai Y (2008) CRL4 regulates crown root formation through auxin transport in rice. Plant Root 2:19-28
46. Liu S, Wang J, Wang L, Wang X, Xue Y, Wu P, Shou H (2009) Adventitious root formation in rice requires OsGNOM1 and is mediated by the OsPINs family. Cell Res 19:1110-1119
47. Geldner N, Anders N, Wolters H, Keicher J, Kornberger W, Muller P, Delbarre A, Ueda T, Nakano A, Jurgens G (2003) The Arabidopsis GNOM ARF-GEF mediates endosomal recycling, auxin transport, and auxin-dependent plant growth. Cell 112:219-230
48. Steinmann T, Geldner N, Grebe M, Mangold S, Jackson CL, Paris S, Galweiler L, Palme K, Jurgens G (1999) Coordinated polar localization of auxin ef fl ux carrier PIN1 by GNOM ARF GEF. Science 286:316-318
49. Friml J, Vieten A, Sauer M, Weijers D, Schwarz H, Hamann T, Offringa R, Jurgens G (2003) Ef fl ux-dependent auxin gradients establish the apical-basal axis of Arabidopsis. Nature 426: 147-153
50. Wang XF, He FF, Ma XX, Mao CZ, Hodgman C, Lu CG, Wu P (2011) OsCAND1 is required for crown root emergence in rice. Mol Plant 4:289-299
51. Chuang HW, Zhang W, Gray WM (2004) Arabidopsis ETA2, an apparent ortholog of the human cullin-interacting protein CAND1, is required for auxin responses mediated by the SCF(TIR1) ubiquitin ligase. Plant Cell 16:1883-1897
52. Feng S, Shen Y, Sullivan JA, Rubio V, Xiong Y, Sun TP, Deng XW (2004) Arabidopsis CAND1, an unmodi fi ed CUL1-interacting protein, is involved in multiple developmental pathways controlled by ubiquitin/proteasomemediated protein degradation. Plant Cell 16: 1870-1882
53. Quint M, Gray WM (2006) Auxin signaling. Curr Opin Plant Biol 9:448-453
54. Woll K, Borsuk LA, Stransky H, Nettleton D, Schnable PS, Hochholdinger F (2005) Isolation, characterization, and pericyclespeci fi c transcriptome analyses of the novel maize lateral and seminal root initiation mutant rum1 . Plant Physiol 139:1255-1267
55. von Behrens I, Komatsu M, Zhang Y, Berendzen KW, Niu X, Sakai H, Taramino G, Hochholdinger F (2011) Rootless with undetectable meristem 1 encodes a monocot-speci fi c AUX/IAA protein that controls embryonic seminal and postembryonic lateral root initiation in maize. Plant J 66:341-353
56. Jia L, Wu Z, Hao X, Carrie C, Zheng L, Whelan J, Wu Y, Wang S, Wu P, Mao C (2011) Identi fi cation of a novel mitochondrial protein, short postembryonic roots 1 (SPR1), involved in root development and iron homeostasis in Oryza sativa . New Phytol 189:843-855
57. Gilroy S, Jones DL (2000) Through form to function: root hair development and nutrient uptake. Trends Plant Sci 5:56-60
58. Sieberer BJ, Ketelaar T, Esseling JJ, Emons AM (2005) Microtubules guide root hair tip growth. New Phytol 167:711-719
59. Wen TJ, Schnable PS (1994) Analyses of mutants of three genes that in fl uence root hair development in Zea mays (Gramineae) suggest that root hairs are dispensable. Am J Bot 81:833-843
60. He B, Guo W (2009) The exocyst complex in polarized exocytosis. Curr Opin Cell Biol 21:537-542
61. Hala M, Cole R, Synek L, Drdova E, Pecenkova T, Nordheim A, Lamkemeyer T, Madlung J, Hochholdinger F, Fowler JE, Zarsky V (2008) An exocyst complex functions in plant cell growth in Arabidopsis and tobacco. Plant Cell 20:1330-1345
62. Hochholdinger F, Wen TJ, Zimmermann R, Chimot-Marolle P, Da Costa e Silva O, Bruce W, Lamkey KR, Wienand U, Schnable PS (2008) The maize ( Zea mays L.) roothairless3 gene encodes a putative GPI-anchored, monocot-speci fi c, COBRA-like protein that signi fi cantly affects grain yield. Plant J 54:888-898
63. Brady SM, Song S, Dhugga KS, Rafalski JA, Benfey PN (2007) Combining expression and comparative evolutionary analysis. The COBRA gene family. Plant Physiol 143:172-187
64. Suzuki N, Taketa S, Ichii M (2003) Morphological and phiosiological characteristics of a root-hairless mutant in rice. Plant Soil 255:9-17
65. Yuo T, Toyota S, Ichii M, Taketa S (2009) Molecular cloning of a root hairless gene rth1 in rice. Breed Sci 59:13-20
66. Shibata K, Morita Y, Abe S, Stankovic B, Davies E (1999) Apyrase from pea stems: isolation, puri fi cation, characterization and identi fi cation of a NTPase from the cytoskeleton fraction of pea stem tissue. Plant Physiol Biochem 37:881-888
67. Kwasniewski M, Szarejko I (2006) Molecular cloning and characterization of ǎ-expansin gene related to root hair formation in barley. Plant Physiol 141:1149-1158
68. Sampedro J, Cosgrove DJ (2005) The expansin superfamily. Genome Biol 6:242
69. Zhiming Y, Bo K, Xiaowei H, Shaolei L, Youhuang B, Wona D, Ming C, Hyung-Taeg C, Ping W (2011) Root hair-speci fi c EXPANSINs modulate root hair elongation in rice. Plant J 66:725-734
70. Kwasniewski M, Janiak A, Mueller-Roeber B, Szarejko I (2010) Global analysis of the root hair morphogenesis transcriptome reveals new candidate genes involved in root hair formation in barley. J Plant Physiol 167:1076-1083
71. Goff SA, Ricke D, Lan TH, Presting G, Wang R, Dunn M, Glazebrook J, Sessions A, Oeller P, Varma H, Hadley D, Hutchison D, Martin C, Katagiri F, Lange BM, Moughamer T, Xia Y, Budworth P, Zhong J, Miguel T, Paszkowski U, Zhang S, Colbert M, Sun WL, Chen L, Cooper B, Park S, Wood TC, Mao L, Quail P, Wing R, Dean R, Yu Y, Zharkikh A, Shen R, Sahasrabudhe S, Thomas A, Cannings R, Gutin A, Pruss D, Reid J, Tavtigian S, Mitchell J, Eldredge G, Scholl T, Miller RM, Bhatnagar S, Adey N, Rubano T, Tusneem N, Robinson R, Feldhaus J, Macalma T, Oliphant A, Briggs S (2002) A draft sequence of the rice genome ( Oryza sativa L. ssp. japonica ). Science 296:92-100
72. Schnable PS, Ware D, Fulton RS, Stein JC, Wei F, Pasternak S, Liang C, Zhang J, Fulton L, Graves TA, Minx P, Reily AD, Courtney L, Kruchowski SS, Tomlinson C, Strong C, Delehaunty K, Fronick C, Courtney B, Rock SM, Belter E, Du F, Kim K, Abbott RM, Cotton M, Levy A, Marchetto P, Ochoa K, Jackson SM, Gillam B, Chen W, Yan L, Higginbotham J, Cardenas M, Waligorski J, Applebaum E, Phelps L, Falcone J, Kanchi K, Thane T, Scimone A, Thane N, Henke J, Wang T, Ruppert J, Shah N, Rotter K, Hodges J, Ingenthron E, Cordes M, Kohlberg S, Sgro J, Delgado B, Mead K, Chinwalla A, Leonard S, Crouse K, Collura K, Kudrna D, Currie J, He R, Angelova A, Rajasekar S, Mueller T, Lomeli R, Scara G, Ko A, Delaney K, Wissotski M, Lopez G, Campos D, Braidotti M, Ashley E, Golser W, Kim H, Lee S, Lin J, Dujmic Z, Kim W, Talag J, Zuccolo A, Fan C, Sebastian A, Kramer M, Spiegel L, Nascimento L, Zutavern T, Miller B, Ambroise C, Muller S, Spooner W, Narechania A, Ren L, Wei S, Kumari S, Faga B, Levy MJ, McMahan L, Van Buren P, Vaughn MW et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326:1112-1115
73. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Li J, Liu Z, Qi Q, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Zhao W, Li P, Chen W, Zhang Y, Hu J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Tao M, Zhu L, Yuan L, Yang H (2002) A draft sequence of the rice genome ( Oryza sativa L. ssp. indica ). Science 296:79-92
74. Schulte D, Close TJ, Graner A, Langridge P, Matsumoto T, Muehlbauer G, Sato K, Schulman AH, Waugh R, Wise RP, Stein N (2009) The international barley sequencing consortium-at the threshold of ef fi cient access to the barley genome. Plant Physiol 149:142-147