Getting to the root of plant biology: impact of the Arabidopsis genome sequence on root research.
Prior to the availability of the genome sequence, the root of Arabidopsis had attracted a small but ardent group of researchers drawn to its accessibility and developmental simplicity. Roots are easily observed when grown on the surface of nutrient agar media, facilitating analysis of responses to stimuli such as gravity and touch. Developmental biologists were attracted to the simple radial organization of primary root tissues, which form a series of concentric cylinders around the central vascular tissue. Equally attractive was the mode of propagation, with stem cells at the tip giving rise to progeny that were confined to cell files. These properties of root development reduced the normal four-dimensional problem of development (three spatial dimensions and time) to a two-dimensional problem, with cell type on the radial axis and developmental time along the longitudinal axis. The availability of the complete Arabidopsis genome sequence has dramatically accelerated traditional genetic research on root biology, and has also enabled entirely new experimental strategies to be applied. Here we review examples of the ways in which availability of the Arabidopsis genome sequence has enhanced progress in understanding root biology.
Benfey
Philip N
PN
Department of Biology, Institute for Genome Sciences & Policy, Center for Systems Biology, Duke University, Durham, NC, USA. philip.benfey@duke.edu
Bennett
Malcolm
M
Schiefelbein
John
J
D017360:Arabidopsis / Q000235:genetics* / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D023281:Genomics; D018517:Plant Roots / Q000235:genetics* / Q000254:growth & development
Science. 2007 Nov 2;318(5851):801-6
17975066
Curr Opin Genet Dev. 1995 Aug;5(4):432-8
7580133
Curr Opin Genet Dev. 2008 Aug;18(4):354-61
18617392
Biochem J. 2007 Jul 1;405(1):191-8
17376028
Plant Cell Physiol. 2005 Jun;46(6):817-26
15795220
Dev Cell. 2008 Dec;15(6):913-22
19081078
Development. 2005 Nov;132(21):4765-75
16207757
Plant Cell Physiol. 2006 Jun;47(6):788-92
16621846
Curr Biol. 2009 Jun 9;19(11):909-14
19398337
Curr Opin Plant Biol. 2009 Oct;12(5):580-6
19695946
Nature. 2007 Oct 25;449(7165):1053-7
17960244
Nat Cell Biol. 2005 Nov;7(11):1057-65
16244669
Curr Opin Plant Biol. 2008 Feb;11(1):70-4
18006363
Plant Physiol. 2005 Jun;138(2):624-35
15955926
Plant Cell. 2007 Jan;19(1):118-30
17259263
Proc Natl Acad Sci U S A. 2005 Aug 16;102(33):11934-9
16085708
Plant Cell. 2005 Jul;17(7):1908-25
15937229
Trends Genet. 1994 Mar;10(3):84-8
8178369
Plant Cell. 2005 May;17(5):1387-96
15829602
Plant Physiol. 2003 May;132(1):27-35
12746508
Development. 2009 Jun;136(12):2059-67
19465596
Development. 2005 Dec;132(24):5387-98
16291794
Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13693-8
16157886
Nature. 2001 Sep 20;413(6853):307-11
11565032
PLoS Biol. 2008 Dec 16;6(12):e307
19090618
Plant Physiol. 2007 Apr;143(4):1789-801
17322336
Nature. 2007 Oct 25;449(7165):1008-13
17960234
Plant J. 2005 Jul;43(1):47-56
15960615
Plant J. 2004 Feb;37(3):398-414
14731265
Development. 2005 Jan;132(2):291-8
15590742
Science. 2003 Dec 12;302(5652):1956-60
14671301
Science. 2008 Oct 24;322(5901):594-7
18948541
Semin Cell Dev Biol. 2008 Dec;19(6):580-5
18824115
Curr Biol. 2009 Sep 15;19(17):1485-90
19646874
Science. 2008 May 16;320(5878):942-5
18436742
Proc Natl Acad Sci U S A. 2008 Jan 15;105(2):803-8
18180456
Nature. 2006 Sep 28;443(7110):458-61
17006513
Nat Genet. 2009 Feb;41(2):258-63
19122662
Dev Biol. 2007 Nov 15;311(2):566-78
17931617
Nat Biotechnol. 2003 Oct;21(10):1215-21
12949535
Plant J. 2009 Mar;57(5):945-56
19000163
J Exp Bot. 2005 Sep;56(419):2433-42
16043452
PLoS Genet. 2009 May;5(5):e1000492
19461889
Nat Genet. 2007 Jun;39(6):792-6
17496893
Plant Physiol. 2009 Jul;150(3):1459-73
19448035
PLoS Biol. 2008 Sep 23;6(9):e235
18816165
Genes Dev. 1997 Mar 15;11(6):799-811
9087433
Development. 2008 Apr;135(7):1335-45
18305006
Plant J. 2006 Jan;45(1):83-100
16367956
Genome Res. 2003 Jun;13(6A):1250-7
12799357
Plant Physiol. 2007 Sep;145(1):147-59
17631527
Bull Math Biol. 2010 Aug;72(6):1383-407
20135237
Trends Plant Sci. 2004 Jan;9(1):42-8
14729218
PLoS Biol. 2005 Jul;3(7):e196
15907155
Plant J. 2009 Nov;60(3):564-74
19619157
Nat Cell Biol. 2008 Aug;10(8):946-54
18622388
J Exp Bot. 2007;58(14):3829-40
18162628
Cell. 2004 Oct 1;119(1):109-20
15454085
Development. 2002 Dec;129(23):5409-19
12403712
Science. 2007 Jul 20;317(5836):338-42
17641193
Nat Chem Biol. 2008 Nov;4(11):674-81
18936752
PLoS Biol. 2006 May;4(5):e143
16640459
Cell. 2005 Dec 29;123(7):1337-49
16377572
Annu Rev Plant Biol. 2008;59:365-86
18257710
New Phytol. 2007;176(1):37-43
17692076
Plant J. 2009 Nov;60(4):666-78
19682286
Nat Cell Biol. 2009 Jan;11(1):78-84
19079245
PLoS Genet. 2008 Feb 29;4(2):e1000004
18454190
Annu Rev Plant Biol. 2007;58:93-113
17177637
Proc Natl Acad Sci U S A. 2006 Feb 21;103(8):2994-9
16481625
Cell. 2009 Aug 7;138(3):549-61
19665976