| Environmental stimuli |
| Gravity |
Normal |
Growth toward the gravity vector |
ARG1 and 2, PIN3 (At) |
Auxin |
Boonsirichai et al. (2003), Harrison and Masson (2008a),b
|
| Light (direct root exposure) |
Presence |
Negative growth to blue light; positive to red/far red light |
PHOT1, NPH1, PhyA, PhyB (At) |
Auxin, JA |
Huala et al. (1997), Kurata and Yamamoto (1997), Christie et al. (1998), Correll et al. (2003), Kiss et al. (2003), Galen et al. (2007), Costigan et al. (2011)
|
| Water/oxygen |
Root system submergence/hypoxia |
CR primordia development and outgrowth (deep-water rice) |
SUB1 (Os) |
GA, ethylene |
Xu et al. (2006), Fukao et al. (2011)
|
|
Drought |
Mixed. General decreased LR and PR growth and LR emergence, but ABA has been shown to stimulate PR elongation and LR emergence in response to drought |
LACS2 (At); SUB1 (Os)
|
ABA |
Sharp et al. (1988), Deak and Malamy (2005), De Smet et al. (2006), Macgregor et al. (2008), Wiegers et al. (2009)
|
| Soil nutrients |
| Nitrogen |
High nitrate availability |
Inhibition of LR outgrowth, development and elongation |
AtNRT1.1, ANR1, AtOCT1 (At) |
Auxin, ABA |
Zhang and Forde (1998), Liu et al. (1999), Zhang et al. (1999), Guo et al. (2002), Munos et al. (2004), Lelandais-Briere et al. (2007), Krouk et al. (2010)
|
|
Low nitrate availability |
Localized stimulation of LR growth, branching in high inorganic N soil patches |
AtNRT1.1, AtNRT2.1, ANR1, AtOCT1 (At) |
Auxin |
Zhang and Forde (1998), Zhang et al. (1999), Malamy and Ryan (2001), Lelandais-Briere et al. (2007), Krouk et al. (2010)
|
| Phosphorus |
High phosphate availability |
PR growth promoted, LR growth prohibited |
PDR2, LPR1, WRKY75 (At)
|
Auxin |
Linkohr et al. (2002); Ticconi et al. (2004), Ticconi et al. (2009), Shane and Lambers (2005), Reymond et al. (2006), Schulze et al. (2006), Devaiah and Raghothama (2007), Devaiah et al. (2007), Perez-Torres et al. (2008)
|
| Phosphorus (con’t) |
Low phosphate availability |
Root foraging: increased LR initiation, outgrowth, forming a shallow, highly branched system |
PDR2, LPR1, PHR1, AtSIZ1, PHO2 (At), OsPTF1 (Os), PHI2 (Nt)
|
Auxin, CK, ethylene, GA, SLs |
Schmidt and Schikora (2001), Williamson et al. (2001), Franco-Zorrilla et al. (2002), López-Bucio et al. (2002), Sano and Nagata (2002), Ma et al. (2003), Shimizu et al. (2004), Ticconi et al. (2004), Ticconi et al. (2009), Miura et al. (2005), Shane and Lambers (2005), Yi et al. (2005), Bari et al. (2006), Reymond et al. (2006), Schulze et al. (2006), Devaiah and Raghothama (2007), Devaiah et al. (2007), Jiang et al. (2007), Perez-Torres et al. (2008)
|
| Sulfur |
High sulfate availability/sufficiency |
Not highly studied |
SULTR1;2, SLIM1 (At)
|
Auxin, JA, CK |
Ohkama et al. (2002), Hirai et al. (2003), Maruyama-Nakashita et al. (2003), Nikiforova et al. (2003), Buchner et al. (2004), Hoefgen and Nikiforova (2008), Lewandowska and Sirko (2008), Takahashi (2010)
|
|
Low sulfate availability |
Mixed. Short-term sulfur limitation proposed to stimulate LR growth with longer-term deficiency causing overall decreased growth |
SULTR1;1, SULTR1;2, SLIM, OAS, NIT3, BIG, IAAs (At)
|
Auxin, JA, CK |
Leustek et al. (2000), Saito (2000), Takahashi et al. (2000), Kutz et al. (2002), Ohkama et al. (2002), Yoshimoto et al. (2002), Maruyama-Nakashita et al. (2003), Maruyama-Nakashita et al. (2004), Nikiforova et al. (2003), Buchner et al. (2004), Bouranis et al. (2008), Hoefgen and Nikiforova (2008), Lewandowska and Sirko (2008)
|
| Phytotoxins |
| Aluminum |
High Al3+
|
Inhibition of LR initiation and outgrowth, swollen, malformed root tips |
ETR1, EIN2, AtACSs, AtACOs, AtPIN, AUX1, PME, AtCHIA, CALS, ALS1 (At); EXPA10, STAR1 and 2, ART1 (Os) |
Auxin, ethylene |
Foy (1984), Delhaize et al. (1993), Kochian (1995), Alonso et al. (1999), Matsumoto (2000), Lee and Kende (2002), Tsuchisaka and Theologis (2004), Yokoyama and Nishitani (2004), Eticha et al. (2005), O’Malley et al. (2005), Jones et al. (2006), Sivaguru et al. (2006), Larsen et al., 2007, Sun et al. (2010)
|
| Sodium chloride |
High salinity |
Mixed. General decrease in root growth due to slower epidermal cell division and elongation |
HKTs, GLRs, NSCCs, CNGCs, SOS1–3, NX1 (At) |
Auxin, ABA, CK, ethylene, GA |
Kuiper et al. (1990), Zidan et al. (1990), Liu and Zhu (1998), Apse et al. (1999), Gaxiola et al. (1999), Leng et al. (2002), Quintero et al. (2002), Tester and Davenport (2003), He et al. (2005), Mahajan and Tuteja (2005), Khadri et al. (2006), Cao et al. (2008), Bano (2010)
|
| Symbioses |
| Root nodulation |
Pre-symbiosis Nod factor-induced |
None known |
|
High colonization |
Nodule formation, putative suppression of LR emergence |
Nodulins, LHK1 (Lj), MtCRE, ARR, NSP1 and 2, NIN, ENOD11, ERFs (Mt) |
Auxin, ABA, BRs, CK, ethylene, GA, SA |
Nutman (1948), Nap and Bisseling (1990), Verma et al. (1992), Catoira (2000), Journet et al. (2001), Borisov et al. (2003), Charron et al. (2004), Lohar et al. (2004), Kalo et al. (2005), Smit et al. (2005), Gonzalez-Rizzo et al. (2006), Marsh et al. (2007), Middleton et al. (2007), Frugier et al. (2008), Vernie et al. (2008), Ding and Oldroyd (2009), Markmann and Parniske (2009), Ferguson et al. (2010)
|
| Arbuscular mycorrhizal |
Pre-symbiosis Myc-factor-induced |
LR elongation |
DMI1 and 2, MtENOD11 (Mt), OsPOLLUX2, OsCCAMK2, CYCLOPS1 (Os, Mt, Lj)
|
Auxin, ABA, CK, SLs |
Endre et al. (2002), Stracke et al. (2002), Kosuta et al. (2003), Olah et al. (2005), Hogg et al. (2006), Gutjahr et al. (2009); Messinese et al., 2007; Yano et al., 2008; Horváth et al. (2011)
|
|
High AM colonization |
Variable increases in root mass, thickness, length, and LR number dependant on host species |
LRT1 (Zm) |
Auxin, ABA, CK, ethylene |
Hetrick et al. (1988), Berta et al. (1990), Berta et al. (1995), Berta et al. (2002), Dixon (1990), Hetrick (1991), Barker and Tagu (2000), Paszkowski and Boller (2002), Vierheilig et al. (2002), Fitze et al. (2005), Olah et al. (2005), Ludwig-Muller and Guther (2007), Parniske (2008), Gutjahr et al. (2009)
|
