TABLE 1.
Selection of transcription factors and components of phytohormone signaling evidently or putatively involved in DNRR further indicating their role in primary and lateral root development or callus formation.
| DNRR phases and stages | ||||||||||||
| Genes | PR | LR | Callus | I | II | III: | Pr | In | Pa | Em | Pro F | Comments |
| ABCB19 (MDR1) | ∙ | ∙Δ | Δ | IAA Tra | LFM display shorter LRs and reduced DNRR from hypocotyl explants, but DNRR is not impaired from intact hypocotyls (Wu et al., 2007; Sukumar et al., 2013) | |||||||
| ALF4 | ∙ | ∙Δ | Δ | Δ | Δ | IAA Sig | Regulator of SCF-TIR1 receptor, LFM acumulate IAAs, Exp in PR and LRs (Bagchi et al., 2018); LFM fail to produce LRs, callus and DNRR (Celenza et al., 1995; Sugimoto et al., 2010; Liu et al., 2014; Bustillo-Avendaño et al., 2018) | |||||
| ARF7,19 | ∙ | ∙Δ | Δ | nd | nd | nd | IAA Sig TFs | Directly activate LBD16/29 (Okushima et al., 2007), ARF7 LFM have less LRs, double mutants fail to produce any LRs, whereas DNRR is normal but callus formation is reduced, Exp in the root vasculature, LRPs and developing LRs (Okushima et al., 2005; 2007; Liu et al., 2014; Lee et al., 2017) | ||||
| ASA1 | ∙nd | ∙neΔ | Δ | IAA Syn | LFM have less DNRR (Zhang et al., 2019), less LRs in response to JA (Sun et al., 2009); Directly activated by ERF109 (Cai et al., 2014; Zhang et al., 2019) | |||||||
| AUX1, LAX3 | ∙ | ∙Δ | ∙Δ | IAA Tra | LFM have less LRs and detached mutant hypocotyls show a reduced rooting capacity for ARs, Exp in PR, LRs and ARP (Marchant et al., 2002; Swarup et al., 2008; Della Rovere et al., 2013; 2015; Bustillo-Avendaño et al., 2018) | |||||||
| COI1 | ∙(Δ) | Δ | Δ | JA Sig | JA receptor, LFM causes reduced DNRR (Zhang et al., 2019) and LR formation in response to JA (Raya-González et al., 2012); Exp in RAM, LFM are insensitive to root growth inhibition by JA (Chen et al., 2011) | |||||||
| ERF109 | nd | ∙Δ | ∙Δ | TF | JA induced after leaf detachment, LFM have reduced DNRR (Zhang et al., 2019); LFM have less LRs, ativates ASA1 and YUC2 (Cai et al., 2014) | |||||||
| ERF115 | ∙Δ | ∙Δ | (Δ) | ? | ? | TF | Induced by JA, IAA and ERF109 in protoxylem and QC cells, involved in root cell regeneration (Zhou et al., 2019); ERF115-SRDX blocks callus formation (Ikeuchi et al., 2017); controls QC cell devision (Heyman et al., 2013) | |||||
| FUS3, LEC2 | ∙Δ | ∙Δ | ? | TFs | Two homologous B3 TFs interact to activate directly YUC4 during LR formation (Tang et al., 2017); precocious growth of PR during embryogenesis (Vicente-Carbajosa and Carbonero, 2005) | |||||||
| GA1 (CPS1), GA5 (GA20OX1) | ∙Δ | GA Syn | Ent-Copalyl Diphosphate Synthetase and GA 20-Oxidase, respectively; involved in vascular proliferation in DNRR, LFM have less AR capacity (Ibáñez et al., 2019) | |||||||||
| GAI | ∙Δ | GA Sig | gai-1 is insensitive to GAs, involved in vascular proliferation during DNRR, LFM have reducted AR capacity (Ibáñez et al., 2019) | |||||||||
| IAA14 (SLR) | ∙(Δ) | Δ | Δ | Δ | Δ | IAA Sig TF | GFM, fail to produce LRs (Fukaki et al., 2002); less callus and DNRR (Shang et al., 2016; Bustillo-Avendaño et al., 2018); PR has less root hairs, Exp in RAM of PR and LRP (Fukaki et al., 2002; Vanneste et al., 2005) | |||||
| LBD16,29 | ∙ | ∙Δ | Δ | ∙Δ | ∙Δ | (∙) | TFs | OE enhances AR formation (Liu et al., 2014); Direct target of ARF7/19 (Okushima et al., 2007); LFM have less LRs and callus (Fan et al., 2012) | ||||
| NAC1 | ∙Δ | ∙Δ | ∙Δ | TF | Dominant-negative lines (NAC1-SRDX) have less LRs (Xie et al., 2000) and less ARs (Chen X. et al., 2016) | |||||||
| PIN 1,2,3,7 | ∙Δ | ∙Δ | ∙Δ | IAA Tra | Exp in leaf vasculature after excision, LFM have less ARs (Bustillo-Avendaño et al., 2018); Invoved PR and LR development (Petrásek and Friml, 2009) | |||||||
| PLT1,2 | ∙Δ | ∙Δ | Δ | Δ | TFs | Activate WOX5 (Shimotohno et al., 2018); double mutants: less DNRR (Bustillo-Avendaño et al., 2018), shorter PR but more LRs (Aida et al., 2004); Exp in LRPs and RAM of PR (Hofhuis et al., 2013; Du and Scheres, 2017) | ||||||
| PLT3,5,7 | ∙Δ | ∙ | ? | ? | ? | TFs | Promotes LR emergence, triple mutants have less LRs, Exp in a subset of pericycle cells requiring ARF7/19 as activators (Hofhuis et al., 2013) | |||||
| SCR | ∙Δ | ∙ | ∙ | ∙Δ | ∙ | ∙ | ∙ | TF | AR formation from hypocotyl is inhibited in LFM (Della Rovere et al., 2015); Involved in positioning the stem cell niche of RAMs, Exp in endodermis, QC and callus (Sabatini et al., 2003; Sugimoto et al., 2010; Kim et al., 2018) | |||
| SHR | ∙Δ | ∙Δ | ∙ | Δ | Δ | TF | LFM have reduced AR and LR formation as well as growth of the PR, Exp in the stelle, shr plt1,2 triple mutants fails to produce ARs (Helariutta et al., 2000; Lucas et al., 2011; Della Rovere et al., 2015; Bustillo-Avendaño et al., 2018) | |||||
| TAA1 (WEI8), TAR2 | ∙ | ∙Δ | ∙ | IAA Syn | Ubiquitously induced in leaf explants, double mutants are impaired in DNRR (Sun et al., 2016); Exp in RAM of PR (Stepanova et al., 2008) | |||||||
| TCP20,21 | (∙Δ) | ? | ? | TFs | Interact with PLT1/3 and SCR to bind and induce WOX5, Exp in precursor QC cells (in embryos) (Shimotohno et al., 2018) | |||||||
| WOX5,7 | ∙Δ | ∙Δ | ∙nd | ∙Δ | ∙Δ | ∙Δ | ∙ | TF | Activated by WOX11/12, WOX5 LFM have reduced DNRR, which is enhanced in double mutants (Hu and Xu, 2016); WOX5 maintains the stem cell niche of RAM, Exp in QC and callus (Sarkar et al., 2007; Sugimoto et al., 2010; Kim et al., 2018), whereas WOX7 is involved in LR initiation (Kong et al., 2016) | |||
| WOX11,12 | (Δ) | ∙Δ | ∙Δ | TF | LFM have less ARs, whereas OE inhibits AR and callus formation, Exp in AR founder cells, promotes LBD16/19 (Liu et al., 2014; Sheng et al., 2017) | |||||||
| YUC1,2,4,6 | ∙Δ | ∙Δ | IAA Syn | Induced in mesophyll cells of leaf explants, double mutants are partially, quadruple mutants severely impaired in DNRR (Chen L. et al., 2016), LFM of YUC4 reduces LR formation (Tang et al., 2017) | ||||||||
∙, expressed; ∆, mutant phenotype; ?, assumed involvement in DNRR; I, Phase I; II, Phase II; III:, Phase III:; Pr, Priming; In, Initiation; Pa, Patterning; En, Emergence; AR, adventitious root; ARP, adventitious root primordia; Exp, Expressed; GA sig, GA signaling; GA syn, GA biosynthesis; GFM, gain of function mutants; IAA sig, auxin signaling; IAA syn, auxin biosynthesis; IAA tra, auxin transport; JA sig, JA signaling; LFM, loss of function mutants; LR, lateral root formation; LRP, lateral root primordia; methylase, histone lysine methyl-transferase; nd, no defects observed; ne, not expressed; OE, overexpression; PR, primary (main) root; Pro F, protein function; QC, quiescent center; RAM, root apical meristem; TF(s), transcription factor(s).