Trehalose-6-phosphate signaling regulates lateral root formation in Arabidopsis thaliana.

Plant roots explore the soil for water and nutrients, thereby determining plant fitness and agricultural yield, as well as determining ground substructure, water levels, and global carbon sequestration. The colonization of the soil requires investment of carbon and energy, but how sugar and energy signaling are integrated with root branching is unknown. Here, we show through combined genetic and chemical modulation of signaling pathways that the sugar small-molecule signal, trehalose-6-phosphate (T6P) regulates root branching through master kinases SNF1-related kinase-1 (SnRK1) and Target of Rapamycin (TOR) and with the involvement of the plant hormone auxin. Increase of T6P levels both via genetic targeting in lateral root (LR) founder cells and through light-activated release of the presignaling T6P-precursor reveals that T6P increases root branching through coordinated inhibition of SnRK1 and activation of TOR. Auxin, the master regulator of LR formation, impacts this T6P function by transcriptionally down-regulating the T6P-degrader trehalose phosphate phosphatase B in LR cells. Our results reveal a regulatory energy-balance network for LR formation that links the 'sugar signal' T6P to both SnRK1 and TOR downstream of auxin.

Discovery of Novel Hybrid-Type Strigolactone Mimics Derived from Cinnamic Amide.

Strigolactones (SLs) are a class of plant hormones and rhizosphere communication signals of great interest. They perform diverse biological functions including the stimulation of parasitic seed germination and phytohormonal activity. However, their practical use is limited by their low abundance and complex structure, which requires simpler SL analogues and mimics with maintained biological function. Here, new, hybrid-type SL mimics were designed, derived from Cinnamic amide, a new potential plant growth regulator with good germination and rooting-promoting activities. Bioassay results indicated that compound 6 not only displayed good germination activity against the parasitic weed O. aegyptiaca with an EC50 value of 2.36 × 10-8 M, but also exhibited significant inhibitory activity against Arabidopsis root growth and lateral root formation, as well as promoting root hair elongation, similar to the action of GR24. Further morphological experiments on Arabidopsis max2-1 mutants revealed that 6 possessed SL-like physiological functions. Furthermore, molecular docking studies indicated that the binding mode of 6 was similar to that of GR24 in the active site of OsD14. This work provides valuable clues for the discovery of novel SL mimics.

Auxin induces lateral root formation in Bupleurum: A heme oxygenase dependent approach.

Objective: The content of saikosaponins in genus Bupleurum is increased with numbers of lateral root, but the genetic mechanisms are largely unknown. This study aims to identify the heme oxygenase (HO) gene family members of B. chinense and B. scorzonerifolium, and assess their role in the root development in Bupleurum. Methods: The gene sequences of HO family were selected from iso-seq full-length transcriptome data of B. chinense and B. scorzonerifolium, and were analyzed in physicochemical properties, conserved domains, motifs and phylogenetic relationship. In addition, the expression patterns of HO gene in different parts of roots were compared via transcriptome sequencing and qRT-PCR in the two species. Results: Five Bupleurum HO genes (BcHO1-BcHO5) belonging to the HO1 subfamily were identified from the transcriptome data, whereas the HO2 subfamily member was not identified. The expression levels of BcHO1 and BcHO2 were significantly higher than those of other three HO members in the transcriptome analysis. In addition, the expression profile of BcHO1 showed consistency with lateral root development in B. chinense and B. scorzonerifolium. Conclusion: Hos might participate in the auxin-induced morphogenesis of lateral roots. The yield of saikosaponin may be improved by manipulating expression of these genes.

Divergent regulation of auxin responsive genes in root-knot and cyst nematodes feeding sites formed in Arabidopsis.

Cysts (CNs) and root-knot nematodes (RKNs) induce specialized feeding cells, syncytia, and giant cells (GCs), respectively, within plant roots. The plant tissues around the GCs usually by respond forming a root swelling called a gall that contains the GCs. The ontogenesis of feeding cells is different. GC formation is a process of new organogenesis from vascular cells, which are still not well characterized, that differentiate into GCs. In contrast, syncytia formation involves the fusion of adjacent cells that have already differentiated. Nonetheless, both feeding sites show an auxin maximum pertinent to feeding site formation. However, data on the molecular divergences and similarities between the formation of both feeding sites regarding auxin-responsive genes are still scarce. We studied genes from the auxin transduction pathways that are crucial during gall and lateral root (LR) development in the CN interaction by using promoter-reporter (GUS/LUC)transgenic lines, as well as loss of function lines of Arabidopsis. The promoters pGATA23 and several deletions of pmiR390a were active in syncytia, as were in galls, but pAHP6 or putative up-stream regulators as ARF5/7/19 were not active in syncytia. Additionally, none of these genes seemed to play a key role during cyst nematode establishment in Arabidopsis, as the infection rates in loss of function lines did not show significant differences compared to control Col-0 plants. Furthermore, the presence of only canonical AuxRe elements in their proximal promoter regions is highly correlated with their activation in galls/GCs (AHP6, LBD16), but those promoters active in syncytia (miR390, GATA23) carry AuxRe overlapping core cis-elements for other transcription factor families (i.e., bHLH, bZIP). Strikingly, in silico transcriptomic analysis showed very few genes upregulated by auxins common to those induced in GCs and syncytia, despite the high number of upregulated IAA responsive genes in syncytia and galls. The complex regulation of auxin transduction pathways, where different members of the auxin response factor (ARF) family may interact with other factors, and the differences in auxin sensitivity, as indicated by the lower induction of the DR5 sensor in syncytia than galls, among other factors, may explain the divergent regulation of auxin responsive genes in the two types of nematode feeding sites.

Tomato defence against Meloidogyne incognita by jasmonic acid-mediated fine-tuning of kaempferol homeostasis.

Jasmonic acid (JA) is involved in the modulation of defence and growth activities in plants. The best-characterized growth-defence trade-offs stem from antagonistic crosstalk among hormones. In this study, we first confirmed that JA negatively regulates root-knot nematode (RKN) susceptibility via the root exudates (REs) of tomato plants. Omics and toxicological analyses implied that kaempferol, a type of flavonol, from REs has a negative effect on RKN infection. We demonstrated that SlMYB57 negatively regulated kaempferol contents in tomato roots, whereas SlMYB108/112 had the opposite effect. We revealed that JA fine-tuned the homeostasis of kaempferol via SlMYB-mediated transcriptional regulation and the interaction between SlJAZs and SlMYBs, thus ensuring a balance between lateral root (LR) development and RKN susceptibility. Overall, this work provides novel insights into JA-modulated LR development and RKN susceptibility mechanisms and elucidates a trade-off model mediated by JA in plants encountering stress.

CLE3 and its homologs share overlapping functions in the modulation of lateral root formation through CLV1 and BAM1 in Arabidopsis thaliana.

Lateral roots are important for a wide range of processes, including uptake of water and nutrients. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) 1 ~ 7 peptide family and their cognate receptor CLV1 have been shown to negatively regulate lateral root formation under low-nitrate conditions. However, little is known about how CLE signaling regulates lateral root formation. A persistent obstacle in CLE peptide research is their functional redundancies, which makes functional analyses difficult. To address this problem, we generate the cle1 ~ 7 septuple mutant (cle1 ~ 7-cr1, cr stands for mutant allele generated with CRISPR/Cas9). cle1 ~ 7-cr1 exhibits longer lateral roots under normal conditions. Specifically, in cle1 ~ 7-cr1, the lateral root density is increased, and lateral root primordia initiation is found to be accelerated. Further analysis shows that cle3 single mutant exhibits slightly longer lateral roots. On the other hand, plants that overexpress CLE2 and CLE3 exhibit decreased lateral root lengths. To explore cognate receptor(s) of CLE2 and CLE3, we analyze lateral root lengths in clv1 barely any meristem 1(bam1) double mutant. Mutating both the CLV1 and BAM1 causes longer lateral roots, but not in each single mutant. In addition, genetic analysis reveals that CLV1 and BAM1 are epistatic to CLE2 and CLE3. Furthermore, gene expression analysis shows that the LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKE (LBD/ASL) genes, which promote lateral root formation, are upregulated in cle1 ~ 7-cr1 and clv1 bam1. We therefore propose that CLE2 and CLE3 peptides are perceived by CLV1 and BAM1 to mediate lateral root formation through LBDs regulation.

Identification and function of miRNA-mRNA interaction pairs during lateral root development of hemi-parasitic Santalum album L. seedlings.

Sandalwood (Santalum album L.) is a hemi-parasitic tree species famous for its santalol and santalene, which are extracted from its heartwood and roots. The ability to understand root functionality within its branched root system would benefit the regulation of sandalwood growth and enhance the commercial value of sandalwood. Phenotypic and anatomical evidence in this study indicated that seed germination stage 4 (SG4) seemed pivotal for lateral root (LR) morphogenesis. Small RNA (sRNA) high-throughput sequencing of root tissues at three sub-stages of SG4 (lateral root primordia initiation (LRPI), lateral root primordia development (LRPD), and lateral root primordia emergence (LRPE)) was performed to identify microRNAs (miRNAs) associated with LR development. A total of 135 miRNAs, including 70 differentially expressed miRNAs (DEMs), were screened. Ten DEMs were selected to investigate transcript abundance in different organs or developmental stages. Among 100 negative DEM-mRNA interaction pairs, four targets (Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8) were selected for studying cleavage sites by 5' RLM-RACE validation. The expression mode of the four miRNA-mRNA pairs was investigated after indole-3-acetic acid (IAA) treatment. IAA enhanced the abundance of homeobox-leucine-zipper protein 32 (HOX32), laccase 12 (LAC12), myeloblastosis86 (MYB86), and pectin methylesterase inhibitor6 (PMEI6) target transcripts by reducing the expression of Sa-miR166m_2, 408d, 858a, and novel_Sa-miR8 in the first 10 min. A schematic model of miRNA-regulated LR development is proposed for this hemi-parasitic species. This novel genetic information for improving sandalwood root growth and development may allow for the cultivation of fast-growing and high-yielding plantations.

OsAMT1;1 and OsAMT1;2 Coordinate Root Morphological and Physiological Responses to Ammonium for Efficient Nitrogen Foraging in Rice.

Optimal plant growth and development rely on morphological and physiological adaptions of the root system to forage heterogeneously distributed nitrogen (N) in soils. Rice grows mainly in the paddy soil where ammonium (NH4+) is present as the major N source. Although root NH4+ foraging behaviors are expected to be agronomically relevant, the underlying mechanism remains largely unknown. Here, we showed that NH4+ supply transiently enhanced the high-affinity NH4+ uptake and stimulated lateral root (LR) branching and elongation. These synergistic physiological and morphological responses were closely related to NH4+-induced expression of NH4+ transporters OsAMT1;1 and OsAMT1;2 in roots. The two independent double mutants (dko) defective in OsAMT1;1 and OsAMT1;2 failed to induce NH4+ uptake and stimulate LR formation, suggesting that OsAMT1s conferred the substrate-dependent root NH4+ foraging. In dko plants, NH4+ was unable to activate the expression of OsPIN2, and the OsPIN2 mutant (lra1) exhibited a strong reduction in NH4+-triggered LR branching, suggesting that the auxin pathway was likely involved in OsAMT1s-dependent LR branching. Importantly, OsAMT1s-dependent root NH4+ foraging behaviors facilitated rice growth and N acquisition under fluctuating NH4+ supply. These results revealed an essential role of OsAMT1s in synergizing root morphological and physiological processes, allowing for efficient root NH4+ foraging to optimize N capture under fluctuating N availabilities.

Arbuscular mycorrhizal symbiosis enhances tomato lateral root formation by modulating CEP2 peptide expression.

Plant lateral root (LR) growth usually is stimulated by arbuscular mycorrhizal (AM) symbiosis. However, the molecular mechanism is still unclear. We used gene expression analysis, peptide treatment and virus-induced gene alteration assays to demonstrate that C-terminally encoded peptide (CEP2) expression in tomato was downregulated during AM symbiosis to mitigate its negative effect on LR formation through an auxin-related pathway. We showed that enhanced LR density and downregulated CEP2 expression were observed during mycorrhizal symbiosis. Synthetic CEP2 peptide treatment reduced LR density and impaired the expression of genes involved in indole-3-butyric acid (IBA, the precursor of IAA) to IAA conversion, auxin polar transport and the LR-related signaling pathway; however, application of IBA or synthetic auxin 1-naphthaleneacetic acid (NAA) to the roots may rescue both defective LR formation and reduced gene expression. CEP receptor 1 (CEPR1) might be the receptor of CEP2 because its knockdown plants did not respond to CEP2 treatment. Most importantly, the LR density of CEP2 overexpression or knockdown plants could not be further increased by AM inoculation, suggesting that CEP2 was critical for AM-induced LR formation. These results indicated that AM symbiosis may regulate root development by modulating CEP2, which affects the auxin-related pathway.

Serratia marcescens PLR enhances lateral root formation through supplying PLR-derived auxin and enhancing auxin biosynthesis in Arabidopsis.

Plant growth promoting rhizobacteria (PGPR) refer to bacteria that colonize the rhizosphere and contribute to plant growth or stress tolerance. To further understand the molecular mechanism by which PGPR exhibit symbiosis with plants, we performed a high-throughput single colony screening from the rhizosphere, and uncovered a bacterium (named promoting lateral root, PLR) that significantly promotes Arabidopsis lateral root formation. By 16S rDNA sequencing, PLR was identified as a novel sub-species of Serratia marcescens. RNA-seq analysis of Arabidopsis integrated with phenotypic verification of auxin signalling mutants demonstrated that the promoting effect of PLR on lateral root formation is dependent on auxin signalling. Furthermore, PLR enhanced tryptophan-dependent indole-3-acetic acid (IAA) synthesis by inducing multiple auxin biosynthesis genes in Arabidopsis. Genome-wide sequencing of PLR integrated with the identification of IAA and its precursors in PLR exudates showed that tryptophan treatment significantly enhanced the ability of PLR to produce IAA and its precursors. Interestingly, PLR induced the expression of multiple nutrient (N, P, K, S) transporter genes in Arabidopsis in an auxin-independent manner. This study provides evidence of how PLR enhances plant growth through fine-tuning auxin biosynthesis and signalling in Arabidopsis, implying a potential application of PLR in crop yield improvement through accelerating root development.

Glutathione produced by γ-glutamyl cysteine synthetase acts downstream of hydrogen to positively influence lateral root branching.

Hydrogen gas (H2) mediation of lateral root (LR) branching was previously described. However, related signaling pathway is largely unexplored. In this study, we discovered that application with H2 using hydrogen-rich water, mimicking the responses of exogenous glutathione (GSH), not only enhanced GSH synthesis, but also induced tomato LR development. The changes in the transcripts of auxin signaling-related genes and cell cycle regulatory genes were matched with above phenotypes. The addition of H2 could trigger higher transcript levels of SlGSH1 and SlGSH2, encoding γ-glutamylcysteine synthetase (γ-ECS) and glutathione synthetase (GS), confirming the stimulation of GSH synthesis. These responses were greatly abolished when the inhibitor of γ-ECS was applied. The inhibition in lateral root primordium development, especially in emergence stage, was also observed. Genetic evidence revealed that the defects in GSH production and lateral rooting in Arabidopsis cad2-1, a γ-ECS defective mutant, were obviously abolished in the presence of GSH compared to those in the presence of H2. Further evidence revealed that mRNA levels of target genes elicited by H2 in wild-type, were differentially impaired in mutant plants. Together, above data clearly demonstrated that γ-ECS-dependent GSH production might be closely associated with H2 control of LR branching.

Glutathione Enhances Auxin Sensitivity in Arabidopsis Roots.

Root development is regulated by the tripeptide glutathione (GSH), a strong non-enzymatic antioxidant found in plants but with a poorly understood function in roots. Here, Arabidopsis mutants deficient in GSH biosynthesis (cad2, rax1, and rml1) and plants treated with the GSH biosynthesis inhibitor buthionine sulfoximine (BSO) showed root growth inhibition, significant alterations in the root apical meristem (RAM) structure (length and cell division), and defects in lateral root formation. Investigation of the molecular mechanisms of GSH action showed that GSH deficiency modulated total ubiquitination of proteins and inhibited the auxin-related, ubiquitination-dependent degradation of Aux/IAA proteins and the transcriptional activation of early auxin-responsive genes. However, the DR5 auxin transcriptional response differed in root apical meristem (RAM) and pericycle cells. The RAM DR5 signal was increased due to the up-regulation of the auxin biosynthesis TAA1 protein and down-regulation of PIN4 and PIN2, which can act as auxin sinks in the root tip. The transcription auxin response (the DR5 signal and expression of auxin responsive genes) in isolated roots, induced by a low (0.1 µM) auxin concentration, was blocked following GSH depletion of the roots by BSO treatment. A higher auxin concentration (0.5 µM) offset this GSH deficiency effect on DR5 expression, indicating that GSH deficiency does not completely block the transcriptional auxin response, but decreases its sensitivity. The ROS regulation of GSH, the active GSH role in cell proliferation, and GSH cross-talk with auxin assume a potential role for GSH in the modulation of root architecture under stress conditions.

TDIF peptides regulate root growth by affecting auxin homeostasis and PINs expression in Arabidopsis thaliana.

MAIN CONCLUSION: TDIF and TDIF-like peptides in excess simultaneously facilitate primary root elongation and lateral root formation through regulating auxin distribution and transport. Tracheary element differentiation inhibitory factor (TDIF) plays key roles in mediating cell-cell communication and stem cell maintenance during vascular development. Recently, TDIF has also been linked to lateral root (LR) organogenesis through Brassinosteroid Insensitive 2 (BIN2) action. In this work, by comparing the in vitro and in vivo activities of AtCLE41-encoded TDIF and one poplar-derived TDIF-like peptide in Arabidopsis thaliana, we demonstrated that both TDIFs promoted primary root (PR) growth and stimulated LR formation. Without affecting auxin biosynthesis and catabolism, TDIFs suppressed the auxin maxima at PR apex but intensified the auxin accumulation at LR initiation sites along the longitudinal axis of PR. TDIF did not alter root sensitivity to exogenous auxin and mutants with varied endogenous auxin levels responded to TDIF peptides in a wild-type manner but to a lesser extent. Intriguingly, TDIF specifically upregulated the transcript abundance of PINs and multiple pin mutants displayed insensitivity to TDIF, demonstrating that PIN-mediated polar auxin transport (PAT) is indispensably required for the TDIF-induced root phenotypes. Taken together, our results revealed that TDIF might target PAT via mobilizing auxin efflux carriers to dynamically regulate the auxin signaling output and hence facilitate PR growth and LR formation.

The dynamic nature and regulation of the root clock.

Plants explore the soil by continuously expanding their root system, a process that depends on the production of lateral roots (LRs). Sites where LRs can be produced are specified in the primary root axis through a pre-patterning mechanism, determined by a biological clock that is coordinated by temporal signals and positional cues. This 'root clock' generates an oscillatory signal that is translated into a developmental cue to specify a set of founder cells for LR formation. In this Review, we summarize recent findings that shed light on the mechanisms underlying the oscillatory signal and discuss how a periodic signal contributes to the conversion of founder cells into LR primordia. We also provide an overview of the phases of the root clock that may be influenced by endogenous factors, such as the plant hormone auxin, and by exogenous environmental cues. Finally, we discuss additional aspects of the root-branching process that act independently of the root clock.

Methane-induced lateral root formation requires the participation of nitric oxide signaling.

Although methane (CH4)-induced lateral root (LR) formation has been discovered, the identification of downstream signaling compounds has yet to be fully elucidated. Here, we report a unique mechanism for the involvement of nitric oxide (NO) in the above CH4-mediated pathway in tomato (Solanum lycopersicum L.) and Arabidopsis thaliana. NO was produced rapidly in the root tissues of tomato seedlings when CH4 was administrated exogenously. The scavenging of NO with its scavengers prevented lateral root primordia formation and thereafter lateral rooting triggered by CH4. Gene expression analysis revealed that similar to the responses of sodium nitroprusside (SNP; a NO-releasing compound), CH4-induced SlCYCA2;1, SlCYCA3;1, and SlCDKA1 transcripts, and -downregulated SlKRP2 mRNA, were differentially abolished when endogenous NO was removed by its scavengers. Changes in the lateral root-related miRNA genes (SlmiR160 and SlmiR390a) and their target genes (SlARF16 and SlARF4), exhibited similar tendencies. Similar to those results in tomato, the addition of CH4 and SNP could obviously induce NO production and LR formation in Arabidopsis seedlings, which were correlated with the transcriptional profiles of representative LR-related genes. Combine with these findings in tomato and Arabidopsis thaliana, our results showed that NO might act, at least partially, as the downstream signaling molecule for CH4 control of lateral rooting.

Brachypodium distachyon tar2lhypo mutant shows reduced root developmental response to symbiotic signal but increased arbuscular mycorrhiza.

Auxin is a major phytohormone that controls root development. A role for auxin is also emerging in the control of plant-microbe interactions, including for the establishment of root endosymbiosis between plants and arbuscular mycorrhizal fungi (AMF). Auxin perception is important both for root colonization by AMF and for arbuscule formation. AMF produce symbiotic signals called lipo-chitooligosaccharides (LCOs) that can modify auxin homeostasis and promote lateral root formation (LRF). Since Brachypodium distachyon (Brachypodium) has a different auxin sensitivity compared to other plant species, we wondered whether this would interfere with the effect of auxin in arbuscular mycorrhizal (AM) symbiosis. Here we tested whether tar2lhypo a Brachypodium mutant with an increase in endogenous auxin content is affected in LRF stimulation by LCOs and in AM symbiosis. We found that, in contrast to control plants, LCO treatment inhibited LRF of the tar2lhypo mutant. However, the level of AMF colonization and the abundance of arbuscules were increased in tar2lhypo compared to control plants, suggesting that auxin also plays a positive role in both AMF colonization and arbuscule formation in Brachypodium.

Cytoskeleton Dynamics Are Necessary for Early Events of Lateral Root Initiation in Arabidopsis.

How plant cells re-establish differential growth to initiate organs is poorly understood. Morphogenesis of lateral roots relies on the asymmetric cell division of initially symmetric founder cells. This division is preceded by the tightly controlled asymmetric radial expansion of these cells. The cellular mechanisms that license and ensure the coordination of these events are unknown. Here, we quantitatively analyze microtubule and F-actin dynamics during lateral root initiation. Using mutants and pharmacological and tissue-specific genetic perturbations, we show that dynamic reorganization of both microtubule and F-actin networks is necessary for the asymmetric expansion of the founder cells. This cytoskeleton remodeling intertwines with auxin signaling in the pericycle and endodermis in order for founder cells to acquire a basic polarity required for initiating lateral root development. Our results reveal the conservation of cell remodeling and polarization strategies between the Arabidopsis zygote and lateral root founder cells. We propose that coordinated, auxin-driven reorganization of the cytoskeleton licenses asymmetric cell growth and divisions during embryonic and post-embryonic organogenesis.

PUCHI regulates very long chain fatty acid biosynthesis during lateral root and callus formation.

Lateral root organogenesis plays an essential role in elaborating plant root system architecture. In Arabidopsis, the AP2 family transcription factor PUCHI controls cell proliferation in lateral root primordia. To identify potential targets of PUCHI, we analyzed a time course transcriptomic dataset of lateral root formation. We report that multiple genes coding for very long chain fatty acid (VLCFA) biosynthesis enzymes are induced during lateral root development in a PUCHI-dependent manner. Significantly, several mutants perturbed in VLCFA biosynthesis show similar lateral root developmental defects as puchi-1 Moreover, puchi-1 roots display the same disorganized callus formation phenotype as VLCFA biosynthesis-deficient mutants when grown on auxin-rich callus-inducing medium. Lipidomic profiling of puchi-1 roots revealed reduced VLCFA content compared with WT. We conclude that PUCHI-regulated VLCFA biosynthesis is part of a pathway controlling cell proliferation during lateral root and callus formation.

Deep Sequencing Reveals Early Reprogramming of Arabidopsis Root Transcriptomes Upon Ralstonia solanacearum Infection.

Bacterial wilt caused by the bacterial pathogen Ralstonia solanacearum is one of the most devastating crop diseases worldwide. The molecular mechanisms controlling the early stage of R. solanacearum colonization in the root remain unknown. Aiming to better understand the mechanism of the establishment of R. solanacearum infection in root, we established four stages in the early interaction of the pathogen with Arabidopsis roots and determined the transcriptional profiles of these stages of infection. A total 2,698 genes were identified as differentially expressed genes during the initial 96 h after infection, with the majority of changes in gene expression occurring after pathogen-triggered root-hair development observed. Further analysis of differentially expressed genes indicated sequential activation of multiple hormone signaling cascades, including abscisic acid (ABA), auxin, jasmonic acid, and ethylene. Simultaneous impairment of ABA receptor genes promoted plant wilting symptoms after R. solanacearum infection but did not affect primary root growth inhibition or root-hair and lateral root formation caused by R. solanacearum. This indicated that ABA signaling positively regulates root defense to R. solanacearum. Moreover, transcriptional changes of genes involved in primary root, lateral root, and root-hair formation exhibited high temporal dynamics upon infection. Taken together, our results suggest that successful infection of R. solanacearum on roots is a highly programmed process involving in hormone crosstalk.

A Genome-Wide Association Study Identifies New Loci Involved in Wound-Induced Lateral Root Formation in Arabidopsis thaliana.

Root systems can display variable architectures that contribute to nutrient foraging or to increase the tolerance of abiotic stress conditions. Root tip excision promotes the developmental progression of previously specified lateral root (LR) founder cells, which allows to easily measuring the branching capacity of a given root as regards its genotype and/or growth conditions. Here, we describe the natural variation among 120 Arabidopsis thaliana accessions in root system architecture (RSA) after root tip excision. Wound-induced changes in RSA were associated with 19 genomic loci using genome-wide association mapping. Three candidate loci associated with wound-induced LR formation were investigated. Sequence variation in the hypothetical protein encoded by the At4g01090 gene affected wound-induced LR development and its loss-of-function mutants displayed a reduced number of LRs after root tip excision. Changes in a histidine phosphotransfer protein putatively involved in cytokinin signaling were significantly associated with LR number variation after root tip excision. Our results provide a better understanding of some of the genetic components involved in LR capacity variation among accessions.