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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Expression quantitative trait loci mapping identified PtrXB38 as a key hub gene in adventitious root development in Populus

Summary Plant establishment requires the formation and development of an extensive root system with architecture modulated by complex genetic networks. Here, we report the identification of the PtrXB38 gene as an expression quantitative trait loci (eQTL) hotspot, mapped using 390 leaf and 444 xylem Populus trichocarpa transcriptomes. Among predicted targets of this trans ‐eQTL were genes involved in plant hormone responses and root development. Overexpression of PtrXB38 in Populus led to significant increases in callusing and formation of both stem‐born roots and base‐born adventitious roots. Omics studies revealed that genes and proteins controlling auxin transport and signaling were involved in PtrXB38‐mediated adventitious root formation. Protein–protein interaction assays indicated that PtrXB38 interacts with components of endosomal sorting complexes required for transport machinery, implying that PtrXB38‐regulated root development may be mediated by regulating endocytosis pathway. Taken together, this work identified a crucial root development regulator and sheds light on the discovery of other plant developmental regulators through combining eQTL mapping and omics approaches.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Influence of PRE-emergence herbicides on soybean development, root nodulation and symbiotic nitrogen fixation

We report widespread occurrence of herbicide-resistant weeds has further limited effective POST-emergence herbicide options in soybean (Glycine max (L.) Merr.) leading to an increased adoption of PRE-emergence herbicides. The objective of this study was to investigate the influence of 11 commonly used PRE herbicides on soybean development, root nodulation, and symbiotic N fixation. Soybean plants were grown under greenhouse conditions in pots (10 L; 4 plants per pot) filled with silt loam soil and treated one day after planting with a labeled field rate of imazethapyr, chlorimuron-ethyl, cloransulam-methyl, metribuzin, sulfentrazone, flumioxazin, saflufenacil, acetochlor, S-metolachlor, dimethenamid-P, pyroxasulfone and no herbicide (nontreated control). Sulfentrazone reduced soybean canopy at the VC growth stage but no canopy reduction was observed at the V2 growth stage from any of the herbicide treatments. At the R2 growth stage, herbicides had no effect on soybean development (root and shoot biomass), root nodulation (# nodule per plant, nodule diameter, and nodule biomass) and symbiotic N fixation (acetylene reduction assay and 15 N natural abundance). According to our findings, although PRE herbicides may slightly affect early-season soybean development, the impacts on plant growth, root nodulation, and symbiotic N fixation were negligible. Thus, when sprayed according to the label, the benefits of PRE herbicides for weed control likely outweigh any potential concern regarding soybean development, root nodulation, and N fixation.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

KARRIKIN INSENSITIVE2 regulates leaf development, root system architecture and arbuscular‐mycorrhizal symbiosis in Brachypodium distachyon

SUMMARY KARRIKIN INSENSITIVE2 (KAI2) is an α/β‐hydrolase required for plant responses to karrikins, which are abiotic butenolides that can influence seed germination and seedling growth. Although represented by four angiosperm species, loss‐of‐function kai2 mutants are phenotypically inconsistent and incompletely characterised, resulting in uncertainties about the core functions of KAI2 in plant development. Here we characterised the developmental functions of KAI2 in the grass Brachypodium distachyon using molecular, physiological and biochemical approaches. Bdkai2 mutants exhibit increased internode elongation and reduced leaf chlorophyll levels, but only a modest increase in water loss from detached leaves. Bdkai2 shows increased numbers of lateral roots and reduced root hair growth, and fails to support normal root colonisation by arbuscular‐mycorrhizal (AM) fungi. The karrikins KAR 1 and KAR 2 , and the strigolactone (SL) analogue rac ‐GR24, each elicit overlapping but distinct changes to the shoot transcriptome via BdKAI2. Finally, we show that BdKAI2 exhibits a clear ligand preference for desmethyl butenolides and weak responses to methyl‐substituted SL analogues such as GR24. Our findings suggest that KAI2 has multiple roles in shoot development, root system development and transcriptional regulation in grasses. Although KAI2‐dependent AM symbiosis is likely conserved within monocots, the magnitude of the effect of KAI2 on water relations may vary across angiosperms.

Meng, Yongjie↗
DOE OSTI2025

Two deeply conserved non-coding sequences control PLETHORA1/2 expression and coordinate embryo and root development

Conserved non-coding sequences (CNSs) are integral elements of transcriptional regulation. Transcriptional tuning of PLETHORA (PLT) genes that encode master regulators of plant development is vital for embryogenesis and meristematic function. However, how the expression of PLT genes is modulated through CNSs remains unclear. Through motif-based mining of upstream sequences in 120 angiosperm genomes, we identified 21 conserved and lineage-specific CNSs, two of which are unusually long, similar, and colinear within eudicots. Using Arabidopsis thaliana, we demonstrate that these two deeply conserved elements, which we named BOX1 and BOX2, control PLT1 and PLT2 expression. CRISPR mutants within these elements specifically reduced PLT expression levels, and reporter lines revealed that deletion of either or both BOXes altered and/or abrogated the PLT2 expression pattern in the root tip, affecting the ability to rescue the plt1 plt2 double mutant. We further show that the influence of these elements on expression patterns is already exerted during embryogenesis and functional in the context of the early embryo. Finally, we reveal the existence of a BOX-mediated autoregulatory feedback loop that, in large part, explains CNS influence on expression patterns. We thus uncover a transcriptional mechanism by which genes encoding master regulators of embryo and root meristem development are regulated.

PLETHORA↗
DOE OSTI2022

Nitrogen fixation and mucilage production on maize aerial roots is controlled by aerial root development and border cell functions

Exploring natural diversity for biological nitrogen fixation in maize and its progenitors is a promising approach to reducing our dependence on synthetic fertilizer and enhancing the sustainability of our cropping systems. We have shown previously that maize accessions from the Sierra Mixe can support a nitrogen-fixing community in the mucilage produced by their abundant aerial roots and obtain a significant fraction of their nitrogen from the air through these associations. In this study, we demonstrate that mucilage production depends on root cap and border cells sensing water, as observed in underground roots. The diameter of aerial roots correlates with the volume of mucilage produced and the nitrogenase activity supported by each root. Young aerial roots produce more mucilage than older ones, probably due to their root cap’s integrity and their ability to produce border cells. Transcriptome analysis on aerial roots at two different growth stages before and after mucilage production confirmed the expression of genes involved in polysaccharide synthesis and degradation. Genes related to nitrogen uptake and assimilation were up-regulated upon water exposure. Altogether, our findings suggest that in addition to the number of nodes with aerial roots reported previously, the diameter of aerial roots and abundance of border cells, polysaccharide synthesis and degradation, and nitrogen uptake are critical factors to ensure efficient nitrogen fixation in maize aerial roots.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Rational Modulation of Plant Root Development Using Engineered Cytokinin Regulators

Achieving precise control over quantitative developmental phenotypes is a key objective in plant biology. Recent advances in synthetic biology have enabled tools to reprogram entire developmental pathways; however, the complexity of designing synthetic genetic programs and the inherent interactions between various signaling processes remains a critical challenge. Here, we leverage Type-B response regulators to modulate the expression of genes involved in cytokinin-dependent growth and development processes. We rationally engineered these regulators to modulate their transcriptional activity (i.e., repression or activation) and potency while reducing their sensitivity to cytokinin. By localizing the expression of these engineered transcription factors using tissue-specific promoters, we can predictably tune cytokinin-regulated traits. As a proof of principle, we deployed this synthetic system in Arabidopsis thaliana to either decrease or increase the number of lateral roots. The simplicity and modularity of our approach makes it an ideal system for controlling other developmental phenotypes of agronomic interest in plants.

Cell signaling↗
DOE OSTI2024

Bioenergy sorghum nodal root bud development: morphometric, transcriptomic and gene regulatory network analysis

Bioenergy sorghum’s large and deep nodal root system and associated microbiome enables uptake of water and nutrients from and deposition of soil organic carbon into soil profiles, key contributors to the crop’s resilience and sustainability. The goal of this study was to increase our understanding of bioenergy sorghum nodal root bud development. Sorghum nodal root bud initiation was first observed on the stem node of the 7 th phytomer below the shoot apex. Buds were initiated near the upper end of the stem node pulvinus on the side of the stem opposite the tiller bud, then additional buds were added over the next 6-8 days forming a ring of 10-15 nascent nodal root buds around the stem. Later in plant development, a second ring of nodal root buds began forming on the 17 th stem node immediately above the first ring of buds. Overall, nodal root bud development can take ~40 days from initiation to onset of nodal root outgrowth. Nodal root buds were initiated in close association with vascular bundles in the rind of the pulvinus. Stem tissue forming nascent nodal root buds expressed sorghum homologs of genes associated with root initiation (WOX4), auxin transport (LAX2, PIN4), meristem activation (NGAL2), and genes involved in cell proliferation. Expression of WOX11 and WOX5, genes involved in root stem niche formation, increased early in nodal root bud development followed by genes encoding PLTs, LBDs (LBD29), LRP1, SMB, RGF1 and root cap LEAs later in development. A nodal root bud gene regulatory network module expressed during nodal root bud initiation predicted connections linking PFA5, SPL9 and WOX4 to genes involved in hormone signaling, meristem activation, and cell proliferation. A network module expressed later in development predicted connections among SOMBRERO, a gene involved in root cap formation, and GATA19, BBM, LBD29 and RITF1/RGF1 signaling. Overall, this study provides a detailed description of bioenergy sorghum nodal root bud development and transcriptome information useful for understanding the regulation of sorghum nodal root bud formation and development.

09 BIOMASS FUELS↗
DOE OSTI2021

Summary of the the 11th Symposium of the International Society of Root Research

11th Symposium of the International Society of Root Research (ISRR11) and the 9th International Symposium on Root Development (Rooting2021) - Root Biology Never Sleeps virtual meeting May 24 - 28. These meetings are generally held in separate years. However, because of travel restrictions imposed by the COVID-19 pandemic, the organizing committees of both symposia decided to host the two meetings as a fully-joint and virtual-only conference. Various time zones were considered when developing the schedule, as live interactions was an important focus. Scientific sessions were held from 3 a.m. to 10 p.m. US Central Daylight Time (CDT) to meet the international demand. More than 700 participants from 52 countries virtually attend both events which featured 74 talks in 16 sessions including: 10 plenary lectures, 16 keynote speakers and 48 selected talks. Additionally, nearly 300 posters were presented in nine poster sessions. The meeting also featured an Ambassador Program with 21 ambassadors from 10 countries. These ambassadors organized a half-day pre-symposium workshop and produced a review of the meeting for “New Phytologist”. The meeting also awarded a Lifetime Award to Dr. Wendy Silk (Prof. Emerita University of California, Davis). Committee Members: • Bob Sharp (Chair) – University of Missouri • Felix Fritschi (Chair, Int’l Program Committee) – University of Missouri • David Braun – University of Missouri • Vicki Bryan – University of Missouri • Rich Ferrieri – University of Missouri • Laura Greeley – University of Missouri (postdoctoral representative) • Ali Housh – University of Missouri (graduate student representative) • Allison Miller – Donald Danforth Plant Science Center and St Louis University • Mel Oliver – University of Missouri • Jonathan Stemmle – University of Missouri • Gus Thies – University of Missouri & Donald Danforth Plant Science Center (graduate student representative) • Chris Topp - Donald Danforth Plant Science Center

Root Biology↗
DOE OSTI2023

BUZZ : an essential gene for postinitiation root hair growth and a mediator of root architecture in Brachypodium distachyon

Here, we discover a player in root development. Recovered from a forward-genetic screen in Brachypodium distachyon, the buzz mutant initiates root hairs but they fail to elongate. In addition, buzz roots grow twice as fast as wild-type roots. Also, lateral roots show increased sensitivity to nitrate, whereas primary roots are less sensitive to nitrate. Using whole-genome resequencing, we identified the causal single nucleotide polymorphism as occurring in a conserved but previously uncharacterized cyclin-dependent kinase (CDK)-like gene. The buzz mutant phenotypes are rescued by the wild-type B. distachyon BUZZ coding sequence and by an apparent homolog in Arabidopsis thaliana. Moreover, T-DNA mutants in A. thaliana BUZZ have shorter root hairs. BUZZ mRNA localizes to epidermal cells and develops root hairs and, in the latter, partially colocalizes with the NRT1.1A nitrate transporter. Based on qPCR and RNA-Seq, buzz overexpresses ROOT HAIRLESS LIKE SIX-1 and -2 and misregulates genes related to hormone signaling, RNA processing, cytoskeletal, and cell wall organization, and to the assimilation of nitrate. Overall, these data demonstrate that BUZZ is required for tip growth after root hair initiation and root architectural responses to nitrate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Two Alternative Splicing Variants of AtERF73/HRE1, HRE1α and HRE1β, Have Differential Transactivation Activities in Arabidopsis

AtERF73/HRE1 is an AP2/ERF transcription factor in Arabidopsis and has two distinct alternative splicing variants, HRE1α and HRE1β. In this study, we examined the differences between the molecular functions of HRE1α and HRE1β. We found that HRE1α and HRE1β are both involved in hypoxia response and root development and have transactivation activity. Two conserved motifs in the C-terminal region of HRE1α and HRE1β, EELL and LWSY-like, contributed to their transactivation activity, specifically the four E residues in the EELL motif and the MGLWS amino acid sequence at the end of the LWSY-like motif. The N-terminal region of HRE1β also showed transactivation activity, mediated by the VDDG motif, whereas that of HRE1α did not. The transactivation activity of HRE1β was stronger than that of HRE1α in Arabidopsis protoplasts. Both transcription factors transactivated downstream genes via the GCC box. RNA-sequencing analysis further supported that both HRE1α and HRE1β might regulate gene expression associated with the hypoxia stress response, although they may transactivate different subsets of genes in downstream pathways. Our results, together with previous studies, suggested that HRE1α and HRE1β differentially transactivate downstream genes in hypoxia response and root development in Arabidopsis.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Drought Drives Spatial Variation in the Millet Root Microbiome

Efforts to boost crop yield and meet global food demands while striving to reach sustainability goals are hindered by the increasingly severe impacts of abiotic stress, such as drought. One strategy for alleviating drought stress in crops is to utilize rootassociated bacteria, yet knowledge concerning the relationship between plant hosts and their microbiomes during drought remain under-studied. One broad pattern that has recently been reported in a variety of monocot and dicot species from both native and agricultural environments, is the enrichment of Actinobacteria within the drought-stressed root microbiome. In order to better understand the causes of this phenomenon, we performed a series of experiments in millet plants to explore the roles of drought severity, drought localization, and root development in provoking Actinobacteria enrichment within the root endosphere. Through 16S rRNA ampliconbased sequencing, we demonstrate that the degree of drought is correlated with levels of Actinobacterial enrichment in four species of millet. Additionally, we demonstrate that the observed drought-induced enrichment of Actinobacteria occurs along the length of the root, but the response is localized to portions of the root experiencing drought. Finally, we demonstrate that Actinobacteria are depleted in the dead root tissue of Japanese millet, suggesting saprophytic activity is not the main cause of observed shifts in drought-treated root microbiome structure. Collectively, these results help narrow the list of potential causes of drought-induced Actinobacterial enrichment in plant roots by showing that enrichment is dependent upon localized drought responses but not root developmental stage or root death.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

An LCO-responsive homolog of NODULE INCEPTION positively regulates lateral root formation in Populus sp.

Abstract The transcription factor NODULE INCEPTION (NIN) has been studied extensively for its multiple roles in root nodule symbiosis within plants of the nitrogen-fixing clade (NFC) that associate with soil bacteria, such as rhizobia and Frankia. However, NIN homologs are present in plants outside the NFC, suggesting a role in other developmental processes. Here, we show that the biofuel crop Populus sp., which is not part of the NFC, contains eight copies of NIN with diversified protein sequence and expression patterns. Lipo-chitooligosaccharides (LCOs) are produced by rhizobia and a wide range of fungi, including mycorrhizal ones, and act as symbiotic signals that promote lateral root formation. RNAseq analysis of Populus sp. treated with purified LCO showed induction of the PtNIN2 subfamily. Moreover, the expression of PtNIN2b correlated with the formation of lateral roots and was suppressed by cytokinin treatment. Constitutive expression of PtNIN2b overcame the inhibition of lateral root development by cytokinin under high nitrate conditions. Lateral root induction in response to LCOs likely represents an ancestral function of NIN retained and repurposed in nodulating plants, as we demonstrate that the role of NIN in LCO-induced root branching is conserved in both Populus sp. and legumes. We further established a visual marker of LCO perception in Populus sp. roots, the putative sulfotransferase PtSS1 that can be used to study symbiotic interactions with the bacterial and fungal symbionts of Populus sp.

Irving, Thomas B. (ORCID:0000000330404543)↗
DOE OSTI2024

Quantitative phenotyping of crop roots with spectral electrical impedance tomography: a rhizotron study with optimized measurement design

Background: Root systems are key contributors to plant health, resilience, and, ultimately, yield of agricultural crops. To optimize plant performance, phenotyping trials are conducted to breed plants with diverse root traits. However, traditional analysis methods are often labour-intensive and invasive to the root system, therefore limiting high-throughput phenotyping. Spectral electrical impedance tomography (sEIT) could help as a non-invasive and cost-efficient alternative to optical root analysis, potentially providing 2D or 3D spatio-temporal information on root development and activity. Although impedance measurements have been shown to be sensitive to root biomass, nutrient status, and diurnal activity, only few attempts have been made to employ tomographic algorithms to recover spatially resolved information on root systems. In this study, we aim to establish relationships between tomographic electrical polarization signatures and root traits of different fine root systems (maize, pinto bean, black bean, and soy bean) under hydroponic conditions. Results: Our results show that, with the use of an optimized data acquisition scheme, sEIT is capable of providing spatially resolved information on root biomass and root surface area for all investigated root systems. We found strong correlations between the total polarization strength and the root biomass (R 2 = 0.82) and root surface area (R 2 = 0.8). Our findings suggest that the captured polarization signature is dominated by cell-scale polarization processes. Additionally, we demonstrate that the resolution characteristics of the measurement scheme can have a significant impact on the tomographic reconstruction of root traits. Conclusion: Our findings showcase that sEIT is a promising tool for the tomographic reconstruction of root traits in high-throughput root phenotyping trials and should be evaluated as a substitute for traditional, often time-consuming, root characterization methods.

59 BASIC BIOLOGICAL SCIENCES↗