GTL1 and DF1 regulate root hair growth through transcriptional repression of ROOT HAIR DEFECTIVE 6-LIKE 4 in Arabidopsis

Whole-Genome Sequencing and Analysis of Tumour-Forming Radish (Raphanus sativus L.) Line

Spontaneous tumour formation in higher plants can occur in the absence of pathogen invasion, depending on the plant genotype. Spontaneous tumour formation on the taproots is consistently observed in certain inbred lines of radish (Raphanus sativus var. radicula Pers.). In this paper, using Oxford Nanopore and Illumina technologies, we have sequenced the genomes of two closely related radish inbred lines that differ in their ability to spontaneously form tumours. We identified a large number of single nucleotide variants (amino acid substitutions, insertions or deletions, SNVs) that are likely to be associated with the spontaneous tumour formation. Among the genes involved in the trait, we have identified those that regulate the cell cycle, meristem activity, gene expression, and metabolism and signalling of phytohormones. After identifying the SNVs, we performed Sanger sequencing of amplicons corresponding to SNV-containing regions to validate our results. We then checked for the presence of SNVs in other tumour lines of the radish genetic collection and found the ERF118 gene, which had the SNVs in the majority of tumour lines. Furthermore, we performed the identification of the CLAVATA3/ESR (CLE) and WUSCHEL (WOX) genes and, as a result, identified two unique radish CLE genes which probably encode proteins with multiple CLE domains. The results obtained provide a basis for investigating the mechanisms of plant tumour formation and also for future genetic and genomic studies of radish.

Transcriptional repression of GTL1 under water-deficit stress promotes anthocyanin biosynthesis to enhance drought tolerance

The transcription factor GT2-LIKE 1 (GTL1) has been implicated in orchestrating a transcriptional network of diverse physiological, biochemical, and developmental processes. In response to water-limiting conditions, GTL1 is a negative regulator of stomatal development, but its potential rolein other water-deficit responses is unknown. We hypothesized that GTL1 regulates transcriptome changes associated with drought tolerance over leaf developmental stages. To test the hypothesis, gene expression was profiled by RNA-seq analysis in emerging and expanding leaves of wild-type and a drought-tolerant gtl1-4 knockout mutant under well-watered and water-deficit conditions. Our comparative analysis of genotype-treatment combinations within leaf developmental age identified 459 and 1073 differentially expressed genes in emerging and expanding leaves, respectively, as water-deficit responsive GTL1-regulated genes. Transcriptional profiling identified a potential role of GTL1 in two important pathways previously linked to drought tolerance: flavonoid and polyamine biosynthesis. In expanding leaves, negative regulation of GTL1 under water-deficit conditions promotes biosynthesis of flavonoids and anthocyanins that may contribute to drought tolerance. Quantification of polyamines did not support a role for GTL1 in these drought-responsive pathways, but this is likely due to the complex nature of polyamine synthesis and turnover. Our global transcriptome analysis suggests that transcriptional repression of GTL1 by water deficit allows plants to activate diverse pathways that collectively contribute to drought tolerance.

An LRH-RSL4 feedback regulatory loop controls the determinate growth of root hairs in Arabidopsis

Root hairs are tubular-shaped outgrowths of epidermal cells essential for plants acquiring water and nutrients from the soil. Despite their importance, the growth of root hairs is finite. How this determinate growth is precisely regulated remains largely unknown. Here we identify LONG ROOT HAIR (LRH), a GYF domain-containing protein, as a unique repressor of root hair growth. We show that LRH inhibits the association of eukaryotic translation initiation factor 4Es (eIF4Es) with the mRNA of ROOT HAIR DEFECTIVE6-LIKE4 (RSL4) that encodes the master regulator of root hair growth, repressing RSL4 translation and thus root hair elongation. RSL4 in turn directly transactivates LRH expression to maintain a proper LRH gradient in the trichoblasts. Our findings reveal a previously uncharacterized LRH-RSL4 feedback regulatory loop that limits root hair growth, shedding new light on the mechanism underlying the determinate growth of root hairs.

GLABROUS INFLORESCENCE STEMS3 binds to and activates RHD2 and RHD4 genes to promote root hair elongation in Arabidopsis

Root hairs are crucial in the uptake of essential nutrients and water in plants. This study showed that a zinc finger protein, GIS3 is involved in root hair growth in Arabidopsis. The loss-of-function gis3 and GIS3 RNAi transgenic line exhibited a significant reduction in root hairs compared to the wild type. The application of 1-aminocyclopropane-1-carboxylic acid (ACC), an exogenous ethylene precursor, and 6-benzyl amino purine (BA), a synthetic cytokinin, significantly restored the percentage of hair cells in the epidermis in gis3 and induced GIS3 expression in the wild type. More importantly, molecular and genetic studies revealed that GIS3 acts upstream of ROOT HAIR DEFECTIVE 2 (RHD2) and RHD4 by binding to their promoters. Furthermore, exogenous ACC and BA application significantly induced the expression of RHD2 and RHD4, while root hair phenotype of rhd2-1, rhd4-1, and rhd4-3 was insensitive to ACC and BA treatment. We can therefore conclude that GIS3 modulates root hair development by directly regulating RHD2 and RHD4 expression through ethylene and cytokinin signals in Arabidopsis.

Circadian Clock Controls Root Hair Elongation through Long-Distance Communication

Plants adapt to periodic environmental changes, such as day and night, by using circadian clocks. Cell division and elongation are primary steps to adjust plant development according to their environments. In Arabidopsis, hypocotyl elongation has been studied as a representative model to understand how the circadian clock regulates cell elongation. However, it remains unknown whether similar phenomena exist in other organs, such as roots, where circadian clocks regulate physiological responses. Here, we show that root hair elongation is controlled by both light and the circadian clock. By developing machine-learning models to automatically analyze the images of root hairs, we found that genes encoding major components of the central oscillator, such as TIMING OF CAB EXPRESSION1 (TOC1) or CIRCADIAN CLOCK ASSOCIATED1 (CCA1), regulate the rhythmicity of root hair length. The partial illumination of light to either shoots or roots suggested that light received in shoots is mainly responsible for the generation of root hair rhythmicity. Furthermore, grafting experiments between wild-type (WT) and toc1 plants demonstrated that TOC1 in shoots is responsible for the generation of root hair rhythmicity. Our results illustrate the combinational effects of long-distance signaling and the circadian clock on the regulation of root hair length.

OsUGE1 is directly targeted by OsGRF6 to regulate root hair length in rice

KEY MESSAGE

Root hairs are required for water and nutrient acquisition in plants. Here, we report a novel mechanism that OsUGE1 is negatively controlled by OsGRF6 to regulate root hair elongation in rice. Root hairs are tubular outgrowths generated by the root epidermal cells. They effectively enlarge the soil-root contact area and play essential roles for nutrient and water absorption. Here, in this study, we demonstrated that the Oryza sativa UDP-glucose 4-epimerase 1-like (OsUGE1) negatively regulated root hair elongation and was directly targeted by Oryza sativa growth regulating factor 6 (OsGRF6). Knockout mutants of OsUGE1 using CRISPR-Cas9 technology showed longer root hairs than those of wild type. In contrast, overexpression lines of OsUGE1 displayed shorter root hair compared with those of wild type. GUS staining showed that it could specifically express in root hair. Subcellular localization analysis indicates that OsUGE1 is located in endoplasmic reticulum, nucleus and plasma membrane. More importantly, ChIP-qPCR, Yeast-one-hybrid and BiFC experiments revealed that OsGRF6 could bind to the promoter of OsUGE1. Furthermore, knockout mutants of OsGRF6 showed shorter root hair than those of wild type, and OsGRF6 dominantly expressed in root. In addition, the expression level of OsUGE1 is significantly downregulated in Osgrf6 mutant. Taken together, our study reveals a novel pathway that OsUGE1 is negatively controlled by OsGRF6 to regulate root hair elongation in rice.

Overexpression of cotton Trihelix transcription factor GhGT-3b_A04 enhances resistance to Verticillium dahliae and affects plant growth in Arabidopsis thaliana

Verticillium wilt is a soil-borne fungal disease that severely affects cotton fiber yield and quality. Herein, a cotton Trihelix family gene, GhGT-3b_A04, was strongly induced by the fungal pathogen Verticillium dahliae. Overexpression of the gene in Arabidopsis thaliana enhanced the plant's resistance to Verticillium wilt but inhibited the growth of rosette leaves. In addition, the primary root length, root hair number, and root hair length increased in GhGT-3b_A04-overexpressing plants. The density and length of trichomes on the rosette leaves also increased. GhGT-3b_A04 localized to the nucleus, and transcriptome analysis revealed that it induced gene expression for salicylic acid synthesis and signal transduction and activated gene expression for disease resistance. The gene expression for auxin signal transduction and trichome development was reduced in GhGT-3b_A04-overexpressing plants. Our results highlight important regulatory genes for Verticillium wilt resistance and cotton fiber quality improvement. The identification of GhGT-3b_A04 and other important regulatory genes can provide crucial reference information for future research on transgenic cotton breeding.

Brassinosteroid gene regulatory networks at cellular resolution in the Arabidopsis root

Brassinosteroids are plant steroid hormones that regulate diverse processes, such as cell division and cell elongation, through gene regulatory networks that vary in space and time. By using time series single-cell RNA sequencing to profile brassinosteroid-responsive gene expression specific to different cell types and developmental stages of the Arabidopsis root, we identified the elongating cortex as a site where brassinosteroids trigger a shift from proliferation to elongation associated with increased expression of cell wall-related genes. Our analysis revealed HOMEOBOX FROM ARABIDOPSIS THALIANA 7 (HAT7) and GT-2-LIKE 1 (GTL1) as brassinosteroid-responsive transcription factors that regulate cortex cell elongation. These results establish the cortex as a site of brassinosteroid-mediated growth and unveil a brassinosteroid signaling network regulating the transition from proliferation to elongation, which illuminates aspects of spatiotemporal hormone responses.

A translatome-transcriptome multi-omics gene regulatory network reveals the complicated functional landscape of maize

BACKGROUND

Maize (Zea mays L.) is one of the most important crops worldwide. Although sophisticated maize gene regulatory networks (GRNs) have been constructed for functional genomics and phenotypic dissection, a multi-omics GRN connecting the translatome and transcriptome is lacking, hampering our understanding and exploration of the maize regulatome.

RESULTS

We collect spatio-temporal translatome and transcriptome data and systematically explore the landscape of gene transcription and translation across 33 tissues or developmental stages of maize. Using this comprehensive transcriptome and translatome atlas, we construct a multi-omics GRN integrating mRNAs and translated mRNAs, demonstrating that translatome-related GRNs outperform GRNs solely using transcriptomic data and inter-omics GRNs outperform intra-omics GRNs in most cases. With the aid of the multi-omics GRN, we reconcile some known regulatory networks. We identify a novel transcription factor, ZmGRF6, which is associated with growth. Furthermore, we characterize a function related to drought response for the classic transcription factor ZmMYB31.

CONCLUSIONS

Our findings provide insights into spatio-temporal changes across maize development at both the transcriptome and translatome levels. Multi-omics GRNs represent a useful resource for dissection of the regulatory mechanisms underlying phenotypic variation.

Molecular Mechanisms of Regulation of Root Development by Plant Peptides

Peptides perform many functions, participating in the regulation of cell differentiation, regulating plant growth and development, and also involved in the response to stress factors and in antimicrobial defense. Peptides are an important class biomolecules for intercellular communication and in the transmission of various signals. The intercellular communication system based on the ligand-receptor bond is one of the most important molecular bases for creating complex multicellular organisms. Peptide-mediated intercellular communication plays a critical role in the coordination and determination of cellular functions in plants. The intercellular communication system based on the receptor-ligand is one of the most important molecular foundations for creating complex multicellular organisms. Peptide-mediated intercellular communication plays a critical role in the coordination and determination of cellular functions in plants. The identification of peptide hormones, their interaction with receptors, and the molecular mechanisms of peptide functioning are important for understanding the mechanisms of both intercellular communications and for regulating plant development. In this review, we drew attention to some peptides involved in the regulation of root development, which implement this regulation by the mechanism of a negative feedback loop.

Genome-wide characterization and identification of Trihelix transcription factors and expression profiling in response to abiotic stresses in Chinese Willow (Salix matsudana Koidz)

Trihelix transcription factors (TTF) are a class of light-responsive proteins with a typical triple-helix structure (helix-loop-helix-loop-helix). Members of this gene family play an important role in plant growth and development, especially in various abiotic stress responses. Salix matsudana Koidz is an allotetraploid ornamental forest tree that is widely planted for its excellent resistance to stress, but no studies on its Trihelix gene family have been reported. In this study, the Trihelix gene family was analyzed at the genome-wide level in S. matsudana. A total of 78 S. matsudana Trihelix transcription factors (SmTTFs) were identified, distributed on 29 chromosomes, and classified into four subfamilies (GT-1, GT-2, SH4, SIP1) based on their structural features. The gene structures and conserved functional domains of these Trihelix genes are similar in the same subfamily and differ between subfamilies. The presence of multiple stress-responsive cis-elements on the promoter of the S. matsudana Trihelix gene suggests that the S. matsudana Trihelix gene may respond to abiotic stresses. Expression pattern analysis revealed that Trihelix genes have different functions during flooding stress, salt stress, drought stress and low temperature stress in S. matsudana. Given that SmTTF30, as a differentially expressed gene, has a faster response to flooding stress, we selected SmTTF30 for functional studies. Overexpression of SmTTF30 in Arabidopsis thaliana (Arabidopsis) enhances its tolerance to flooding stress. Under flooding stress, the leaf cell activity and peroxidase activity (POD) of the overexpression strain were significantly higher than the leaf cell activity and POD of the wild type, and the malondialdehyde (MDA) content was significantly lower than the MDA content of the wild type. Thus, these results suggest that SmTTF30 enhances plant flooding tolerance and plays a positive regulatory role in plant flooding tolerance.

Coregulation of glutamine synthetase1;2 (GLN1;2) and NADH-dependent glutamate synthase (GLT1) gene expression in Arabidopsis roots in response to ammonium supply

Ammonium absorbed by roots is assimilated into amino acids. The glutamine synthetase/glutamate synthase (glutamine 2-oxoglutarate aminotransferase) (GS/GOGAT) cycle is essential to this biological process. In Arabidopsis thaliana, GLN1;2 and GLT1 are the GS and GOGAT isoenzymes induced in response to ammonium supply and playing key roles in ammonium utilization. Although recent studies suggest gene regulatory networks involved in transcriptional regulation of ammonium-responsive genes, direct regulatory mechanisms for ammonium-induced expression of GS/GOGAT remain unclear. In this study, we revealed that the expression of GLN1;2 and GLT1 in Arabidopsis is not directly induced by ammonium but is regulated by glutamine or post-glutamine metabolites produced by ammonium assimilation. Previously, we identified a promoter region required for ammonium-responsive expression of GLN1;2. In this study, we further dissected the ammonium-responsive region of the GLN1;2 promoter and also performed a deletion analysis of the GLT1 promoter, which led to the identification of a conserved ammonium-responsive region. Yeast one-hybrid screening using the ammonium-responsive region of the GLN1;2 promoter as a decoy sequence revealed a trihelix family transcription factor DF1 that binds to this region. A putative DF1 binding site was also found in the ammonium-responsive region of the GLT1 promoter.

Genome-wide analysis of the 6B-INTERACTING PROTEIN1 gene family with functional characterization of MdSIP1-2 in Malus domestica

Trihelix transcription factors consist of five subfamilies, including GT-1, GT-2, SH4, GTγ, and SIP1, which play important roles in the responses to biotic and abiotic stresses, however, seldom is known about the role of the SIP1 genes in apples. In this study, 12 MdSIP1 genes were first identified in apples by genome-wide analysis, and contained conserved MYB/SANT-like domains. Expression patterns analyses showed that the MdSIP1 genes had different tissue expression patterns, and different transcription levels in response to abiotic stresses, indicating that MdSIP1s may play multiple roles under various abiotic stresses. Among them, the MdSIP1-2 gene was cloned and ectopic transformed into Arabidopsis, and its biology function was identified. The subcellular localization showed that MdSIP1-2 protein was specifically localized in the nucleus, and that overexpression of MdSIP1-2 promoted the development of lateral roots, increased abscisic acid (ABA) sensitivity, and improved salt and drought tolerance. These findings suggested that MdSIP1-2 plays an important role in root development, ABA synthesis, and salt and drought stress tolerance. In conclusion, these results lay a solid foundation for determining the role of MdSIP1 in the growth and development and abiotic stress tolerance of apples.

Dynamics of alkannin/shikonin biosynthesis in response to jasmonate and salicylic acid in Lithospermum officinale

Alkannin/shikonin and their derivatives are specialised metabolites of high pharmaceutical and ecological importance exclusively produced in the periderm of members of the plant family Boraginaceae. Previous studies have shown that their biosynthesis is induced in response to methyl jasmonate but not salicylic acid, two phytohormones that play important roles in plant defence. However, mechanistic understanding of induction and non-induction remains largely unknown. In the present study, we generated the first comprehensive transcriptomic dataset and metabolite profiles of Lithospermum officinale plants treated with methyl jasmonate and salicylic acid to shed light on the underlying mechanisms. Our results highlight the diverse biological processes activated by both phytohormones and reveal the important regulatory role of the mevalonate pathway in alkannin/shikonin biosynthesis in L. officinale. Furthermore, by modelling a coexpression network, we uncovered structural and novel regulatory candidate genes connected to alkannin/shikonin biosynthesis. Besides providing new mechanistic insights into alkannin/shikonin biosynthesis, the generated methyl jasmonate and salicylic acid elicited expression profiles together with the coexpression networks serve as important functional genomic resources for the scientific community aiming at deepening the understanding of alkannin/shikonin biosynthesis.

Trihelix transcription factors GTL1 and DF1 prevent aberrant root hair formation in an excess nutrient condition

Root hair growth is tuned in response to the environment surrounding plants. While most previous studies focused on the enhancement of root hair growth during nutrient starvation, few studies investigated the root hair response in the presence of excess nutrients. We report that the post-embryonic growth of wild-type Arabidopsis plants is strongly suppressed with increasing nutrient availability, particularly in the case of root hair growth. We further used gene expression profiling to analyze how excess nutrient availability affects root hair growth, and found that RHD6 subfamily genes, which are positive regulators of root hair growth, are downregulated in this condition. However, defects in GTL1 and DF1, which are negative regulators of root hair growth, cause frail and swollen root hairs to form when excess nutrients are supplied. Additionally, we observed that the RHD6 subfamily genes are mis-expressed in gtl1-1 df1-1. Furthermore, overexpression of RSL4, an RHD6 subfamily gene, induces swollen root hairs in the face of a nutrient overload, while mutation of RSL4 in gtl1-1 df1-1 restore root hair swelling phenotype. In conclusion, our data suggest that GTL1 and DF1 prevent unnecessary root hair formation by repressing RSL4 under excess nutrient conditions.

Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) under abiotic stress conditions

Background

The trihelix family of transcription factors plays essential roles in the growth, development, and abiotic stress response of plants. Although several studies have been performed on the trihelix gene family in several dicots and monocots, this gene family is yet to be studied in Chenopodium quinoa (quinoa).

Results

In this study, 47 C. quinoa trihelix (CqTH) genes were in the quinoa genome. Phylogenetic analysis of the CqTH and trihelix genes from Arabidopsis thaliana and Beta vulgaris revealed that the genes were clustered into five subfamilies: SIP1, GTγ, GT1, GT2, and SH4. Additionally, synteny analysis revealed that the CqTH genes were located on 17 chromosomes, with the exception of chromosomes 8 and 11, and 23 pairs of segmental duplication genes were detected. Furthermore, expression patterns of 10 CqTH genes in different plant tissues and at different developmental stages under abiotic stress and phytohormone treatment were examined. Among the 10 genes, CqTH02, CqTH25, CqTH18, CqTH19, CqTH25, CqTH31, and CqTH36, were highly expressed in unripe achenes 21 d after flowering and in mature achenes compared with other plant tissues. Notably, the 10 CqTH genes were upregulated in UV-treated leaves, whereas CqTH36 was consistently upregulated in the leaves under all abiotic stress conditions.

Conclusions

The findings of this study suggest that gene duplication could be a major driver of trihelix gene evolution in quinoa. These findings could serve as a basis for future studies on the roles of CqTH transcription factors and present potential genetic markers for breeding stress-resistant and high-yielding quinoa varieties.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08726-y.

A DE1 BINDING FACTOR 1-GLABRA2 module regulates rhamnogalacturonan I biosynthesis in Arabidopsis seed coat mucilage

The mucilage surrounding hydrated Arabidopsis thaliana seeds is a specialized extracellular matrix composed mainly of the pectic polysaccharide rhamnogalacturonan I (RG-I). Although, several genes responsible for RG-I biosynthesis have been identified, the transcriptional regulatory mechanisms controlling RG-I production remain largely unknown. Here we report that the trihelix transcription factor DE1 BINDING FACTOR 1 (DF1) is a key regulator of mucilage RG-I biosynthesis. RG-I biosynthesis is significantly reduced in loss-of-function mutants of DF1. DF1 physically interacts with GLABRA2 (GL2) and both proteins transcriptionally regulate the expression of the RG-I biosynthesis genes MUCILAGE MODIFIED 4 (MUM4) and GALACTURONOSYLTRANSFERASE-LIKE5 (GATL5). Through chromatin immunoprecipitation-quantitative PCR and transcriptional activation assays, we uncover a cooperative mechanism of the DF1-GL2 module in activating MUM4 and GATL5 expression, in which DF1 binds to the promoters of MUM4 and GATL5 through interacting with GL2 and facilitates the transcriptional activity of GL2. The expression of DF1 and GL2 is directly regulated by TRANSPARENT TESTA GLABRA2 (TTG2) and, in turn, DF1 directly represses the expression of TTG2. Taken together, our data reveal that the transcriptional regulation of mucilage RG-I biosynthesis involves a regulatory module, comprising DF1, GL2, and TTG2.

Short Peptides Induce Development of Root Hair Nicotiana tabacum

Root hairs absorb soil nutrients and water, and anchor the plant in the soil. Treatment of tobacco (Nicotiana tabacum) roots with glycine (Gly) amino acid, and glycilglycine (GlyGly) and glycilaspartic acid (GlyAsp) dipeptides (10⁻⁷ M concentration) significantly increased the development of root hairs. In the root, peptide accumulation was tissue-specific, with predominant localization to the root cap, meristem, elongation zone, and absorption zone. Peptides penetrated the epidermal and cortical cell and showed greater localization to the nucleus than to the cytoplasm. Compared with the control, tobacco plants grown in the presence of Gly, GlyGly, and GlyAsp exhibited the activation of WER, CPC, bHLH54, and bHLH66 genes and suppression of GTL1 and GL2 genes during root hair lengthening. Although Gly, GlyGly, and GlyAsp have a similar structure, the mechanism of regulation of root hair growth in each case were different, and these differences are most likely due to the fact that neutral Gly and GlyGly and negatively charged GlyAsp bind to different motives of functionally important proteins. Short peptides site-specifically interact with DNA, and histones. The molecular mechanisms underlying the effect of exogenous peptides on cellular processes remain unclear. Since these compounds acted at low concentrations, gene expression regulation by short peptides is most likely of epigenetic nature.

A phosphorus-limitation induced, functionally conserved DUF506 protein is a repressor of root hair elongation in plants

Root hairs (RHs) function in nutrient and water acquisition, root metabolite exudation, soil anchorage and plant-microbe interactions. Longer or more abundant RHs are potential breeding traits for developing crops that are more resource-use efficient and can improve soil health. While many genes are known to promote RH elongation, relatively little is known about genes and mechanisms that constrain RH growth. Here we demonstrate that a DOMAIN OF UNKNOWN FUNCTION 506 (DUF506) protein, AT3G25240, negatively regulates Arabidopsis thaliana RH growth. The AT3G25240 gene is strongly and specifically induced during phosphorus (P)-limitation. Mutants of this gene, which we call REPRESSOR OF EXCESSIVE ROOT HAIR ELONGATION 1 (RXR1), have much longer RHs, higher phosphate content and seedling biomass, while overexpression of the gene exhibits opposite phenotypes. Co-immunoprecipitation, pull-down and bimolecular fluorescence complementation (BiFC) analyses reveal that RXR1 physically interacts with a RabD2c GTPase in nucleus, and a rabd2c mutant phenocopies the rxr1 mutant. Furthermore, N-terminal variable region of RXR1 is crucial for inhibiting RH growth. Overexpression of a Brachypodium distachyon RXR1 homolog results in repression of RH elongation in Brachypodium. Taken together, our results reveal a novel DUF506-GTPase module with a prominent role in repression of plant RH elongation especially under P stress.

Future Challenges in Plant Systems Biology

Plant systems biology is currently facing several important challenges, whose nature depend on the considered frame of reference and associated scale. This review covers some of the issues associated respectively with the molecular, tissue, and whole-plant scales, as well as discusses the potential for latest advances in synthetic biology and machine-learning methods to be of use in the future of plant systems biology.

A Tree Peony Trihelix Transcription Factor PrASIL1 Represses Seed Oil Accumulation

In many higher plants, seed oil accumulation is governed by complex multilevel regulatory networks including transcriptional regulation, which primarily affects fatty acid biosynthesis. Tree peony (Paeonia rockii), a perennial deciduous shrub endemic to China is notable for its seed oil that is abundant in unsaturated fatty acids. We discovered that a tree peony trihelix transcription factor, PrASIL1, localized in the nucleus, is expressed predominantly in developing seeds during maturation. Ectopic overexpression of PrASIL1 in Nicotiana benthamiana leaf tissue and Arabidopsis thaliana seeds significantly reduced total fatty acids and altered the fatty acid composition. These changes were in turn associated with the decreased expression of multitudinous genes involved in plastidial fatty acid synthesis and oil accumulation. Thus, we inferred that PrASIL1 is a critical transcription factor that represses oil accumulation by down-regulating numerous key genes during seed oil biosynthesis. In contrary, up-regulation of oil biosynthesis genes and a significant increase in total lipids and several major fatty acids were observed in PrASIL1-silenced tree peony leaves. Together, these results provide insights into the role of trihelix transcription factor PrASIL1 in controlling seed oil accumulation. PrASIL1 can be targeted potentially for oil enhancement in tree peony and other crops through gene manipulation.

HOMEOBOX PROTEIN 24 mediates the conversion of indole-3-butyric acid to indole-3-acetic acid to promote root hair elongation

Indole-3-acetic acid (IAA) is a predominant form of active auxin in plants. In addition to de novo biosynthesis and release from its conjugate forms, IAA can be converted from its precursor indole-3-butyric acid (IBA). The IBA-derived IAA may help drive root hair elongation in Arabidopsis thaliana seedlings, but how the IBA-to-IAA conversion is regulated and affects IAA function requires further investigation. In this study, HOMEOBOX PROTEIN 24 (HB24), a transcription factor in the zinc finger-homeodomain family (ZF-HD family) of proteins, was identified. With loss of HB24 function, defective growth occurred in root hairs. INDOLE-3-BUTYRIC ACID RESPONSE 1 (IBR1), which encodes an enzyme involved in the IBA-to-IAA conversion, was identified as a direct target of HB24 for the control of root hair elongation. The exogenous IAA or auxin analogue 1-naphthalene acetic acid (NAA) both rescued the root hair growth phenotype of hb24 mutants, but IBA did not, suggesting a role for HB24 in the IBA-to-IAA conversion. Therefore, HB24 participates in root hair elongation by upregulating the expression of IBR1 and subsequently promoting the IBA-to-IAA conversion. Moreover, IAA also elevated the expression of HB24, suggesting a feedback loop is involved in IBA-to-IAA conversion-mediated root hair elongation.

Real-time tracking of root hair nucleus morphodynamics using a microfluidic approach

Root hairs (RHs) are tubular extensions of root epidermal cells that favour nutrient uptake and microbe interactions. RHs show a fast apical growth, constituting a unique single cell model system for analysing cellular morphodynamics. In this context, live cell imaging using microfluidics recently developed to analyze root development is appealing, although high-resolution imaging is still lacking to enable an investigation of the accurate spatiotemporal morphodynamics of organelles. Here, we provide a powerful coverslip based microfluidic device (CMD) that enables us to capture high resolution confocal imaging of Arabidopsis RH development with real-time monitoring of nuclear movement and shape changes. To validate the setup, we confirmed the typical RH growth rates and the mean nuclear positioning previously reported with classical methods. Moreover, to illustrate the possibilities offered by the CMD, we have compared the real-time variations in the circularity, area and aspect ratio of nuclei moving in growing and mature RHs. Interestingly, we observed higher aspect ratios in the nuclei of mature RHs, correlating with higher speeds of nuclear migration. This observation opens the way for further investigations of the effect of mechanical constraints on nuclear shape changes during RH growth and nuclear migration and its role in RH and plant development.

Spatial and temporal localization of SPIRRIG and WAVE/SCAR reveal roles for these proteins in actin-mediated root hair development

Root hairs are single-cell protrusions that enable roots to optimize nutrient and water acquisition. These structures attain their tubular shapes by confining growth to the cell apex, a process called tip growth. The actin cytoskeleton and endomembrane systems are essential for tip growth; however, little is known about how these cellular components coordinate their activities during this process. Here, we show that SPIRRIG (SPI), a beige and Chediak Higashi domain-containing protein involved in membrane trafficking, and BRK1 and SCAR2, subunits of the WAVE/SCAR (W/SC) actin nucleating promoting complex, display polarized localizations in Arabidopsis thaliana root hairs during distinct developmental stages. SPI accumulates at the root hair apex via post-Golgi compartments and positively regulates tip growth by maintaining tip-focused vesicle secretion and filamentous-actin integrity. BRK1 and SCAR2 on the other hand, mark the root hair initiation domain to specify the position of root hair emergence. Consistent with the localization data, tip growth was reduced in spi and the position of root hair emergence was disrupted in brk1 and scar1234. BRK1 depletion coincided with SPI accumulation as root hairs transitioned from initiation to tip growth. Taken together, our work uncovers a role for SPI in facilitating actin-dependent root hair development in Arabidopsis through pathways that might intersect with W/SC.

Nitrate triggered phosphoproteome changes and a PIN2 phosphosite modulating root system architecture

Nitrate commands genome‐wide gene expression changes that impact metabolism, physiology, plant growth, and development. In an effort to identify new components involved in nitrate responses in plants, we analyze the Arabidopsis thaliana root phosphoproteome in response to nitrate treatments via liquid chromatography coupled to tandem mass spectrometry. 176 phosphoproteins show significant changes at 5 or 20 min after nitrate treatments. Proteins identified by 5 min include signaling components such as kinases or transcription factors. In contrast, by 20 min, proteins identified were associated with transporter activity or hormone metabolism functions, among others. The phosphorylation profile of NITRATE TRANSPORTER 1.1 (NRT1.1) mutant plants was significantly altered as compared to wild‐type plants, confirming its key role in nitrate signaling pathways that involves phosphorylation changes. Integrative bioinformatics analysis highlights auxin transport as an important mechanism modulated by nitrate signaling at the post‐translational level. We validated a new phosphorylation site in PIN2 and provide evidence that it functions in primary and lateral root growth responses to nitrate.

Recognizing the hidden half in wheat: root system attributes associated with drought tolerance

Improving drought tolerance in wheat is crucial for maintaining productivity and food security. Roots are responsible for the uptake of water from soil, and a number of root traits are associated with drought tolerance. Studies have revealed many quantitative trait loci and genes controlling root development in plants. However, the genetic dissection of root traits in response to drought in wheat is still unclear. Here, we review crop root traits associated with drought, key genes governing root development in plants, and quantitative trait loci and genes regulating root system architecture under water-limited conditions in wheat. Deep roots, optimal root length density and xylem diameter, and increased root surface area are traits contributing to drought tolerance. In view of the diverse environments in which wheat is grown, the balance among root and shoot traits, as well as individual and population performance, are discussed. The known functions of key genes provide information for the genetic dissection of root development of wheat in a wide range of conditions, and will be beneficial for molecular marker development, marker-assisted selection, and genetic improvement in breeding for drought tolerance.

Characterization of the development dynamics within the linear growth bamboo leaf

The leaf is the main photosynthetic organ in plants, such as bamboo. Leaves from bamboo are used as a food additive. However, according to our investigation, to date there have been no reports concerning the leaf development of bamboo. By measuring over 7500 parenchymal cells, we discovered that the linear leaf growth of Pseudosasa japonica could be divided into three growth sections. The first one is a roughly 1-cm long division zone (DZ), containing about 1580 cells, located at the bottom of the leaf; the second one is an about 3-cm long elongation zone (EZ), with ~1905 cells, located above the DZ; and the last is a mature zone (MZ) in which cell elongation is completed. The cell production rate of the DZ was 25.33-35.81 cells per hour, with an average of 29.73; and the cell division rate was ~0.45 cells per cell every 24 h. PacBio and Illumina transcriptome sequencing found 21 933 unigenes expressed in these zones. Further analysis revealed a dynamic transcriptome, with transcripts for cell division in the DZ changing to transcripts for cell elongation, photosynthetic development, secondary metabolism, stress resistance, and nutrition transport toward the leaf distal. Those transcriptome transformations correlated well with the changes of relative water content, biomass accumulation, and cellulose crystal degree and were supported by quantitative polymerase chain reaction data. These results revealed a developmental gradient of the bamboo linear growth leaf, which offers a foundation to elucidate and engineer leaf development in bamboo, an economically valuable plant.

Inferring and analyzing gene regulatory networks from multi-factorial expression data: a complete and interactive suite

Background

High-throughput transcriptomic datasets are often examined to discover new actors and regulators of a biological response. To this end, graphical interfaces have been developed and allow a broad range of users to conduct standard analyses from RNA-seq data, even with little programming experience. Although existing solutions usually provide adequate procedures for normalization, exploration or differential expression, more advanced features, such as gene clustering or regulatory network inference, often miss or do not reflect current state of the art methodologies.

Results

We developed here a user interface called DIANE (Dashboard for the Inference and Analysis of Networks from Expression data) designed to harness the potential of multi-factorial expression datasets from any organisms through a precise set of methods. DIANE interactive workflow provides normalization, dimensionality reduction, differential expression and ontology enrichment. Gene clustering can be performed and explored via configurable Mixture Models, and Random Forests are used to infer gene regulatory networks. DIANE also includes a novel procedure to assess the statistical significance of regulator-target influence measures based on permutations for Random Forest importance metrics. All along the pipeline, session reports and results can be downloaded to ensure clear and reproducible analyses.

Conclusions

We demonstrate the value and the benefits of DIANE using a recently published data set describing the transcriptional response of Arabidopsis thaliana under the combination of temperature, drought and salinity perturbations. We show that DIANE can intuitively carry out informative exploration and statistical procedures with RNA-Seq data, perform model based gene expression profiles clustering and go further into gene network reconstruction, providing relevant candidate genes or signalling pathways to explore. DIANE is available as a web service (https://diane.bpmp.inrae.fr), or can be installed and locally launched as a complete R package.

Supplementary Information

The online version contains supplementary material available at (10.1186/s12864-021-07659-2).

Auxin-Environment Integration in Growth Responses to Forage for Resources

Plant fitness depends on the adequate morphological adjustment to the prevailing conditions of the environment. Therefore, plants sense environmental cues through their life cycle, including the presence of full darkness, light, or shade, the range of ambient temperatures, the direction of light and gravity vectors, and the presence of water and mineral nutrients (such as nitrate and phosphate) in the soil. The environmental information impinges on different aspects of the auxin system such as auxin synthesis, degradation, transport, perception, and downstream transcriptional regulation to modulate organ growth. Although a single environmental cue can affect several of these points, the relative impacts differ significantly among the various growth processes and cues. While stability in the generation of precise auxin gradients serves to guide the basic developmental pattern, dynamic changes in the auxin system fine-tune body shape to optimize the capture of environmental resources.

The Wheat GENIE3 Network Provides Biologically-Relevant Information in Polyploid Wheat

Gene regulatory networks are powerful tools which facilitate hypothesis generation and candidate gene discovery. However, the extent to which the network predictions are biologically relevant is often unclear. Recently a GENIE3 network which predicted targets of wheat transcription factors was produced. Here we used an independent RNA-Seq dataset to test the predictions of the wheat GENIE3 network for the senescence-regulating transcription factor NAM-A1 (TraesCS6A02G108300). We re-analyzed the RNA-Seq data against the RefSeqv1.0 genome and identified a set of differentially expressed genes (DEGs) between the wild-type and nam-a1 mutant which recapitulated the known role of NAM-A1 in senescence and nutrient remobilisation. We found that the GENIE3-predicted target genes of NAM-A1 overlap significantly with the DEGs, more than would be expected by chance. Based on high levels of overlap between GENIE3-predicted target genes and the DEGs, we identified candidate senescence regulators. We then explored genome-wide trends in the network related to polyploidy and found that only homeologous transcription factors are likely to share predicted targets in common. However, homeologs which vary in expression levels across tissues are less likely to share predicted targets than those that do not, suggesting that they may be more likely to act in distinct pathways. This work demonstrates that the wheat GENIE3 network can provide biologically-relevant predictions of transcription factor targets, which can be used for candidate gene prediction and for global analyses of transcription factor function. The GENIE3 network has now been integrated into the KnetMiner web application, facilitating its use in future studies.

Network-based approaches for understanding gene regulation and function in plants

Expression reprogramming directed by transcription factors is a primary gene regulation underlying most aspects of the biology of any organism. Our views of how gene regulation is coordinated are dramatically changing thanks to the advent and constant improvement of high-throughput profiling and transcriptional network inference methods: from activities of individual genes to functional interactions across genes. These technical and analytical advances can reveal the topology of transcriptional networks in which hundreds of genes are hierarchically regulated by multiple transcription factors at systems level. Here we review the state of the art of experimental and computational methods used in plant biology research to obtain large-scale datasets and model transcriptional networks. Examples of direct use of these network models and perspectives on their limitations and future directions are also discussed.

Autocrine regulation of root hair size by the RALF-FERONIA-RSL4 signaling pathway

Root hair (RH) size has vital physiological implications, since it influences the surface area of the root and thus the ability of the plant to absorb water and nutrients from the soil. Arabidopsis ROOT HAIR DEFECTIVE 6-LIKE 4 (RSL4), a bHLH transcription factor, controls the expression of hundreds of RH genes, and RSL4 expression itself can trigger ectopic RH growth. Recent studies reveal an autocrine mechanism governing plant RH cell growth in which the extracellular peptide RAPID ALKALINIZATION FACTOR 1 (RALF1) and receptor FERONIA (FER) act as a central hub between the cell surface and downstream signaling events. RALF1-FER promotes the phosphorylation of eIF4E1. Then, phosphorylated eIF4E1 further regulates the synthesis of RH proteins, including RSL4, to promote RH growth. High levels of RSL4 exert a negative feedback on RALF1 expression via directly binding to the RALF1 gene promoter, slowing RH growth and determining final RH cell size.

Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation

Root architecture varies widely between species; it even varies between ecotypes of the same species, despite strong conservation of the coding portion of their genomes. By contrast, noncoding RNAs evolve rapidly between ecotypes and may control their differential responses to the environment, since several long noncoding RNAs (lncRNAs) are known to quantitatively regulate gene expression. Roots from ecotypes Columbia and Landsberg erecta of Arabidopsis (Arabidopsis thaliana) respond differently to phosphate starvation. Here, we compared transcriptomes (mRNAs, lncRNAs, and small RNAs) of root tips from these two ecotypes during early phosphate starvation. We identified thousands of lncRNAs that were largely conserved at the DNA level in these ecotypes. In contrast to coding genes, many lncRNAs were specifically transcribed in one ecotype and/or differentially expressed between ecotypes independent of phosphate availability. We further characterized these ecotype-related lncRNAs and studied their link with small interfering RNAs. Our analysis identified 675 lncRNAs differentially expressed between the two ecotypes, including antisense RNAs targeting key regulators of root-growth responses. Misregulation of several lincRNAs showed that at least two ecotype-related lncRNAs regulate primary root growth in ecotype Columbia. RNA-sequencing analysis following deregulation of lncRNA NPC48 revealed a potential link with root growth and transport functions. This exploration of the noncoding transcriptome identified ecotype-specific lncRNA-mediated regulation in root apexes. The noncoding genome may harbor further mechanisms involved in ecotype adaptation of roots to different soil environments.

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions

The regulation of gene expression is central to many biological processes. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes and represent maps of potential transcriptional regulation. Here, we analyzed a large number of publically available maize (Zea mays) transcriptome data sets including >6000 RNA sequencing samples to generate 45 coexpression-based GRNs that represent potential regulatory relationships between TFs and other genes in different populations of samples (cross-tissue, cross-genotype, and tissue-and-genotype samples). While these networks are all enriched for biologically relevant interactions, different networks capture distinct TF-target associations and biological processes. By examining the power of our coexpression-based GRNs to accurately predict covarying TF-target relationships in natural variation data sets, we found that presence/absence changes rather than quantitative changes in TF gene expression are more likely associated with changes in target gene expression. Integrating information from our TF-target predictions and previous expression quantitative trait loci (eQTL) mapping results provided support for 68 TFs underlying 74 previously identified trans-eQTL hotspots spanning a variety of metabolic pathways. This study highlights the utility of developing multiple GRNs within a species to detect putative regulators of important plant pathways and provides potential targets for breeding or biotechnological applications.

A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virus

Resistance genes are an effective means for disease control in plants. They predominantly function by inducing a hypersensitive reaction, which results in localized cell death restricting pathogen spread. Some resistance genes elicit an atypical response, termed extreme resistance, where resistance is not associated with a hypersensitive reaction and its standard defense responses. Unlike hypersensitive reaction, the molecular regulatory mechanism(s) underlying extreme resistance is largely unexplored. One of the few known, naturally occurring, instances of extreme resistance is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent Soybean mosaic virus strains. To discern the regulatory mechanism underlying Rsv3-mediated extreme resistance, we generated a gene regulatory network using transcriptomic data from time course comparisons of Soybean mosaic virus-G7-inoculated resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. Our results show Rsv3 begins mounting a defense by 6 hpi via a complex phytohormone network, where abscisic acid, cytokinin, jasmonic acid, and salicylic acid pathways are suppressed. We identified putative regulatory interactions between transcription factors and genes in phytohormone regulatory pathways, which is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. One such transcription factor identified as a putative transcriptional regulator was MYC2 encoded by Glyma.07G051500. Known as a master regulator of abscisic acid and jasmonic acid signaling, MYC2 specifically recognizes the G-box motif ("CACGTG"), which was significantly enriched in our data among differentially expressed genes implicated in abscisic acid- and jasmonic acid-related activities. This suggests an important role for Glyma.07G051500 in abscisic acid- and jasmonic acid-derived defense signaling in Rsv3. Resultantly, the findings from our network offer insights into genes and biological pathways underlying the molecular defense mechanism of Rsv3-mediated extreme resistance against Soybean mosaic virus. The computational pipeline used to reconstruct the gene regulatory network in this study is freely available at https://github.com/LiLabAtVT/rsv3-network.

A transcriptional regulatory network of Rsv3-mediated extreme resistance against Soybean mosaic virus

Resistance genes are an effective means for disease control in plants. They predominantly function by inducing a hypersensitive reaction, which results in localized cell death restricting pathogen spread. Some resistance genes elicit an atypical response, termed extreme resistance, where resistance is not associated with a hypersensitive reaction and its standard defense responses. Unlike hypersensitive reaction, the molecular regulatory mechanism(s) underlying extreme resistance is largely unexplored. One of the few known, naturally occurring, instances of extreme resistance is resistance derived from the soybean Rsv3 gene, which confers resistance against the most virulent Soybean mosaic virus strains. To discern the regulatory mechanism underlying Rsv3-mediated extreme resistance, we generated a gene regulatory network using transcriptomic data from time course comparisons of Soybean mosaic virus-G7-inoculated resistant (L29, Rsv3-genotype) and susceptible (Williams82, rsv3-genotype) soybean cultivars. Our results show Rsv3 begins mounting a defense by 6 hpi via a complex phytohormone network, where abscisic acid, cytokinin, jasmonic acid, and salicylic acid pathways are suppressed. We identified putative regulatory interactions between transcription factors and genes in phytohormone regulatory pathways, which is consistent with the demonstrated involvement of these pathways in Rsv3-mediated resistance. One such transcription factor identified as a putative transcriptional regulator was MYC2 encoded by Glyma.07G051500. Known as a master regulator of abscisic acid and jasmonic acid signaling, MYC2 specifically recognizes the G-box motif ("CACGTG"), which was significantly enriched in our data among differentially expressed genes implicated in abscisic acid- and jasmonic acid-related activities. This suggests an important role for Glyma.07G051500 in abscisic acid- and jasmonic acid-derived defense signaling in Rsv3. Resultantly, the findings from our network offer insights into genes and biological pathways underlying the molecular defense mechanism of Rsv3-mediated extreme resistance against Soybean mosaic virus. The computational pipeline used to reconstruct the gene regulatory network in this study is freely available at https://github.com/LiLabAtVT/rsv3-network.

Integrated multi-omics framework of the plant response to jasmonic acid

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.

Integrated multi-omics framework of the plant response to jasmonic acid

Understanding the systems-level actions of transcriptional responses to hormones provides insight into how the genome is reprogrammed in response to environmental stimuli. Here, we investigated the signalling pathway of the hormone jasmonic acid (JA), which controls a plethora of critically important processes in plants and is orchestrated by the transcription factor MYC2 and its closest relatives in Arabidopsis thaliana. We generated an integrated framework of the response to JA, which spans from the activity of master and secondary regulatory transcription factors, through gene expression outputs and alternative splicing, to protein abundance changes, protein phosphorylation and chromatin remodelling. We integrated time-series transcriptome analysis with (phospho)proteomic data to reconstruct gene regulatory network models. These enabled us to predict previously unknown points of crosstalk of JA to other signalling pathways and to identify new components of the JA regulatory mechanism, which we validated through targeted mutant analysis. These results provide a comprehensive understanding of how a plant hormone remodels cellular functions and plant behaviour, the general principles of which provide a framework for analyses of cross-regulation between other hormone and stress signalling pathways.

tuxnet: a simple interface to process RNA sequencing data and infer gene regulatory networks

Predicting gene regulatory networks (GRNs) from expression profiles is a common approach for identifying important biological regulators. Despite the increased use of inference methods, existing computational approaches often do not integrate RNA-sequencing data analysis, are not automated or are restricted to users with bioinformatics backgrounds. To address these limitations, we developed tuxnet, a user-friendly platform that can process raw RNA-sequencing data from any organism with an existing reference genome using a modified tuxedo pipeline (hisat 2 + cufflinks package) and infer GRNs from these processed data. tuxnet is implemented as a graphical user interface and can mine gene regulations, either by applying a dynamic Bayesian network (DBN) inference algorithm, genist, or a regression tree-based pipeline, rtp-star. We obtained time-course expression data of a PERIANTHIA (PAN) inducible line and inferred a GRN using genist to illustrate the use of tuxnet while gaining insight into the regulations downstream of the Arabidopsis root stem cell regulator PAN. Using rtp-star, we inferred the network of ATHB13, a downstream gene of PAN, for which we obtained wild-type and mutant expression profiles. Additionally, we generated two networks using temporal data from developmental leaf data and spatial data from root cell-type data to highlight the use of tuxnet to form new testable hypotheses from previously explored data. Our case studies feature the versatility of tuxnet when using different types of gene expression data to infer networks and its accessibility as a pipeline for non-bioinformaticians to analyze transcriptome data, predict causal regulations, assess network topology and identify key regulators.

Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks

Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play a crucial role in cell renewal, regeneration, and organization. A number of stem cell type-specific genes have a known role in stem cell maintenance, identity, and/or division. Yet, how genes expressed across different stem cell types, referred to here as stem-cell-ubiquitous genes, contribute to stem cell regulation is less understood. Here, we find that, in the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks. Development of a mathematical model of TCX2 expression allows us to show that TCX2 orchestrates the coordinated division of different stem cell types. Our results highlight that genes expressed across different stem cell types ensure cross-communication among cells, allowing them to divide and develop harmonically together.

Stem-cell-ubiquitous genes spatiotemporally coordinate division through regulation of stem-cell-specific gene networks

Stem cells are responsible for generating all of the differentiated cells, tissues, and organs in a multicellular organism and, thus, play a crucial role in cell renewal, regeneration, and organization. A number of stem cell type-specific genes have a known role in stem cell maintenance, identity, and/or division. Yet, how genes expressed across different stem cell types, referred to here as stem-cell-ubiquitous genes, contribute to stem cell regulation is less understood. Here, we find that, in the Arabidopsis root, a stem-cell-ubiquitous gene, TESMIN-LIKE CXC2 (TCX2), controls stem cell division by regulating stem cell-type specific networks. Development of a mathematical model of TCX2 expression allows us to show that TCX2 orchestrates the coordinated division of different stem cell types. Our results highlight that genes expressed across different stem cell types ensure cross-communication among cells, allowing them to divide and develop harmonically together.

Challenges of Translating Gene Regulatory Information into Agronomic Improvements

Improvement of agricultural species has exploited the genetic variation responsible for complex quantitative traits. Much of the functional variation is regulatory, in cis-regulatory elements and trans-acting factors that ultimately contribute to gene expression differences. However, the identification of gene regulatory network components that, when modulated, will increase plant productivity or resilience, is challenging, yet essential to provide increased predictive power for genome engineering approaches that are likely to benefit useful traits. Here, we discuss the opportunities and limitations of using data obtained from gene coexpression, transcription factor binding, and genome-wide association mapping analyses to predict regulatory interactions that impact crop improvement. It is apparent that a combination of information from these data types is necessary for the reliable identification and utilization of important regulatory interactions that underlie complex agronomic traits.

Inhibition of Pre-mRNA Splicing Promotes Root Hair Development in Arabidopsis thaliana

Root hairs protruding from epidermal cells increase the surface area for water absorption and nutrient uptake. Various environmental factors including light, oxygen concentration, carbon dioxide concentration, calcium and mycorrhizal associations promote root hair formation in Arabidopsis thaliana. Light regulates the expression of a large number of genes at the transcriptional and post-transcriptional levels; however, there is little information linking the light response to root hair development. In this study, we describe a novel mutant, light-sensitive root-hair development 1 (lrh1), that displays enhanced root hair development in response to light. Hypocotyl and root elongation was inhibited in the lrh1 mutant, which had a late flowering phenotype. We identified the gene encoding the p14 protein, a putative component of the splicing factor 3b complex essential for pre-mRNA splicing, as being responsible for the lrh1 phenotype. Indeed, regulation of alternative splicing was affected in lrh1 mutants and treatment with a splicing inhibitor mimicked the lrh1 phenotype. Genome-wide alterations in pre-mRNA splicing patterns including differential splicing events of light signaling- and circadian clock-related genes were found in lrh1 as well as a difference in transcriptional regulation of multiple genes including upregulation of essential genes for root hair development. These results suggest that pre-mRNA splicing is the key mechanism regulating root hair development in response to light signals.

Transcriptome profiling of Gossypium arboreum during fiber initiation and the genome-wide identification of trihelix transcription factors

Cotton fiber initiation is the first step in fiber development, and it determines the yield. Here, genome-wide transcriptome profiling of Gossypium arboreum was performed to determine the molecular basis of cotton fiber initiation. A comparison of the transcriptomes of fiber-bearing ovules at -0.5, 0, 0.5, 1, 1.5, 2, 2.5 and 3 d post-anthesis detected 12,049 differentially expressed genes that mainly participated in ribosome, carbon metabolism and amino acid biosynthesis pathways. Genes encoding alcohol dehydrogenase 1 and hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase, involving in fatty acid degradation and flavonoid biosynthesis, were enriched. Furthermore, 1049 differentially expressed transcription factors were identified. Among these, 17 were trihelix family transcription factors, which play important roles in plant development and responses to biotic and abiotic stresses. In total, 52 full-length trihelix genes, named as GaGTs, were identified in G. arboreum and located in 12 of the 13 cotton chromosomes. Transcriptomic data and a quantitative real-time PCR analysis indicated that several GaGTs were significantly induced during fiber initiation in G. arboreum. Thus, the genome-wide comprehensive analysis of gene expression in G. arboreum fiber initiation will serve as a useful resource for unraveling the functions of specific genes. The phylogenetic relationships and expression analyses of the G. arboreum trihelix genes established a solid foundation for future comprehensive functional analyses of the GaGTs.

A gene regulatory network for root hair development

Root hairs play important roles for the acquisition of nutrients, microbe interaction and plant anchorage. In addition, root hairs provide an excellent model system to study cell patterning, differentiation and growth. Arabidopsis root hairs have been thoroughly studied to understand how plants regulate cell fate and growth in response to environmental signals. Accumulating evidence suggests that a multi-layered gene regulatory network is the molecular secret to enable the flexible and adequate response to multiple signals. In this review, we describe the key transcriptional regulators controlling cell fate and/or cell growth of root hairs. We also discuss how plants integrate phytohormonal and environmental signals, such as auxin, ethylene and phosphate availability, and modulate the level of these transcriptional regulators to tune root hair development.

Plant Synthetic Biology: Quantifying the "Known Unknowns" and Discovering the "Unknown Unknowns"

Biosensors, advanced microscopy, and single- cell transcriptomics are advancing plant synthetic biology.

Recent advances in gene function prediction using context-specific coexpression networks in plants

Predicting gene functions from genome sequence alone has been difficult, and the functions of a large fraction of plant genes remain unknown. However, leveraging the vast amount of currently available gene expression data has the potential to facilitate our understanding of plant gene functions, especially in determining complex traits. Gene coexpression networks-created by integrating multiple expression datasets-connect genes with similar patterns of expression across multiple conditions. Dense gene communities in such networks, commonly referred to as modules, often indicate that the member genes are functionally related. As such, these modules serve as tools for generating new testable hypotheses, including the prediction of gene function and importance. Recently, we have seen a paradigm shift from the traditional "global" to more defined, context-specific coexpression networks. Such coexpression networks imply genetic correlations in specific biological contexts such as during development or in response to a stress. In this short review, we highlight a few recent studies that attempt to fill the large gaps in our knowledge about cellular functions of plant genes using context-specific coexpression networks.

Computational prediction of gene regulatory networks in plant growth and development

Plants integrate a wide range of cellular, developmental, and environmental signals to regulate complex patterns of gene expression. Recent advances in genomic technologies enable differential gene expression analysis at a systems level, allowing for improved inference of the network of regulatory interactions between genes. These gene regulatory networks, or GRNs, are used to visualize the causal regulatory relationships between regulators and their downstream target genes. Accordingly, these GRNs can represent spatial, temporal, and/or environmental regulations and can identify functional genes. This review summarizes recent computational approaches applied to different types of gene expression data to infer GRNs in the context of plant growth and development. Three stages of GRN inference are described: first, data collection and analysis based on the dataset type; second, network inference application based on data availability and proposed hypotheses; and third, validation based on in silico, in vivo, and in planta methods. In addition, this review relates data collection strategies to biological questions, organizes inference algorithms based on statistical methods and data types, discusses experimental design considerations, and provides guidelines for GRN inference with an emphasis on the benefits of integrative approaches, especially when a priori information is limited. Finally, this review concludes that computational frameworks integrating large-scale heterogeneous datasets are needed for a more accurate (e.g. fewer false interactions), detailed (e.g. discrimination between direct versus indirect interactions), and comprehensive (e.g. genetic regulation under various conditions and spatial locations) inference of GRNs.