LATERAL ROOT PRIMORDIA 1 of maize acts as a transcriptional activator in auxin signalling downstream of the Aux/IAA gene rootless with undetectable meristem 1

ZmPILS6 is an auxin efflux carrier required for maize root morphogenesis

Plant root systems play a pivotal role in plant physiology and exhibit diverse phenotypic traits. Understanding the genetic mechanisms governing root growth and development in model plants like maize is crucial for enhancing crop resilience to drought and nutrient limitations. This study focused on identifying and characterizing ZmPILS6, an annotated auxin efflux carrier, as a key regulator of various crown root traits in maize. ZmPILS6-modified roots displayed reduced network area and suppressed lateral root formation, which are desirable traits for the "steep, cheap, and deep" ideotype. The research revealed that ZmPILS6 localizes to the endoplasmic reticulum and plays a vital role in controlling the spatial distribution of indole-3-acetic acid (IAA or "auxin") in primary roots. The study also demonstrated that ZmPILS6 can actively efflux IAA when expressed in yeast. Furthermore, the loss of ZmPILS6 resulted in significant proteome remodeling in maize roots, particularly affecting hormone signaling pathways. To identify potential interacting partners of ZmPILS6, a weighted gene coexpression analysis was performed. Altogether, this research contributes to the growing knowledge of essential genetic determinants governing maize root morphogenesis, which is crucial for guiding agricultural improvement strategies.

Lateral root primordium: Formation, influencing factors and regulation

Roots are the primary determinants of water and nutrient uptake by plants. The structure of roots is largely determined by the repeated formation of new lateral roots (LR). A new lateral root primordium (LRP) is formed between the beginning and appearance of LR, which defines the organization and function of LR. Therefore, proper LRP morphogenesis is a crucial process for lateral root formation. The development of LRP is regulated by multiple factors, including hormone and environmental signals. Roots integrate signals and regulate growth and development. At the molecular level, many genes regulate the growth and development of root organs to ensure stable development plans, while also being influenced by various environmental factors. To gain a better understanding of the LRP formation and its influencing factors, this study summarizes previous research. The cell cycle involved in LRP formation, as well as the roles of ROS, auxin, other auxin-related plant hormones, and genetic regulation, are discussed in detail. Additionally, the effects of gravity, mechanical stress, and cell death on LRP formation are explored. Throughout the text unanswered or poorly understood questions are identified to guide future research in this area.

The fungal pathogen Ustilago maydis targets the maize corepressor RELK2 to modulate host transcription for tumorigenesis

Ustilago maydis is a biotrophic fungus that causes tumor formation on all aerial parts of maize. U. maydis secretes effector proteins during penetration and colonization to successfully overcome the plant immune response and reprogram host physiology to promote infection. In this study, we functionally characterized the U. maydis effector protein Topless (TPL) interacting protein 6 (Tip6). We found that Tip6 interacts with the N-terminus of RELK2 through its two Ethylene-responsive element binding factor-associated amphiphilic repression (EAR) motifs. We show that the EAR motifs are essential for the virulence function of Tip6 and critical for altering the nuclear distribution pattern of RELK2. We propose that Tip6 mimics the recruitment of RELK2 by plant repressor proteins, thus disrupting host transcriptional regulation. We show that a large group of AP2/ERF B1 subfamily transcription factors are misregulated in the presence of Tip6. Our study suggests a regulatory mechanism where the U. maydis effector Tip6 utilizes repressive domains to recruit the corepressor RELK2 to disrupt the transcriptional networks of the host plant.

Paenibacillus lentimorbus alleviates nutrient deficiency-induced stress in Zea mays by modulating root system architecture, auxin signaling, and metabolic pathways

KEY MESSAGE

Paenibacillus lentimorbus reprograms auxin signaling and metabolic pathways for modulating root system architecture to mitigate nutrient deficiency in maize crops. The arable land across the world is having deficiency and disproportionate nutrients, limiting crop productivity. In this study, the potential of plant growth-promoting rhizobacteria (PGPR) viz., Pseudomonas putida, Paenibacillus lentimorbus, and their consortium was explored for growth promotion in maize (Zea mays) under nutrient-deficient conditions. PGPR inoculation improved the overall health of plants under nutrient-deficient conditions. The PGPR inoculation significantly improved the root system architecture and also induced changes in root cortical aerenchyma. Based on plant growth and physiological parameters inoculation with P. lentimorbus performed better as compared to P. putida, consortium, and uninoculated control. Furthermore, expression of auxin signaling (rum1, rul1, lrp1, rtcs, rtcl) and root hair development (rth)-related genes modulated the root development process to improve nutrient acquisition and tolerance to nutrient-deficient conditions in P. lentimorbus inoculated maize plants. Further, GC-MS analysis indicated the involvement of metabolites including carbohydrates and organic acids due to the interaction between maize roots and P. lentimorbus under nutrient-deficient conditions. These findings affirm that P. lentimorbus enhance overall plant growth by modulating the root system of maize to provide better tolerance to nutrient-deficient condition.

Identification of SRS transcription factor family in Solanum lycopersicum, and functional characterization of their responses to hormones and abiotic stresses

The SHI RELATED SEQUENCE (SRS) family plays a vital role in the development of multiple plant organs such as floral meristem determinacy, organ morphogenesis, and signal transduction. Nevertheless, there is little understanding of the biological significance of tomato SRS family at this point. Our research identified eight SlSRS family members and classified them into three subfamilies based on phylogenetics, conserved motifs, and characteristic domain analysis. The intraspecies and interspecies collinearity analysis revealed clues of SRS family evolution. Many cis-elements related to hormones, stresses, and plant development can be found in the promoter region of SlSRS genes. All of eight SlSRS proteins were located in the nucleus and possessed transcriptional activity, half of which were transcriptional activators, and the other half were transcriptional repressors. Except for SlSRS1, which showed high transcript accumulation in vegetative organs, most SlSRS genes expressed ubiquitously in all flower organs. In addition, all SlSRS genes could significantly respond to at least four different plant hormones. Further, expression of SlSRS genes were regulated by various abiotic stress conditions. In summary, we systematically analyzed and characterized the SlSRS family, reviewed the expression patterns and preliminarily investigated the protein function, and provided essential information for further functional research of the tomato SRS genes in the determination of reproductive floral organs and the development of plants, and possibly other plants.

Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus

SRS (SHI-related sequence) transcription factors play a crucial role in plant growth, development, and abiotic stress response. Although Brassica napus (B. napus) is one of the most important oil crops in the world, the role of SRS genes in B. napus (BnSRS) has not been well investigated. Therefore, we employed a bioinformatics approach to identify BnSRS genes from genomic data and investigated their characteristics, functions, and expression patterns, to gain a better understanding of how this gene family is involved in plant development and growth. The results revealed that there were 34 BnSRS gene family members in the genomic sequence of B. napus, unevenly distributed throughout the sequence. Based on the phylogenetic analysis, these BnSRS genes could be divided into four subgroups, with each group sharing comparable conserved motifs and gene structure. Analysis of the upstream promoter region showed that BnSRS genes may regulate hormone responses, biotic and abiotic stress response, growth, and development in B. napus. The protein-protein interaction analysis revealed the involvement of BnSRS genes in various biological processes and metabolic pathways. Our analysis of BnSRS gene expression showed that 23 BnSRS genes in the callus tissue exhibited a dominant expression pattern, suggesting their critical involvement in cell dedifferentiation, cell division, and tissue development. In addition, association analysis between genotype and agronomic traits revealed that BnSRS genes may be linked to some important agronomic traits in B. napus, suggesting that BnSRS genes were widely involved in the regulation of important agronomic traits (including C16.0, C18.0, C18.1, C18.2 C18.3, C20.1, C22.1, GLU, protein, TSW, and FFT). In this study, we predicted the evolutionary relationships and potential functions of BnSRS gene family members, providing a basis for the development of BnSRS gene functions which could facilitate targeted functional studies and genetic improvement for elite breeding in B. napus.

A Wox3-patterning module organizes planar growth in grass leaves and ligules

Grass leaves develop from a ring of primordial initial cells within the periphery of the shoot apical meristem, a pool of organogenic stem cells that generates all of the organs of the plant shoot. At maturity, the grass leaf is a flattened, strap-like organ comprising a proximal supportive sheath surrounding the stem and a distal photosynthetic blade. The sheath and blade are partitioned by a hinge-like auricle and the ligule, a fringe of epidermally derived tissue that grows from the adaxial (top) leaf surface. Together, the ligule and auricle comprise morphological novelties that are specific to grass leaves. Understanding how the planar outgrowth of grass leaves and their adjoining ligules is genetically controlled can yield insight into their evolutionary origins. Here we use single-cell RNA-sequencing analyses to identify a 'rim' cell type present at the margins of maize leaf primordia. Cells in the leaf rim have a distinctive identity and share transcriptional signatures with proliferating ligule cells, suggesting that a shared developmental genetic programme patterns both leaves and ligules. Moreover, we show that rim function is regulated by genetically redundant Wuschel-like homeobox3 (WOX3) transcription factors. Higher-order mutations in maize Wox3 genes greatly reduce leaf width and disrupt ligule outgrowth and patterning. Together, these findings illustrate the generalizable use of a rim domain during planar growth of maize leaves and ligules, and suggest a parsimonious model for the homology of the grass ligule as a distal extension of the leaf sheath margin.

Genome-Wide Identification and Expression Analysis of the SHI-Related Sequence Family in Cassava

The SHORT INTERNODES (SHI)-related sequences (SRS) are plant-specific transcription factors that have been quantitatively characterized during plant growth, regeneration, and stress responses. However, the genome-wide discovery of SRS family genes and their involvement in abiotic stress-related activities in cassava have not been documented. A genome-wide search strategy was used to identify eight family members of the SRS gene family in cassava (Manihot esculenta Crantz). Based on their evolutionary linkages, all MeSRS genes featured homologous RING-like zinc finger and IXGH domains. Genetic architecture and conserved motif analysis validated the categorization of MeSRS genes into four groups. Eight pairs of segmental duplications were detected, resulting in an increase in the number of MeSRS genes. Orthologous studies of SRS genes among cassava and three different plant species (Arabidopsis thaliana, Oryza sativa, and Populus trichocarpa) provided important insights into the probable history of the MeSRS gene family. The functionality of MeSRS genes was elucidated through the prediction of protein–protein interaction networks and cis-acting domains. RNA-seq data demonstrated tissue/organ expression selectivity and preference of the MeSRS genes. Furthermore, qRT-PCR investigation of MeSRS gene expression after exposure to salicylic acid (SA) and methyl jasmonate (MeJA) hormone treatments, as well as salt (NaCl) and osmotic (polyethylene glycol, PEG) stresses, showed their stress-responsive patterns. This genome-wide characterization and identification of the evolutionary relationships and expression profiles of the cassava MeSRS family genes will be helpful for further research into this gene family and its function in stress response. It may also assist future agricultural efforts to increase the stress tolerance of cassava.

Positional cloning and characterization reveal the role of a miRNA precursor gene ZmLRT in the regulation of lateral root number and drought tolerance in maize

Lateral roots play essential roles in drought tolerance in maize (Zea mays L.). However, the genetic basis for the variation in the number of lateral roots in maize remains elusive. Here, we identified a major quantitative trait locus (QTL), qLRT5-1, controlling lateral root number using a recombinant inbred population from a cross between the maize lines Zong3 (with many lateral roots) and 87-1 (with few lateral roots). Fine-mapping and functional analysis determined that the candidate gene for qLRT5-1, ZmLRT, expresses the primary transcript for the microRNA miR166a. ZmLRT was highly expressed in root tips and lateral root primordia, and knockout and overexpression of ZmLRT increased and decreased lateral root number, respectively. Compared with 87-1, the ZmLRT gene model of Zong3 lacked the second and third exons and contained a 14 bp deletion at the junction between the first exon and intron, which altered the splicing site. In addition, ZmLRT expression was significantly lower in Zong3 than in 87-1, which might be attributed to the insertions of a transposon and over large DNA fragments in the Zong3 ZmLRT promoter region. These mutations decreased the abundance of mature miR166a in Zong3, resulting in increased lateral roots at the seedling stage. Furthermore, miR166a post-transcriptionally repressed five development-related class-III homeodomain-leucine zipper genes. Moreover, knockout of ZmLRT enhanced drought tolerance of maize seedlings. Our study furthers our understanding of the genetic basis of lateral root number variation in maize and highlights ZmLRT as a target for improving drought tolerance in maize.

The plant specific SHORT INTERNODES/STYLISH (SHI/STY) proteins: Structure and functions

Plant specific SHORT INTERNODES/STYLISH (SHI/STY) protein is a transcription factor involved in the formation and development of early lateral organs in plants. However, research on the SHI/STY protein family is not focused enough. In this article, we review recent studies on SHI/STY genes and explore the evolution and structure of SHI/STY. The biological functions of SHI/STYs are discussed in detail in this review, and the application of each biological function to modern agriculture is discussed. All SHI/STY proteins contain typical conserved RING-like zinc finger domain and IGGH domain. SHI/STYs are involved in the formation and development of lateral root, stem extension, leaf morphogenesis, and root nodule development. They are also involved in the regulation of pistil and stamen development and flowering time. At the same time, the regulation of some GA, JA, and auxin signals also involves these family proteins. For each aspect, unanswered or poorly understood questions were identified to help define future research areas. This review will provide a basis for further functional study of this gene family.

Genome-wide dissection of changes in maize root system architecture during modern breeding

Appropriate root system architecture (RSA) can improve maize yields in densely planted fields, but little is known about its genetic basis in maize. Here we performed root phenotyping of 14,301 field-grown plants from an association mapping panel to study the genetic architecture of maize RSA. A genome-wide association study identified 81 high-confidence RSA-associated candidate genes and revealed that 28 (24.3%) of known root-related genes were selected during maize domestication and improvement. We found that modern maize breeding has selected for a steeply angled root system. Favourable alleles related to steep root system angle have continuously accumulated over the course of modern breeding, and our data pinpoint the root-related genes that have been selected in different breeding eras. We confirm that two auxin-related genes, ZmRSA3.1 and ZmRSA3.2, contribute to the regulation of root angle and depth in maize. Our genome-wide identification of RSA-associated genes provides new strategies and genetic resources for breeding maize suitable for high-density planting.

Transcription Factor IAA27 Positively Regulates P Uptake through Promoted Adventitious Root Development in Apple Plants

Phosphate (P) deficiency severely limits the growth and production of plants. Adventitious root development plays an essential role in responding to low phosphorus stress for apple plants. However, the molecular mechanisms regulating adventitious root growth and development in response to low phosphorus stress have remained elusive. In this study, a mutation (C-T) in the coding region of the apple AUXIN/INDOLE-3-ACETIC ACID 27 (IAA27) gene was identified. MdIAA27T-overexpressing transgenic apple improved the tolerance to phosphorus deficiency, which grew longer and denser adventitious roots and presented higher phosphorous content than the control plants under low phosphorus conditions, while the overexpression of MdIAA27C displayed the opposite trend. Moreover, the heterologous overexpression of MdIAA27 in tobacco yielded the same results, supporting the aforementioned findings. In vitro and in vivo assays showed that MdIAA27 directly interacted with AUXIN RESPONSE FACTOR (ARF8), ARF26 and ARF27, which regulated Small Auxin-Up RNA 76 (MdSAUR76) and lateral organ boundaries domain 16 (MdLBD16) transcription. The mutation in IAA27 resulted in altered interaction modes, which in turn promoted the release of positive ARFs to upregulate SAUR76 and LBD16 expression in low phosphorus conditions. Altogether, our studies provide insights into how the allelic variation of IAA27 affects adventitious root development in response to low phosphorus stress.

Maize Seedling Growth and Hormone Response Assays Using the Rolled Towel Method

Root system architecture is a critical factor in maize health and stress resilience. Determining the genetic and environmental factors that shape maize root system architecture is an active research area. However, the ability to phenotype juvenile root systems is hindered by the use of field-grown and soil-based systems. An alternative to soil- and field-based growing conditions for maize seedlings is a controlled environment with a soil-free medium, which can facilitate root system phenotyping. Here, we describe how to grow maize under soil-free conditions for up to 12 days to facilitate root phenotyping. Maize seeds are sterilized and planted on specialized seed germination paper to minimize fungal contamination and ensure synchronized seedling growth, followed by imaging at the desired time point. The root images are then analyzed to quantify traits of interest, such as primary root length, lateral root density, seminal root length, and seminal root number. In addition, juvenile shoot traits can be quantified using manual annotation methods. We also outline the steps for performing rigorous hormone response assays for four classical phytohormones: auxin, brassinosteroid, cytokinin, and jasmonic acid. This protocol can be rapidly scaled up and is compatible with genetic screens and sample collection for downstream molecular analyses such as transcriptomics and proteomics. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Maize seedling rolled towel assay and phenotyping Basic Protocol 2: Maize seedling hormone response assays using the rolled towel assay.

Genome-wide identification, structural analysis and expression profiles of short internodes related sequence gene family in quinoa

Based on the whole genome data information of Chenopodium quinoa Willd, the CqSRS gene family members were systematically identified and analyzed by bioinformatics methods, and the responses of CqSRS genes to NaCl (100 mmol/L), salicylic acid (200 umol/L) and low temperature (4°C) were detected by qRT-PCR. The results showed that a total of 10 SHI related sequence genes were identified in quinoa, and they were distributed on 9 chromosomes, and there were four pairs of duplicated genes. The number of amino acids encoded ranged from 143 aa to 370 aa, and the isoelectric point ranged from 4.81 to 8.90. The secondary structure was mainly composed of random coil (Cc). Most of the SRS gene encoding proteins were located in the cytoplasm (5 CqSRS). Phylogenetic analysis showed that the CqSRS genes were divided into three groups, and the gene structure showed that the number of exons of CqSRS was between two-five. Promoter analysis revealed that there are a total of 44 elements related to plant hormone response elements, light response elements, stress response elements and tissue-specific expression in the upstream regin of the gene. Protein interaction showed that all 10 CqSRS proteins appeared in the known protein interaction network diagram in Arabidopsis. Expression profile analysis showed that CqSRS genes had different expression patterns, and some genes had tissue-specific expression. qRT-PCR showed that all SRS family genes responded to ABA、NaCl、drought and low-temperature treatments, but the expression levels of different CqSRS genes were significantly different under various stresses. This study lays a foundation for further analyzed the function of CqSRS genes.

Molecular evolutionary analysis of the SHI/STY gene family in land plants: A focus on the Brassica species

The plant-specific SHORT INTERNODES/STYLISH (SHI/STY) proteins belong to a family of transcription factors that are involved in the formation and development of early lateral roots. However, the molecular evolution of this family is rarely reported. Here, a total of 195 SHI/STY genes were identified in 21 terrestrial plants, and the Brassica species is the focus of our research. Their physicochemical properties, chromosome location and duplication, motif distribution, exon-intron structures, genetic evolution, and expression patterns were systematically analyzed. These genes are divided into four clades (Clade 1/2/3/4) based on phylogenetic analysis. Motif distribution and gene structure are similar in each clade. SHI/STY proteins are localized in the nucleus by the prediction of subcellular localization. Collinearity analysis indicates that the SHI/STYs are relatively conserved in evolution. Whole-genome duplication is the main factor for their expansion. SHI/STYs have undergone intense purifying selection, but several positive selection sites are also identified. Most promoters of SHI/STY genes contain different types of cis-elements, such as light, stress, and hormone-responsive elements, suggesting that they may be involved in many biological processes. Protein-protein interaction predicted some important SHI/STY interacting proteins, such as LPAT4, MBOATs, PPR, and UBQ3. In addition, the RNA-seq and qRT-PCR analysis were studied in detail in rape. As a result, SHI/STYs are highly expressed in root and bud, and can be affected by Sclerotinia sclerotiorum, drought, cold, and heat stresses. Moreover, quantitative real-time PCR (qRT-PCR) analyses indicates that expression levels of BnSHI/STYs are significantly altered in different treatments (cold, salt, drought, IAA, auxin; ABA, abscisic acid; 6-BA, cytokinin). It provides a new understanding of the evolution and expansion of the SHI/STY family in land plants and lays a foundation for further research on their functions.

Deconstructing the root system of grasses through an exploration of development, anatomy and function

Well-adapted root systems allow plants to grow under resource-limiting environmental conditions and are important determinants of yield in agricultural systems. Important staple crops such as rice and maize belong to the family of grasses, which develop a complex root system that consists of an embryonic root system that emerges from the seed, and a postembryonic nodal root system that emerges from basal regions of the shoot after germination. While early seedling establishment is dependent on the embryonic root system, the nodal root system, and its associated branches, gains in importance as the plant matures and will ultimately constitute the bulk of below-ground growth. In this review, we aim to give an overview of the different root types that develop in cereal grass root systems, explore the different physiological roles they play by defining their anatomical features, and outline the genetic networks that control their development. Through this deconstructed view of grass root system function, we provide a parts-list of elements that function together in an integrated root system to promote survival and crop productivity.

Temporal and spatial auxin responsive networks in maize primary roots

Auxin is a key regulator of root morphogenesis across angiosperms. To better understand auxin-regulated networks underlying maize root development, we have characterized auxin-responsive transcription across two time points (30 and 120 min) and four regions of the primary root: the meristematic zone, elongation zone, cortex and stele. Hundreds of auxin-regulated genes involved in diverse biological processes were quantified in these different root regions. In general, most auxin-regulated genes are region unique and are predominantly observed in differentiated tissues compared with the root meristem. Auxin gene regulatory networks were reconstructed with these data to identify key transcription factors that may underlie auxin responses in maize roots. Additionally, Auxin-Response Factor subnetworks were generated to identify target genes that exhibit tissue or temporal specificity in response to auxin. These networks describe novel molecular connections underlying maize root development and provide a foundation for functional genomic studies in a key crop.

Genome-Wide Identification and Expression Analysis of the SRS Gene Family in Medicago sativa

SHI-related sequence (SRS) transcription factors, specific to plants, act as crucial regulators of plant organ growth and development. Here, we examined the Medicago sativa (alfalfa) SRS gene family (MsSRSs) to analyze the structure and function of MsSRSs using bioinformatics methods, and verify their abiotic stress responses through growth experiments. Twenty-seven MsSRS genes were identified from the genome-wide data of nontransgenic alfalfa. MsSRSs were distributed on 16 chromosomes and classified into seven different subfamilies by phylogenetic analysis. Forty-five cis-regulatory elements related to stress and phytohormone responsiveness, and tissue-specific expression occurred in the promoter sequences of MsSRSs. Ks values and Ka/Ks ratios of duplicate gene pairs showed that purifying selection affected most duplicate genes during their evolutionary history, while rapid recent positive selection strongly influenced MsSRS25 and MsSRS01. Real-time fluorescence quantitative PCR results showed that MsSRS genes could be induced by cold and salt stress. Within 12 h of salt stress exposure, the expression levels of seven and nine MsSRSs showed significant upregulation and downregulation, respectively. Within 12 h of cold stress exposure, the expression levels of the 3 and 13 selected MsSRSs showed significant upregulation and downregulation, respectively. Thus, this study provides novel comprehensive information on the MsSRS gene family, helpful for the study of SRS-mediated tolerance in alfalfa and the functional characteristics of SRS genes in other plants.

Identification and Analysis of Zinc Efficiency-Associated Loci in Maize

Zinc (Zn) deficiency, a globally predominant micronutrient disorder in crops and humans, reduces crop yields and adversely impacts human health. Despite numerous studies on the physiological mechanisms underlying Zn deficiency tolerance, its genetic basis of molecular mechanism is still poorly understood. Thus, the Zn efficiency of 20 maize inbred lines was evaluated, and a quantitative trait locus (QTL) analysis was performed in the recombination inbred line population derived from the most Zn-efficient (Ye478) and Zn-inefficient inbred line (Wu312) to identify the candidate genes associated with Zn deficiency tolerance. On this basis, we analyzed the expression of ZmZIP1-ZmZIP8. Thirteen QTLs for the traits associated with Zn deficiency tolerance were detected, explaining 7.6-63.5% of the phenotypic variation. The genes responsible for Zn uptake and transport across membranes (ZmZIP3, ZmHMA3, ZmHMA4) were identified, which probably form a sophisticated network to regulate the uptake, translocation, and redistribution of Zn. Additionally, we identified the genes involved in the indole-3-acetic acid (IAA) biosynthesis (ZmIGPS) and auxin-dependent gene regulation (ZmIAA). Notably, a high upregulation of ZmZIP3 was found in the Zn-deficient root of Ye478, but not in that of Wu312. Additionally, ZmZIP4, ZmZIP5, and ZmZIP7 were up-regulated in the Zn-deficient roots of Ye478 and Wu312. Our findings provide a new insight into the genetic basis of Zn deficiency tolerance.

Synthesis and regulation of auxin and abscisic acid in maize

Indole-3-acetic acid (IAA), the primary auxin in higher plants, and abscisic acid (ABA) play crucial roles in the ability of maize (Zea mays L.) to acclimatize to various environments by mediating growth, development, defense and nutrient allocation. Although understanding the biochemical reactions for IAA and ABA biosynthesis and signal transduction has progressed, the mechanisms by which auxin and ABA are synthesized and transduced in maize have not been fully elucidated to date. The synthesis and signal transduction pathway of IAA and ABA in maize can be analyzed using an existing model. This article focuses on the research progress toward understanding the synthesis and signaling pathways of IAA and ABA, as well as IAA and ABA regulation of maize growth, providing insight for future development and the significance of IAA and ABA for maize improvement.

Auxin treatment of grapevine (Vitis vinifera L.) berries delays ripening onset by inhibiting cell expansion

Auxin treatment of grape (Vitis vinifera L.) berries delays ripening by inducing changes in gene expression and cell wall metabolism and could combat some deleterious climate change effects. Auxins are inhibitors of grape berry ripening and their application may be useful to delay harvest to counter effects of climate change. However, little is known about how this delay occurs. The expression of 1892 genes was significantly changed compared to the control during a 48 h time-course where the auxin 1-naphthaleneacetic acid (NAA) was applied to pre-veraison grape berries. Principal component analysis showed that the control and auxin-treated samples were most different at 3 h post-treatment when approximately three times more genes were induced than repressed by NAA. There was considerable cross-talk between hormone pathways, particularly between those of auxin and ethylene. Decreased expression of genes encoding putative cell wall catabolic enzymes (including those involved with pectin) and increased expression of putative cellulose synthases indicated that auxins may preserve cell wall structure. This was confirmed by immunochemical labelling of berry sections using antibodies that detect homogalacturonan (LM19) and methyl-esterified homogalacturonan (LM20) and by labelling with the CMB3a cellulose-binding module. Comparison of the auxin-induced changes in gene expression with the pattern of these genes during berry ripening showed that the effect on transcription is a mix of changes that may specifically alter the progress of berry development in a targeted manner and others that could be considered as non-specific changes. Several lines of evidence suggest that cell wall changes and associated berry softening are the first steps in ripening and that delaying cell expansion can delay ripening providing a possible mechanism for the observed auxin effects.

Transcriptomic profiling and discovery of key genes involved in adventitious root formation from green cuttings of highbush blueberry (Vaccinium corymbosum L.)

BACKGROUND

Propagation of cuttings is frequently used in various plant species, including blueberry, which shows special root characteristics that may hinder adventitious root (AR) formation. AR formation is influenced by various factors, and auxin is considered to play a central role; however, little is known of the related regulatory mechanisms. In this study, a comparative transcriptome analysis of green cuttings treated with or without indole-butyric acid (IBA) was performed via RNA_seq to identify candidate genes associated with IBA-induced AR formation.

RESULTS

Rooting phenotypes, especially the rooting rate, were significantly promoted by exogenous auxin in the IBA application. Blueberry AR formation was an auxin-induced process, during which adventitious root primordium initiation (rpi) began at 14 days after cutting (DAC), root primordium (rp) was developed at 21 DAC, mature AR was observed at 28 DAC and finally outgrowth from the stem occurred at 35 DAC. Higher IAA levels and lower ABA and zeatin contents might facilitate AR formation and development. A time series transcriptome analysis identified 14,970 differentially expressed genes (DEGs) during AR formation, of which there were 7467 upregulated and 7503 downregulated genes. Of these, approximately 35 candidate DEGs involved in the auxin-induced pathway and AR formation were further identified, including 10 auxin respective genes (ARFs and SAURs), 13 transcription factors (LOB domain-containing protein (LBDs)), 6 auxin transporters (AUX22, LAX3/5 and PIN-like 6 (PIL6s)) and 6 rooting-associated genes (root meristem growth factor 9 (RGF9), lateral root primordium 1 (LRP1s), and dormancy-associated protein homologue 3 (DRMH3)). All these identified DEGs were highly upregulated in certain stages during AR formation, indicating their potential roles in blueberry AR formation.

CONCLUSIONS

The transcriptome profiling results indicated candidate genes or major regulatory factors that influence adventitious root formation in blueberry and provided a comprehensive understanding of the rooting mechanism underlying the auxin-induced AR formation from blueberry green cuttings.

Auxin signaling modulates LATERAL ROOT PRIMORDIUM1 (LRP1) expression during lateral root development in Arabidopsis

Auxin signaling mediated by various auxin/indole-3-acetic acid (Aux/IAAs) and AUXIN RESPONSE FACTORs (ARFs) regulate lateral root (LR) development by controlling the expression of downstream genes. LATERAL ROOT PRIMORDIUM1 (LRP1), a member of the SHORT INTERNODES/STYLISH (SHI/STY) family, was identified as an auxin-inducible gene. The precise developmental role and molecular regulation of LRP1 in root development remain to be understood. Here we show that LRP1 is expressed in all stages of LR development, besides the primary root. The expression of LRP1 is regulated by histone deacetylation in an auxin-dependent manner. Our genetic interaction studies showed that LRP1 acts downstream of auxin responsive Aux/IAAs-ARFs modules during LR development. We showed that auxin-mediated induction of LRP1 is lost in emerging LRs of slr-1 and arf7arf19 mutants roots. NPA treatment studies showed that LRP1 acts after LR founder cell specification and asymmetric division during LR development. Overexpression of LRP1 (LRP1 OE) showed an increased number of LR primordia (LRP) at stages I, IV and V, resulting in reduced emerged LR density, which suggests that it is involved in LRP development. Interestingly, LRP1-induced expression of YUC4, which is involved in auxin biosynthesis, contributes to the increased accumulation of endogenous auxin in LRP1 OE roots. LRP1 interacts with SHI, STY1, SRS3, SRS6 and SRS7 proteins of the SHI/STY family, indicating their possible redundant role during root development. Our results suggested that auxin and histone deacetylation affect LRP1 expression and it acts downstream of LR forming auxin response modules to negatively regulate LRP development by modulating auxin homeostasis in Arabidopsis thaliana.

Gene coexpression network analysis reveals the role of SRS genes in senescence leaf of maize (Zea mays L.)

Shi-related sequence (SRS) proteins are plant-specific transcription factors that play important roles in developmental processes, including regulating hormone biosynthesis, response or signal transduction. However, systematical analysis of the SRS gene family in maize has not yet been conducted. In this study, 11 SRS genes with 13 transcripts were identified and characterized. The characteristics of the gene family were analysed in terms of phylogenetic relationships, chromosome distribution and gene structure. RNA-sequencing data analysis showed that the expression patterns of SRS genes were quite different from each other in maize, indicating their divergence in function. Interestingly, the GRMZM2G077752 gene is highly expressed in senescent leaves. Using further coexpression network analysis, we determined that the module containing GRMZM2G077752 were over-represented by genes related to abscisic acid (ABA) stimulus and carbohydrate metabolic process. This result indicated that GRMZM2G077752 might perceive ABA signal and cause the activation of carbohydrate remobilization during leaf ageing. This study provides valuable information for understanding the functions of the SRS genes in maize.

Identification and functional characterization of the Aux/IAA gene VcIAA27 in blueberry

Aux/IAA genes are an important class of players in diverse developmental processes in plants, which generally exert their functions through the auxin signaling pathway. Blueberry is an economically and nutritionally important berry-bearing crop. However, Aux/IAA genes remain unknown in blueberry. In the present study, an Aux/IAA gene (VcIAA27) was identified and characterized in blueberry, and it is most closely related to IAA27 in other plant species. Expression analysis indicated that VcIAA27 transcripts accumulate highly in shoot, flower and fruit. Interestingly, VcIAA27 was highly expressed at early fruit developmental stages, and dramatically decreased from the onset of fruit ripening, implying that VcIAA27 possibly plays important roles during fruit enlargement. Meanwhile, the analysis of promoter activity in Arabidopsis showed that strong GUS signal was detected in the trichome and hydathodes of leaves, receptacle of silique, and lateral roots of seedling. Overexpression of VcIAA27 in Arabidopsis leads to auxin-related defects such as downward-curled leaves, short or sterile siliques, shorter stature, and more shoot branches. Moreover, qPCR analysis indicated that VcIAA27 is able to alter the expression patterns of the auxin-related genes BRU6, SAG13, SAUR26 in Arabidopsis, suggesting that VcIAA27 might be negatively involved in the auxin signaling pathway. The findings will greatly contribute to future investigation of Aux/IAA-mediated mechanisms that control blueberry development, especially fruit development and ripening.

Inoculation with the mycorrhizal fungus Rhizophagus irregularis modulates the relationship between root growth and nutrient content in maize (Zea mays ssp. mays L.)

Plant root systems play a fundamental role in nutrient and water acquisition. In resource-limited soils, modification of root system architecture is an important strategy to optimize plant performance. Most terrestrial plants also form symbiotic associations with arbuscular mycorrhizal fungi to maximize nutrient uptake. In addition to direct delivery of nutrients, arbuscular mycorrhizal fungi benefit the plant host by promoting root growth. Here, we aimed to quantify the impact of arbuscular mycorrhizal symbiosis on root growth and nutrient uptake in maize. Inoculated plants showed an increase in both biomass and the total content of twenty quantified elements. In addition, image analysis showed mycorrhizal plants to have denser, more branched root systems. For most of the quantified elements, the increase in content in mycorrhizal plants was proportional to root and overall plant growth. However, the increase in boron, calcium, magnesium, phosphorus, sulfur, and strontium was greater than predicted by root system size alone, indicating fungal delivery to be supplementing root uptake.

Abscisic Acid Regulates Auxin Distribution to Mediate Maize Lateral Root Development Under Salt Stress

Roots are important plant organs. Lateral root (LR) initiation (LRI) and development play a central role in environmental adaptation. The mechanism of LR development has been well investigated in Arabidopsis. When we evaluated the distribution of auxin and abscisic acid (ABA) in maize, we found that the mechanism differed from that in Arabidopsis. The distribution of ABA and auxin within the primary roots (PRs) and LRs was independent of each other. Auxin localization was observed below the quiescent center of the root tips, while ABA localized at the top of the quiescent center. Furthermore, NaCl inhibited LRI by increasing ABA accumulation, which mainly regulates auxin distribution, while auxin biosynthesis was inhibited by ABA in Arabidopsis. The polar localization of ZmPIN1 in maize was disrupted by NaCl and exogenous ABA. An inhibitor of ABA biosynthesis, fluridone (FLU), and the ABA biosynthesis mutant vp14 rescued the phenotype under NaCl treatment. Together, all the evidence suggested that NaCl promoted ABA accumulation in LRs and that ABA altered the polar localization of ZmPIN1, disrupted the distribution of auxin and inhibited LRI and development.

The Quantitative Genetic Control of Root Architecture in Maize

Roots remain an underexplored frontier in plant genetics despite their well-known influence on plant development, agricultural performance and competition in the wild. Visualizing and measuring root structures and their growth is vastly more difficult than characterizing aboveground parts of the plant and is often simply avoided. The majority of research on maize root systems has focused on their anatomy, physiology, development and soil interaction, but much less is known about the genetics that control quantitative traits. In maize, seven root development genes have been cloned using mutagenesis, but no genes underlying the many root-related quantitative trait loci (QTLs) have been identified. In this review, we discuss whether the maize mutants known to control root development may also influence quantitative aspects of root architecture, including the extent to which they overlap with the most recent maize root trait QTLs. We highlight specific challenges and anticipate the impacts that emerging technologies, especially computational approaches, may have toward the identification of genes controlling root quantitative traits.

Role of Phytohormones in Piriformospora indica-Induced Growth Promotion and Stress Tolerance in Plants: More Questions Than Answers

Phytohormones play vital roles in the growth and development of plants as well as in interactions of plants with microbes such as endophytic fungi. The endophytic root-colonizing fungus Piriformospora indica promotes plant growth and performance, increases resistance of colonized plants to pathogens, insects and abiotic stress. Here, we discuss the roles of the phytohormones (auxins, cytokinin, gibberellins, abscisic acid, ethylene, salicylic acid, jasmonates, and brassinosteroids) in the interaction of P. indica with higher plant species, and compare available data with those from other (beneficial) microorganisms interacting with roots. Crosstalks between different hormones in balancing the plant responses to microbial signals is an emerging topic in current research. Furthermore, phytohormones play crucial roles in systemic signal propagation as well as interplant communication. P. indica interferes with plant hormone synthesis and signaling to stimulate growth, flowering time, differentiation and local and systemic immune responses. Plants adjust their hormone levels in the roots in response to the microbes to control colonization and fungal propagation. The available information on the roles of phytohormones in beneficial root-microbe interactions opens new questions of how P. indica manipulates the plant hormone metabolism to promote the benefits for both partners in the symbiosis.

The dehydration stress of couch grass is associated with its lipid metabolism, the induction of transporters and the re-programming of development coordinated by ABA

Background

The wild relatives of crop species represent a potentially valuable source of novel genetic variation, particularly in the context of improving the crop’s level of tolerance to abiotic stress. The mechanistic basis of these tolerances remains largely unexplored. Here, the focus was to characterize the transcriptomic response of the nodes (meristematic tissue) of couch grass (a relative of barley) to dehydration stress, and to compare it to that of the barley crown formed by both a drought tolerant and a drought sensitive barley cultivar.

Results

Many of the genes up-regulated in the nodes by the stress were homologs of genes known to be mediated by abscisic acid during the response to drought, or were linked to either development or lipid metabolism. Transporters also featured prominently, as did genes acting on root architecture. The resilience of the couch grass node arise from both their capacity to develop an altered, more effective root architecture, but also from their formation of a lipid barrier on their outer surface and their ability to modify both their lipid metabolism and transporter activity when challenged by dehydration stress.

Conclusions

Our analysis revealed the nature of dehydration stress response in couch grass. We suggested the tolerance is associated with lipid metabolism, the induction of transporters and the re-programming of development coordinated by ABA. We also proved the applicability of barley microarray for couch grass stress-response analysis.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4700-3) contains supplementary material, which is available to authorized users.

Genome-wide association studies of doubled haploid exotic introgression lines for root system architecture traits in maize (Zea mays L.)

Root system architecture (RSA) is becoming recognized as important for water and nutrient acquisition in plants. This study focuses on finding single nucleotide polymorphisms (SNPs) associated with seedling RSA traits from 300 doubled haploid (DH) lines derived from crosses between Germplasm Enhancement of Maize (GEM) accessions and inbred lines PHB47 and PHZ51. These DH lines were genotyped using 62,077 SNP markers, while root and shoot phenotype data were collected from 14-day old seedlings. Genome-wide association studies (GWAS) were conducted using three models to offset false positives/negatives. Multiple SNPs associated with seedling root traits were detected, some of which were within or linked to gene models that showed expression in seedling roots. Significant trait associations involving the SNP S5_152926936 on Chromosome 5 were detected in all three models, particularly the trait network area. The SNP is within the gene model GRMZM2G021110, which is expressed in roots at seedling stage. SNPs that were significantly associated with seedling root traits, and closely linked to gene models that encode proteins associated with root development were also detected. This study shows that the GEM-DH panel may be a source of allelic diversity for genes controlling seedling root development.

Genetic Control of Root System Development in Maize

The maize root system comprises structurally and functionally different root types. Mutant analyses have revealed that root-type-specific genetic regulators intrinsically determine the maize root system architecture. Molecular cloning of these genes has demonstrated that key elements of auxin signal transduction, such as LOB domain (LBD) and Aux/IAA proteins, are instrumental for seminal, shoot-borne, and lateral root initiation. Moreover, genetic analyses have demonstrated that genes related to exocytotic vesicle docking, cell wall loosening, and cellulose synthesis and organization control root hair elongation. The identification of upstream regulators, protein interaction partners, and downstream targets of these genes together with cell-type-specific transcriptome analyses have provided novel insights into the regulatory networks controlling root development and architecture in maize.

Overexpression of the protein phosphatase 2A regulatory subunit a gene ZmPP2AA1 improves low phosphate tolerance by remodeling the root system architecture of maize

Phosphate (Pi) limitation is a constraint for plant growth and development in many natural and agricultural ecosystems. In this study, a gene encoding Zea mays L. protein phosphatase 2A regulatory subunit A, designated ZmPP2AA1, was induced in roots by low Pi availability. The function of the ZmPP2AA1 gene in maize was analyzed using overexpression and RNA interference. ZmPP2AA1 modulated root gravitropism, negatively regulated primary root (PR) growth, and stimulated the development of lateral roots (LRs). A detailed characterization of the root system architecture (RSA) in response to different Pi concentrations with or without indole-3-acetic acid and 1-N-naphthylphthalamic acid revealed that auxin was involved in the RSA response to low Pi availability. Overexpression of ZmPP2AA1 enhanced tolerance to Pi starvation in transgenic maize in hydroponic and soil pot experiments. An increased dry weight (DW), root-to-shoot ratio, and total P content and concentration, along with a delayed and reduced accumulation of anthocyanin in overexpressing transgenic maize plants coincided with their highly branched root system and increased Pi uptake capability under low Pi conditions. Inflorescence development of the ZmPP2AA1 overexpressing line was less affected by low Pi stress, resulting in higher grain yield per plant under Pi deprivation. These data reveal the biological function of ZmPP2AA1, provide insights into a linkage between auxin and low Pi responses, and drive new strategies for the efficient utilization of Pi by maize.

AhDGR2, an amaranth abiotic stress-induced DUF642 protein gene, modifies cell wall structure and composition and causes salt and ABA hyper-sensibility in transgenic Arabidopsis

An amaranth DGR gene, induced under abiotic stress, modifies cell wall structure and causes hypersensitivity to ABA and salt when overexpressed in Arabidopsis. DUF642 is a highly conserved plant-specific family of unknown cell wall-associated proteins. The AhDGR2 gene, coding for a DUF642 protein, was significantly induced in grain amaranth (Amaranthus hypochondriacus) plants subjected to water-deficit and salinity stress, thereby suggesting its participation in abiotic stress tolerance in this plant. A role in development was also inferred from the higher AhDGR2 expression rates detected in young tissues. Subsequent overexpression of AhDGR2 in transgenic Arabidopsis plants (OE-AhDGR2) supported its possible role in development processes. Thus, OE-AhDGR2 plants generated significantly longer roots when grown in normal MS medium. However, they showed a hypersensitivity to increasing concentrations of abscisic acid or NaCl in the medium, as manifested by shorter root length, smaller and slightly chlorotic rosettes, as well as highly reduced germination rates. Contrary to expectations, OE-AhDGR2 plants were intolerant to abiotic stress. Moreover, cell walls in transgenic plants were thinner, in leaves, and more disorganized, in roots, and had significantly modified pectin levels. Lower pectin methylesterase activity detected in leaves of OE-AhDGR2 plants, but not in roots, was contrary to previous reports associating DUF642 proteins and decreased pectin esterification levels in cell walls. Nonetheless, microarray data identified candidate genes whose expression levels explained the phenotypes observed in leaves of OE-AhDGR2 plants, including several involved in cell wall integrity and extension, growth and development, and resistance to abiotic stress. These results support the role of DUF642 proteins in cell wall-related processes and offer novel insights into their possible role(s) in plants.

Genome-wide analysis of starch metabolism genes in potato (Solanum tuberosum L.)

Background

Starch is the principle constituent of potato tubers and is of considerable importance for food and non-food applications. Its metabolism has been subject of extensive research over the past decades. Despite its importance, a description of the complete inventory of genes involved in starch metabolism and their genome organization in potato plants is still missing. Moreover, mechanisms regulating the expression of starch genes in leaves and tubers remain elusive with regard to differences between transitory and storage starch metabolism, respectively. This study aimed at identifying and mapping the complete set of potato starch genes, and to study their expression pattern in leaves and tubers using different sets of transcriptome data. Moreover, we wanted to uncover transcription factors co-regulated with starch accumulation in tubers in order to get insight into the regulation of starch metabolism.

Results

We identified 77 genomic loci encoding enzymes involved in starch metabolism. Novel isoforms of many enzymes were found. Their analysis will help to elucidate mechanisms of starch biosynthesis and degradation. Expression analysis of starch genes led to the identification of tissue-specific isoenzymes suggesting differences in the transcriptional regulation of starch metabolism between potato leaf and tuber tissues. Selection of genes predominantly expressed in developing potato tubers and exhibiting an expression pattern indicative for a role in starch biosynthesis enabled the identification of possible transcriptional regulators of tuber starch biosynthesis by co-expression analysis.

Conclusions

This study provides the annotation of the complete set of starch metabolic genes in potato plants and their genomic localizations. Novel, so far undescribed, enzyme isoforms were revealed. Comparative transcriptome analysis enabled the identification of tuber- and leaf-specific isoforms of starch genes. This finding suggests distinct regulatory mechanisms in transitory and storage starch metabolism. Putative regulatory proteins of starch biosynthesis in potato tubers have been identified by co-expression and their expression was verified by quantitative RT-PCR.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3381-z) contains supplementary material, which is available to authorized users.

Use of genotype-environment interactions to elucidate the pattern of maize root plasticity to nitrogen deficiency

Maize (Zea mays L.) root morphology exhibits a high degree of phenotypic plasticity to nitrogen (N) deficiency, but the underlying genetic architecture remains to be investigated. Using an advanced BC4 F3 population, we investigated the root growth plasticity under two contrasted N levels and identified the quantitative trait loci (QTLs) with QTL-environment (Q × E) interaction effects. Principal components analysis (PCA) on changes of root traits to N deficiency (ΔLN-HN) showed that root length and biomass contributed for 45.8% in the same magnitude and direction on the first PC, while root traits scattered highly on PC2 and PC3. Hierarchical cluster analysis on traits for ΔLN-HN further assigned the BC4 F3 lines into six groups, in which the special phenotypic responses to N deficiency was presented. These results revealed the complicated root plasticity of maize in response to N deficiency that can be caused by genotype-environment (G × E) interactions. Furthermore, QTL mapping using a multi-environment analysis identified 35 QTLs for root traits. Nine of these QTLs exhibited significant Q × E interaction effects. Taken together, our findings contribute to understanding the phenotypic and genotypic pattern of root plasticity to N deficiency, which will be useful for developing maize tolerance cultivars to N deficiency.

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development

Comprehensive and systematic transcriptome profiling provides valuable insight into biological and developmental processes that occur throughout the life cycle of a plant. We have enhanced our previously published microarray-based gene atlas of maize ( L.) inbred B73 to now include 79 distinct replicated samples that have been interrogated using RNA sequencing (RNA-seq). The current version of the atlas includes 50 original array-based gene atlas samples, a time-course of 12 stalk and leaf samples postflowering, and an additional set of 17 samples from the maize seedling and adult root system. The entire dataset contains 4.6 billion mapped reads, with an average of 20.5 million mapped reads per biological replicate, allowing for detection of genes with lower transcript abundance. As the new root samples represent key additions to the previously examined tissues, we highlight insights into the root transcriptome, which is represented by 28,894 (73.2%) annotated genes in maize. Additionally, we observed remarkable expression differences across both the longitudinal (four zones) and radial gradients (cortical parenchyma and stele) of the primary root supported by fourfold differential expression of 9353 and 4728 genes, respectively. Among the latter were 1110 genes that encode transcription factors, some of which are orthologs of previously characterized transcription factors known to regulate root development in (L.) Heynh., while most are novel, and represent attractive targets for reverse genetics approaches to determine their roles in this important organ. This comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.

Conserved and unique features of the homeologous maize Aux/IAA proteins ROOTLESS WITH UNDETECTABLE MERISTEM 1 and RUM1-like 1

The maize (Zea mays L.) Aux/IAA protein RUM1 (ROOTLESS WITH UNDETECTABLE MERISTEM 1) is a key regulator of lateral and seminal root formation. An ancient maize genome duplication resulted in the emergence of its homeolog rum1-like1 (rul1), which displays 92% amino acid sequence identity with RUM1. Both, RUL1 and RUM1 exhibit the canonical four domain structure of Aux/IAA proteins. Moreover, both are localized to the nucleus, are instable and have similar short half-lives of ~23min. Moreover, RUL1 and RUM1 can be stabilized by specific mutations in the five amino acid degron sequence of domain II. In addition, proteins encoded by both genes interact in vivo with auxin response factors (ARFs) such as ZmARF25 and ZmARF34 in protoplasts. Although it was demonstrated that RUL1 and RUM1 can homo and heterodimerize in vivo, rul1 expression is independent of rum1. Moreover, on average rul1 expression is ~84-fold higher than rum1 in the 12 tested tissues and developmental stages, although the relative expression levels in different root tissues are very similar. While RUM1 and RUL1 display conserved biochemical properties, yeast-two-hybrid in combination with BiFC experiments identified a RUM1-associated protein 1 (RAP1) that specifically interacts with RUM1 but not with RUL1. This suggests that RUM1 and RUL1 are at least in part interwoven into different molecular networks.