Hormonal control of cell division and elongation along differentiation trajectories in roots

Identification of cotton PIP5K genes and role of GhPIP5K9a in primary root development

Phosphatidylinositol 4 phosphate 5-kinase (PIP5K) is crucial for the phosphatidylinositol (PI) signaling pathway. It plays a significant role in plant growth and development, as well as stress response. However, its effects on cotton are unknown. This study identified PIP5K genes from four cotton species and conducted bioinformatic analyses, with a particular emphasis on the functions of GhPIP5K9a in primary roots. The results showed that cotton PIP5Ks were classified into four subgroups. Analysis of gene structure and motif composition showed obvious conservation within each subgroup. Synteny analysis suggested that the PIP5K gene family experienced significant expansion due to both whole-genome duplication (WGD) and segmental duplication. Transcriptomic data analysis revealed that the majority of GhPIP5K genes had the either low or undetectable levels of expression. Moreover, GhPIP5K9a is highly expressed in the root and was located in plasmalemma. Suppression of GhPIP5K9a transcripts resulted in longer primary roots, longer primary root cells and increased auxin polar transport-related genes expression, and decreased abscisic acid (ABA) content, indicating that GhPIP5K9a negatively regulates cotton primary root growth. This study lays the foundation for further exploration of the role of the PIP5K genes in cotton.

Suppression of OsSAUR2 gene expression immobilizes soil arsenic bioavailability by modulating root exudation and rhizosphere microbial assembly in rice

One of the factors influencing the behavior of arsenic (As) in environment is microbial-mediated As transformation. However, the detailed regulatory role of gene expression on the changes of root exudation, rhizosphere microorganisms, and soil As occurrence forms remains unclear. In this study, we evidence that loss-of-function of OsSAUR2 gene, a member of the SMALL AUXIN-UP RNA family in rice, results in significantly higher As uptake in roots but greatly lower As accumulation in grains via affecting the expression of OsLsi1, OsLsi2 in roots and OsABCC1 in stems. Further, the alteration of OsSAUR2 expression extensively affects the metabolomic of root exudation, and thereby leading to the variations in the composition of rhizosphere microbial communities in rice. The microbial community in the rhizosphere of Ossaur2 plants strongly immobilizes the occurrence forms of As in soil. Interestingly, Homovanillic acid (HA) and 3-Coumaric acid (CA), two differential metabolites screened from root exudation, can facilitate soil iron reduction, enhance As bioavailability, and stimulate As uptake and accumulation in rice. These findings add our further understanding in the relationship of OsSAUR2 expression with the release of root exudation and rhizosphere microbial assembly under As stress in rice, and provide potential rice genetic resources and root exudation in phytoremediation of As-contaminated paddy soil.

Cytokinins regulate spatially specific ethylene production to control root growth in Arabidopsis

Two principal growth regulators, cytokinins and ethylene, are known to interact in the regulation of plant growth. However, information about the underlying molecular mechanism and positional specificity of cytokinin/ethylene crosstalk in the control of root growth is scarce. We have identified the spatial specificity of cytokinin-regulated root elongation and root apical meristem (RAM) size, both of which we demonstrate to be dependent on ethylene biosynthesis. Upregulation of the cytokinin biosynthetic gene ISOPENTENYLTRANSFERASE (IPT) in proximal and peripheral tissues leads to both root and RAM shortening. By contrast, IPT activation in distal and inner tissues reduces RAM size while leaving the root length comparable to that of mock-treated controls. We show that cytokinins regulate two steps specific to ethylene biosynthesis: production of the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC) by ACC SYNTHASEs (ACSs) and its conversion to ethylene by ACC OXIDASEs (ACOs). We describe cytokinin- and ethylene-specific regulation controlling the activity of ACSs and ACOs that are spatially discrete along both proximo/distal and radial root axes. Using direct ethylene measurements, we identify ACO2, ACO3, and ACO4 as being responsible for ethylene biosynthesis and ethylene-regulated root and RAM shortening in cytokinin-treated Arabidopsis. Direct interaction between ARABIDOPSIS RESPONSE REGULATOR 2 (ARR2), a member of the multistep phosphorelay cascade, and the C-terminal portion of ETHYLENE INSENSITIVE 2 (EIN2-C), a key regulator of canonical ethylene signaling, is involved in the cytokinin-induced, ethylene-mediated control of ACO4. We propose tight cooperation between cytokinin and ethylene signaling in the spatially specific regulation of ethylene biosynthesis as a key aspect of the hormonal control of root growth.

Ectopic expression of OsWOX9A alters leaf anatomy and plant architecture in rice

MAIN CONCLUSION

Ectopic expression of OsWOX9A induces narrow adaxially rolled rice leaves with larger bulliform cells and fewer large veins, probably through regulating the expression of auxin-related and expansin genes. The WUSCHEL-related homeobox (WOX) family plays a pivotal role in plant development by regulating genes involved in various aspects of growth and differentiation. OsWOX9A (DWT1) has been linked to tiller growth, uniform plant growth, and flower meristem activity. However, its impact on leaf growth and development in rice has not been studied. In this study, we investigated the biological role of OsWOX9A in rice growth and development using transgenic plants. Overexpression of OsWOX9A conferred narrow adaxially rolled rice leaves and altered plant architecture. These plants exhibited larger bulliform cells and fewer larger veins compared to wild-type plants. OsWOX9A overexpression also reduced plant height, tiller number, and seed-setting rate. Comparative transcriptome analysis revealed several differentially expressed auxin-related and expansin genes in OsWOX9A overexpressing plants, consistent with their roles in leaf and plant development. These results indicate that the ectopic expression of OsWOX9A may have multiple effects on the development and growth of rice, providing a more comprehensive picture of how the WOX9 subfamily contributes to leaf development and plant architecture.

Hydrotropism mechanisms and their interplay with gravitropism

Plants partly optimize their water recruitment from the growth medium by directing root growth toward a moisture source, a phenomenon termed hydrotropism. The default mechanism of downward growth, termed gravitropism, often functions to counteract hydrotropism when the water-potential gradient deviates from the gravity vector. This review addresses the identity of the root sites in which hydrotropism-regulating factors function to attenuate gravitropism and the interplay between these various factors. In this context, the function of hormones, including auxin, abscisic acid, and cytokinins, as well as secondary messengers, calcium ions, and reactive oxygen species in the conflict between these two opposing tropisms is discussed. We have assembled the available data on the effects of various chemicals and genetic backgrounds on both gravitropism and hydrotropism, to provide an up-to-date perspective on the interactions that dictate the orientation of root tip growth. We specify the relevant open questions for future research. Broadening our understanding of root mechanisms of water recruitment holds great potential for providing advanced approaches and technologies that can improve crop plant performance under less-than-optimal conditions, in light of predicted frequent and prolonged drought periods due to global climate change.

The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development

The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.

The Slow Growth of Adventitious Roots in Tetraploid Hybrid Poplar (Populus simonii × P. nigra var. italica) May Be Caused by Endogenous Hormone-Mediated Meristem Shortening

Polyploidization produces abundant phenotypic variation. Little is currently known about adventitious root (AR) development variation due to polyploidization. In this study, we analyzed the morphological, cytological, and physiological variations in AR development between tetraploid and diploid Populus plants during in vitro rooting culture. Compared to the diploids, the AR formation times and rooting rates of the tetraploids' stem explants had non-significant changes. However, the tetraploid ARs exhibited significantly slower elongation growth than the diploid ARs. Cytological observation showed that the tetraploid ARs were characterized by shorter root meristems and reduced meristem cell numbers, suggesting the reasons for the slow AR elongation. Analysis of hormones and related metabolites during AR development demonstrated that the total auxin, cytokinin, and jasmonic acid contents were significantly lower in the tetraploid ARs than in those of the diploids, and that the ratio of total auxins to total CKs at 0 h of AR development was also lower in the tetraploids than in the diploids, whereas the total salicylic acid content of the tetraploids was consistently higher than that of the diploids. qPCR analysis showed that the expression levels of several hormone signaling and cell division-related genes in the tetraploid ARs significantly differed from those in the diploids. In conclusion, the slow elongation of the tetraploid ARs may be caused by the endogenous hormone-mediated meristem shortening. Our findings enhance the understanding of polyploidization-induced variation in AR development of forest trees.

Role of calcium signaling in cadmium stress mitigation by indol-3-acetic acid and gibberellin in chickpea seedlings

Given the adverse impacts of heavy metals on plant development and physiological processes, the present research investigated the protective role of indole-3-acetic acid (IAA) and gibberellic acid (GA3) against cadmium (Cd)-induced injury in chickpea seedlings. Therefore, seeds germinated for 6 days in a medium containing 200 μM Cd alone or combined with 10 μM GA3 or 10 μM IAA. Both GA3 and IAA mitigated Cd-imposed growth delays in roots and shoots (80% and 50% increase in root and shoot length, respectively). This beneficial effect was accompanied by a significant reduction in Cd2+ accumulation in both roots (74% for IAA and 38% for GA3) and shoots (68% and 35%, respectively). Furthermore, these phytohormones restored the cellular redox state by reducing the activity of NADPH oxidase and downregulating the transcription level of RbohF and RbohD genes. Likewise, hydrogen peroxide contents were reduced by GA3 and IAA supply. Additionally, GA3 and IAA countered the Cd-induced reduction in total phenols, flavonoids, and reducing sugars in both roots and shoots. The exogenous effectors enhanced the activities of catalase, ascorbate peroxidase, and thioredoxin, as well as the corresponding gene expressions. Interestingly, adding GA3 and IAA to the Cd-contaminated germination media corrected the level of calcium (Ca2+) ion within seedling tissues. This effect coincided with the upregulation of key genes associated with stress sensing and signal transduction, including auxin-binding protein (ABP19a), mitogen-activated protein kinase (MAPK2), calcium-dependent protein kinase (CDPK1), and calmodulin (CaM). Overall, the current results suggest that GA3 and IAA sustain the Ca2+ signaling pathway, resulting in metal phytotoxicity relief. Amendment of agricultural soils contaminated with heavy metals with GA3 or IAA could represent an effective practice to improve crop yield.

Physiological Mechanism through Which Al Toxicity Inhibits Peanut Root Growth

Al (Aluminum) poisoning is a significant limitation to crop yield in acid soil. However, the physiological process involved in the peanut root response to Al poisoning has not been clarified yet and requires further research. In order to investigate the influence of Al toxicity stress on peanut roots, this study employed various methods, including root phenotype analysis, scanning of the root, measuring the physical response indices of the root, measurement of the hormone level in the root, and quantitative PCR (qPCR). This research aimed to explore the physiological mechanism underlying the reaction of peanut roots to Al toxicity. The findings revealed that Al poisoning inhibits the development of peanut roots, resulting in reduced biomass, length, surface area, and volume. Al also significantly affects antioxidant oxidase activity and proline and malondialdehyde contents in peanut roots. Furthermore, Al toxicity led to increased accumulations of Al and Fe in peanut roots, while the contents of zinc (Zn), cuprum (Cu), manganese (Mn), kalium (K), magnesium (Mg), and calcium (Ca) decreased. The hormone content and related gene expression in peanut roots also exhibited significant changes. High concentrations of Al trigger cellular defense mechanisms, resulting in differentially expressed antioxidase genes and enhanced activity of antioxidases to eliminate excessive ROS (reactive oxygen species). Additionally, the differential expression of hormone-related genes in a high-Al environment affects plant hormones, ultimately leading to various negative effects, for example, decreased biomass of roots and hindered root development. The purpose of this study was to explore the physiological response mechanism of peanut roots subjected to aluminum toxicity stress, and the findings of this research will provide a basis for cultivating Al-resistant peanut varieties.

Characterization of Almond Scion/Rootstock Communication in Cultivar and Rootstock Tissues through an RNA-Seq Approach

The rootstock genotype plays a crucial role in determining various aspects of scion development, including the scion three-dimensional structure, or tree architecture. Consequently, rootstock choice is a pivotal factor in the establishment of new almond (Prunus amygdalus (L.) Batsch, syn P. dulcis (Mill.)) intensive planting systems, demanding cultivars that can adapt to distinct requirements of vigor and shape. Nevertheless, considering the capacity of the rootstock genotype to influence scion development, it is likely that the scion genotype reciprocally affects rootstock performance. In the context of this study, we conducted a transcriptomic analysis of the scion/rootstock interaction in young almond trees, with a specific focus on elucidating the scion impact on the rootstock molecular response. Two commercial almond cultivars were grafted onto two hybrid rootstocks, thereby generating four distinct combinations. Through RNA-Seq analysis, we discerned that indeed, the scion genotype exerts an influence on the rootstock expression profile. This influence manifests through the modulation of genes associated with hormonal regulation, cell division, root development, and light signaling. This intricate interplay between scion and rootstock communication plays a pivotal role in the development of both scion and rootstock, underscoring the critical importance of a correct choice when establishing new almond orchards.

Comparative Transcriptome Sequencing and Endogenous Phytohormone Content of Annual Grafted Branches of Zelkova schneideriana and Its Dwarf Variety HenTianGao

Zelkova schneideriana is a fast-growing tree species endemic to China. Recent surveys and reports have highlighted a continued decline in its natural populations; therefore, it is included in the Red List of Threatened Species by The International Union for Conservation of Nature. A new variety "HenTianGao" (H) has been developed with smaller plant height, slow growth, and lower branching points. In this study, we attempted to understand the differences in plant height of Z. schneideriana (J) and its dwarf variety H. We determined the endogenous hormone content in the annual grafted branches of both J and H. J exhibited higher gibberellic acid (GA)-19 and trans-Zeatin (tZ) levels, whereas H had higher levels of indole-3-acetic acid (IAA) catabolite 2-oxindole-3-acetic acid (OxIAA), IAA-Glu conjugate, and jasmonic acid (JA) (and its conjugate JA-Ile). The transcriptome comparison showed differential regulation of 20,944 genes enriched in growth and development, signaling, and metabolism-related pathways. The results show that the differential phytohormone level (IAA, JA, tZ, and GA) was consistent with the expression of the genes associated with their biosynthesis. The differences in relative OxIAA, IAA-Glu, GA19, trans-Zeatin, JA, and JA-Ile levels were linked to changes in respective signaling-related genes. We also observed significant differences in the expression of cell size, number, proliferation, cell wall biosynthesis, and remodeling-related genes in J and H. The differences in relative endogenous hormone levels, expression of biosynthesis, and signaling genes provide a theoretical basis for understanding the plant height differences in Z. schneideriana.

Exploring the Role of the Plant Actin Cytoskeleton: From Signaling to Cellular Functions

The plant actin cytoskeleton is characterized by the basic properties of dynamic array, which plays a central role in numerous conserved processes that are required for diverse cellular functions. Here, we focus on how actins and actin-related proteins (ARPs), which represent two classical branches of a greatly diverse superfamily of ATPases, are involved in fundamental functions underlying signal regulation of plant growth and development. Moreover, we review the structure, assembly dynamics, and biological functions of filamentous actin (F-actin) from a molecular perspective. The various accessory proteins known as actin-binding proteins (ABPs) partner with F-actin to finely tune actin dynamics, often in response to various cell signaling pathways. Our understanding of the significance of the actin cytoskeleton in vital cellular activities has been furthered by comparison of conserved functions of actin filaments across different species combined with advanced microscopic techniques and experimental methods. We discuss the current model of the plant actin cytoskeleton, followed by examples of the signaling mechanisms under the supervision of F-actin related to cell morphogenesis, polar growth, and cytoplasmic streaming. Determination of the theoretical basis of how the cytoskeleton works is important in itself and is beneficial to future applications aimed at improving crop biomass and production efficiency.

RNA polymerase common subunit ZmRPABC5b is transcriptionally activated by Opaque2 and essential for endosperm development in maize

Maize (Zea mays) kernel size is an important factor determining grain yield; although numerous genes regulate kernel development, the roles of RNA polymerases in this process are largely unclear. Here, we characterized the defective kernel 701 (dek701) mutant that displays delayed endosperm development but normal vegetative growth and flowering transition, compared to its wild type. We cloned Dek701, which encoded ZmRPABC5b, a common subunit to RNA polymerases I, II and III. Loss-of-function mutation of Dek701 impaired the function of all three RNA polymerases and altered the transcription of genes related to RNA biosynthesis, phytohormone response and starch accumulation. Consistent with this observation, loss-of-function mutation of Dek701 affected cell proliferation and phytohormone homeostasis in maize endosperm. Dek701 was transcriptionally regulated in the endosperm by the transcription factor Opaque2 through binding to the GCN4 motif within the Dek701 promoter, which was subjected to strong artificial selection during maize domestication. Further investigation revealed that DEK701 interacts with the other common RNA polymerase subunit ZmRPABC2. The results of this study provide substantial insight into the Opaque2-ZmRPABC5b transcriptional regulatory network as a central hub for regulating endosperm development in maize.

Endoreplication-Why Are We Not Using Its Full Application Potential?

Endoreplication-a process that is common in plants and also accompanies changes in the development of animal organisms-has been seen from a new perspective in recent years. In the paper, we not only shed light on this view, but we would also like to promote an understanding of the application potential of this phenomenon in plant cultivation. Endoreplication is a pathway for cell development, slightly different from the classical somatic cell cycle, which ends with mitosis. Since many rounds of DNA synthesis take place within its course, endoreplication is a kind of evolutionary compensation for the relatively small amount of genetic material that plants possess. It allows for its multiplication and active use through transcription and translation. The presence of endoreplication in plants has many positive consequences. In this case, repeatedly produced copies of genes, through the corresponding transcripts, help the plant acquire the favorable properties for which proteins are responsible directly or indirectly. These include features that are desirable in terms of cultivation and marketing: a greater saturation of fruit and flower colors, a stronger aroma, a sweeter fruit taste, an accumulation of nutrients, an increased resistance to biotic and abiotic stress, superior tolerance to adverse environmental conditions, and faster organ growth (and consequently the faster growth of the whole plant and its biomass). The two last features are related to the nuclear-cytoplasmic ratio-the greater the content of DNA in the nucleus, the higher the volume of cytoplasm, and thus the larger the cell size. Endoreplication not only allows cells to reach larger sizes but also to save the materials used to build organelles, which are then passed on to daughter cells after division, thus ending the classic cell cycle. However, the content of genetic material in the cell nucleus determines the number of corresponding organelles. The article also draws attention to the potential practical applications of the phenomenon and the factors currently limiting its use.

Protein-protein interaction (PPI) network analysis reveals important hub proteins and sub-network modules for root development in rice (Oryza sativa)

BACKGROUND

The root system is vital to plant growth and survival. Therefore, genetic improvement of the root system is beneficial for developing stress-tolerant and improved plant varieties. This requires the identification of proteins that significantly contribute to root development. Analyzing protein-protein interaction (PPI) networks is vastly beneficial in studying developmental phenotypes, such as root development, because a phenotype is an outcome of several interacting proteins. PPI networks can be analyzed to identify modules and get a global understanding of important proteins governing the phenotypes. PPI network analysis for root development in rice has not been performed before and has the potential to yield new findings to improve stress tolerance.

RESULTS

Here, the network module for root development was extracted from the global Oryza sativa PPI network retrieved from the STRING database. Novel protein candidates were predicted, and hub proteins and sub-modules were identified from the extracted module. The validation of the predictions yielded 75 novel candidate proteins, 6 sub-modules, 20 intramodular hubs, and 2 intermodular hubs.

CONCLUSIONS

These results show how the PPI network module is organized for root development and can be used for future wet-lab studies for producing improved rice varieties.

Griseofulvin Inhibits Root Growth by Targeting Microtubule-Associated Proteins Rather Tubulins in Arabidopsis

Griseofulvin was considered an effective agent for cancer therapy in past decades. Although the negative effects of griseofulvin on microtubule stability are known, the exact target and mechanism of action in plants remain unclear. Here, we used trifluralin, a well-known herbicide targeting microtubules, as a reference and revealed the differences in root tip morphology, reactive oxygen species production (ROS), microtubule dynamics, and transcriptome analysis between Arabidopsis treated with griseofulvin and trifluralin to elucidate the mechanism of root growth inhibition by griseofulvin. Like trifluralin, griseofulvin inhibited root growth and caused significant swelling of the root tip due to cell death induced by ROS. However, the presence of griseofulvin and trifluralin caused cell swelling in the transition zone (TZ) and meristematic zone (MZ) of root tips, respectively. Further observations revealed that griseofulvin first destroyed cortical microtubules in the cells of the TZ and early elongation zone (EZ) and then gradually affected the cells of other zones. The first target of trifluralin is the microtubules in the root MZ cells. Transcriptome analysis showed that griseofulvin mainly affected the expression of microtubule-associated protein (MAP) genes rather than tubulin genes, whereas trifluralin significantly suppressed the expression of αβ-tubulin genes. Finally, it was proposed that griseofulvin could first reduce the expression of MAP genes, meanwhile increasing the expression of auxin and ethylene-related genes to disrupt microtubule alignment in root tip TZ and early EZ cells, induce dramatic ROS production, and cause severe cell death, eventually leading to cell swelling in the corresponding zones and inhibition of root growth.

Genome-wide survey identified superior and rare haplotypes for plant height in the north-eastern soybean germplasm of China

The proper and efficient utilization of natural genetic diversity can significantly impact crop improvements. Plant height is a quantitative trait governing the plant type as well as the yield and quality of soybean. Here, we used a combined approach including a genome-wide association study (GWAS) and haplotype and candidate gene analyses to explore the genetic basis of plant height in diverse natural soybean populations. For the GWAS analysis, we used the whole-genome resequencing data of 196 diverse soybean cultivars collected from different accumulated temperature zones of north-eastern China to detect the significant single-nucleotide polymorphisms (SNPs) associated with plant height across three environments (E1, E2, and E3). A total of 33 SNPs distributed on four chromosomes, viz., Chr.02, Chr.04, Chr.06, and Chr.19, were identified to be significantly associated with plant height across the three environments. Among them, 23 were consistently detected in two or more environments and the remaining 10 were identified in only one environment. Interestingly, all the significant SNPs detected on the respective chromosomes fell within the physical interval of linkage disequilibrium (LD) decay (± 38.9 kb). Hence, these genomic regions were considered to be four quantitative trait loci (QTLs), viz., qPH2, qPH4, qPH6, and qPH19, regulating plant height. Moreover, the genomic region flanking all significant SNPs on four chromosomes exhibited strong LD. These significant SNPs thus formed four haplotype blocks, viz., Hap-2, Hap-4, Hap-6, and Hap-19. The number of haplotype alleles underlying each block varied from four to six, and these alleles regulate the different phenotypes of plant height ranging from dwarf to extra-tall heights. Nine candidate genes were identified within the four haplotype blocks, and these genes were considered putative candidates regulating soybean plant height. Hence, these stable QTLs, superior haplotypes, and candidate genes (after proper validation) can be deployed for the development of soybean cultivars with desirable plant heights.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01363-7.

New Insights on Endophytic Microbacterium-Assisted Blast Disease Suppression and Growth Promotion in Rice: Revelation by Polyphasic Functional Characterization and Transcriptomics

Plant growth-promoting endophytic microbes have drawn the attention of researchers owing to their ability to confer fitness benefits in many plant species. Here, we report agriculturally beneficial traits of rice-leaf-adapted endophytic Microbacterium testaceum. Our polyphasic taxonomic investigations revealed its identity as M. testaceum. The bacterium displayed typical endophytism in rice leaves, indicated by the green fluorescence of GFP-tagged M. testaceum in confocal laser scanning microscopy. Furthermore, the bacterium showed mineral solubilization and production of IAA, ammonia, and hydrolytic enzymes. Tobacco leaf infiltration assay confirmed its non-pathogenic nature on plants. The bacterium showed antifungal activity on Magnaporthe oryzae, as exemplified by secreted and volatile organic metabolome-mediated mycelial growth inhibition. GC-MS analysis of the volatilome of M. testaceum indicated the abundance of antimicrobial compounds. Bacterization of rice seedlings showed phenotypic traits of MAMP-triggered immunity (MTI), over-expression of OsNPR1 and OsCERK, and the consequent blast suppressive activity. Strikingly, M. testaceum induced the transcriptional tradeoff between physiological growth and host defense pathways as indicated by up- and downregulated DEGs. Coupled with its plant probiotic features and the defense elicitation activity, the present study paves the way for developing Microbacterium testaceum-mediated bioformulation for sustainably managing rice blast disease.

Silicon Palliates Chromium Toxicity through the Formation of Root Hairs in Rice (Oryza sativa) Mediated by GSH and IAA

Along with the rapidly increasing environmental contamination by heavy metals, the exposure of plants to chromium has also magnified, resulting in a declined productivity. Hexavalent chromium [Cr(VI)], the most toxic form of Cr, brings about changes in plant processes at morpho-physiological and biochemical levels. However, silicon (Si) is known to mitigate the impact of abiotic stresses in plants. Here, we demonstrate Si-mediated alleviation of Cr(VI) toxicity and its effects on root hair formation in rice seedlings. Reduced glutathione (GSH) and indole-3 acetic acid (IAA, an important auxin) were assessed for their involvement in root hair formation after the application of Si to Cr(VI)-stressed plants, and our results confirmed their crucial significance in such developmental processes. The expression analysis of genes involved in GSH biosynthesis (OsGS2) and regeneration (OsGR1), and auxin biosynthesis (OsTAA1 and OsYUCCA1) and transport (OsAUX1 and OsPIN1) corroborated their positive role in Si-mediated root hair formation in Cr(VI)-stressed rice seedlings. Moreover, the results indicated that nitric oxide (NO) seems a probable but not fundamental component in Si-mediated formation of roots in rice during exposure to Cr(VI) stress. In this study, the indispensable role of GSH and IAA, redox homeostasis of GSH and IAA biosynthesis and transport are discussed with regard to Si-mediated formation of root hairs in rice under Cr(VI) stress. The results of the study suggest that Si is a protective agent against Cr(VI) stress in rice, and the findings can be used to develop Cr(VI) stress-tolerant varieties of rice with enhanced productivity.

Brassica napus Roots Use Different Strategies to Respond to Warm Temperatures

Elevated growth temperatures are negatively affecting crop productivity by increasing yield losses. The modulation of root traits associated with improved response to rising temperatures is a promising approach to generate new varieties better suited to face the environmental constraints caused by climate change. In this study, we identified several Brassica napus root traits altered in response to warm ambient temperatures. Different combinations of changes in specific root traits result in an extended and deeper root system. This overall root growth expansion facilitates root response by maximizing root-soil surface interaction and increasing roots' ability to explore extended soil areas. We associated these traits with coordinated cellular events, including changes in cell division and elongation rates that drive root growth increases triggered by warm temperatures. Comparative transcriptomic analysis revealed the main genetic determinants of these root system architecture (RSA) changes and uncovered the necessity of a tight regulation of the heat-shock stress response to adjusting root growth to warm temperatures. Our work provides a phenotypic, cellular, and genetic framework of root response to warming temperatures that will help to harness root response mechanisms for crop yield improvement under the future climatic scenario.

Volatile organic compounds from Lysinibacillus macroides regulating the seedling growth of Arabidopsis thaliana

Volatile organic compounds (VOCs) have the characteristics of long distance propagation, low concentration, perception, and indirect contact between organisms. In this experiment, Lysinibacillus macroides Xi9 was isolated from cassava residue, and the VOCs produced by this strain were analyzed by the SPME-GC-MS method, mainly including alcohols, esters, and alkanes. By inoculation of L. macroides Xi9, VOCs can promote the growth and change the root-system architecture of Arabidopsis seedlings. The results showed that the number of lateral roots, root density, and fresh weight of Arabidopsis seedlings were significantly higher (p ≤ 0.01), and the number of roots hair was also increased after exposure to strain Xi9. Compared with the control group, the transcriptome analysis of Arabidopsis seedlings treated with strain Xi9 for 5 days revealed a total of 508 genes differentially expressed (p < 0.05). After Gene Ontology enrichment analysis, it was found that genes encoding nitrate transport and assimilation, and the lateral root-related gene ANR1 were up-regulated. The content of NO3 - and amino acid in Arabidopsis seedlings were significantly higher from control group (p ≤ 0.01). Plant cell wall-related EXPA family genes and pectin lyase gene were up-regulated, resulting cell elongation of leaf. SAUR41 and up-regulation of its subfamily members, as well as the down-regulation of auxin efflux carrier protein PILS5 and auxin response factor 20 (ARF20) led to the accumulation of auxin. These results indicated that VOCs of strain Xi9 promote Arabidopsis seedlings growth and development by promoting nitrogen uptake, regulating auxin synthesis, and improving cell wall modification.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01268-3.

Combined Approach of GWAS and Phylogenetic Analyses to Identify New Candidate Genes That Participate in Arabidopsis thaliana Primary Root Development Using Cellular Measurements and Primary Root Length

Genome-wide association studies (GWAS) have allowed the identification of different loci associated with primary root (PR) growth, and Arabidopsis is an excellent model for these studies. The PR length is controlled by cell proliferation, elongation, and differentiation; however, the specific contribution of proliferation and differentiation in the control of PR growth is still poorly studied. To this end, we analyzed 124 accessions and used a GWAS approach to identify potential causal genomic regions related to four traits: PR length, growth rate, cell proliferation and cell differentiation. Twenty-three genes and five statistically significant SNPs were identified. The SNP with the highest score mapped to the fifth exon of NAC048 and this change makes a missense variant in only 33.3% of the accessions with a large PR, compared with the accessions with a short PR length. Moreover, we detected five more SNPs in this gene and in NAC3 that allow us to discover closely related accessions according to the phylogenetic tree analysis. We also found that the association between genetic variants among the 18 genes with the highest scores in our GWAS and the phenotypic classes into which we divided our accessions are not straightforward and likely follow historical patterns.

Temporal change in chromatin accessibility predicts regulators of nodulation in Medicago truncatula

Background

Symbiotic associations between bacteria and leguminous plants lead to the formation of root nodules that fix nitrogen needed for sustainable agricultural systems. Symbiosis triggers extensive genome and transcriptome remodeling in the plant, yet an integrated understanding of the extent of chromatin changes and transcriptional networks that functionally regulate gene expression associated with symbiosis remains poorly understood. In particular, analyses of early temporal events driving this symbiosis have only captured correlative relationships between regulators and targets at mRNA level. Here, we characterize changes in transcriptome and chromatin accessibility in the model legume Medicago truncatula, in response to rhizobial signals that trigger the formation of root nodules.

Results

We profiled the temporal chromatin accessibility (ATAC-seq) and transcriptome (RNA-seq) dynamics of M. truncatula roots treated with bacterial small molecules called lipo-chitooligosaccharides that trigger host symbiotic pathways of nodule development. Using a novel approach, dynamic regulatory module networks, we integrated ATAC-seq and RNA-seq time courses to predict cis-regulatory elements and transcription factors that most significantly contribute to transcriptomic changes associated with symbiosis. Regulators involved in auxin (IAA4-5, SHY2), ethylene (EIN3, ERF1), and abscisic acid (ABI5) hormone response, as well as histone and DNA methylation (IBM1), emerged among those most predictive of transcriptome dynamics. RNAi-based knockdown of EIN3 and ERF1 reduced nodule number in M. truncatula validating the role of these predicted regulators in symbiosis between legumes and rhizobia.

Conclusions

Our transcriptomic and chromatin accessibility datasets provide a valuable resource to understand the gene regulatory programs controlling the early stages of the dynamic process of symbiosis. The regulators identified provide potential targets for future experimental validation, and the engineering of nodulation in species is unable to establish that symbiosis naturally.

An open source plant kinase chemogenomics set

One hundred twenty-nine protein kinases, selected to represent the diversity of the rice (Oryza sativa) kinome, were cloned and tested for expression in Escherichia coli. Forty of these rice kinases were purified and screened using differential scanning fluorimetry (DSF) against 627 diverse kinase inhibitors, with a range of structures and activities targeting diverse human kinases. Thirty-seven active compounds were then tested for their ability to modify primary root development in Arabidopsis. Of these, 14 compounds caused a significant reduction of primary root length compared with control plants. Two of these inhibitory compounds bind to the predicted orthologue of Arabidopsis PSKR1, one of two receptors for PSK, a small sulfated peptide that positively controls root development. The reduced root length phenotype could not be rescued by the exogenous addition of the PSK peptide, suggesting that chemical treatment may inhibit both PSKR1 and its closely related receptor PSKR2. Six of the compounds acting as root growth inhibitors in Arabidopsis conferred the same effect in rice. Compound RAF265 (CHIR-265), previously shown to bind the human kinase BRAF (B-Raf proto-oncogene, serine/threonine kinase), also binds to nine highly conserved rice kinases tested. The binding of human and rice kinases to the same compound suggests that human kinase inhibitor sets will be useful for dissecting the function of plant kinases.

Sucrose targets clathrin-mediated endocytosis kinetics supporting cell elongation in Arabidopsis thaliana

Sucrose is a central regulator of plant growth and development, coordinating cell division and cell elongation according to the energy status of plants. Sucrose is known to stimulate bulk endocytosis in cultured cells; however, its physiological role has not been described to date. Our work shows that sucrose supplementation induces root cell elongation and endocytosis. Sucrose targets clathrin-mediated endocytosis (CME) in epidermal cells. Its presence decreases the abundance of both the clathrin coating complex and phosphatidylinositol 4,5-biphosphate at the plasma membrane, while increasing clathrin complex abundance in intracellular spaces. Sucrose decreases the plasma membrane residence time of the clathrin complex, indicating that it controls the kinetics of endocytic vesicle formation and internalization. CME regulation by sucrose is inducible and reversible; this on/off mechanism reveals an endocytosis-mediated mechanism for sensing plant energy status and signaling root elongation. The sucrose monosaccharide fructose also induces CME, while glucose and mannitol have no effect, demonstrating the specificity of the process. Overall, our data show that sucrose can mediate CME, which demonstrates that sucrose signaling for plant growth and development is dependent on endomembrane trafficking.

Strigolactone: An Emerging Growth Regulator for Developing Resilience in Plants

Improving plant resilience to changing environmental conditions is the primary focus of today's scientific research globally. It is essential to find various strategies for the better survival of plants with higher resistance potential to climate change. Strigolactones (SLs) are multifunctional β-carotene derivative molecules that determine a range of plant growth and development aspects, such as root architecture, shoot branching, chlorophyll synthesis, and senescence. SLs facilitate strong defense responses against drought, salinity, heavy metal, nutrient starvation, and heat stress. The SLs trigger other hormonal-responsive pathways and determine plant resilience against stressful environments. This review focuses on the mechanisms regulated by SLs and interaction with other plant hormones to regulate plant developmental processes and SLs' influence on the mitigation of plant damage under abiotic stresses. A better understanding of the signaling and perception of SLs may lead to the path for the sustainability of plants in the changing environmental scenario. The SLs may be considered as an opening door toward sustainable agriculture.

Using machine learning to link the influence of transferred Agrobacterium rhizogenes genes to the hormone profile and morphological traits in Centella asiatica hairy roots

Hairy roots are made after the integration of a small set of genes from Agrobacterium rhizogenes in the plant genome. Little is known about how this small set is linked to their hormone profile, which determines development, morphology, and levels of secondary metabolite production. We used C. asiatica hairy root line cultures to determine the putative links between the rol and aux gene expressions with morphological traits, a hormone profile, and centelloside production. The results obtained after 14 and 28 days of culture were processed via multivariate analysis and machine-learning processes such as random forest, supported vector machines, linear discriminant analysis, and neural networks. This allowed us to obtain models capable of discriminating highly productive root lines from their levels of genetic expression (rol and aux genes) or from their hormone profile. In total, 12 hormones were evaluated, resulting in 10 being satisfactorily detected. Within this set of hormones, abscisic acid (ABA) and cytokinin isopentenyl adenosine (IPA) were found to be critical in defining the morphological traits and centelloside content. The results showed that IPA brings more benefits to the biotechnological platform. Additionally, we determined the degree of influence of each of the evaluated genes on the individual hormone profile, finding that aux1 has a significant influence on the IPA profile, while the rol genes are closely linked to the ABA profile. Finally, we effectively verified the gene influence on these two specific hormones through feeding experiments that aimed to reverse the effect on root morphology and centelloside content.

How Metabolic Rate Relates to Cell Size

Simple Summary

The metabolic conversion of resources into living structures and processes is fundamental to all living systems. The rate of metabolism (‘fire of life’) is critical for supporting the rates of various biological processes (‘pace of life’), but why it varies considerably within and among species is little understood. Much of this variation is related to body size, but such ‘metabolic scaling’ relationships also vary extensively. Numerous explanations have been offered, but no consensus has yet been reached. Here, I critically review explanations concerning how cell size and number and their establishment by cell expansion and multiplication may affect metabolic rate and its scaling with body mass. Numerous lines of evidence suggest that cell size and growth can affect metabolic rate at any given body mass, as well as how it changes with increasing body mass during growth or evolution. Mechanisms causing negative associations between cell size and metabolic rate may involve reduced resource supply and/or demand in larger cells, but more research is needed. A cell-size perspective not only helps to explain some (but not all) variation in metabolic rate and its body-mass scaling, but may also foster the conceptual integration of studies of ontogenetic development and body-mass scaling.

Abstract

Metabolic rate and its covariation with body mass vary substantially within and among species in little understood ways. Here, I critically review explanations (and supporting data) concerning how cell size and number and their establishment by cell expansion and multiplication may affect metabolic rate and its scaling with body mass. Cell size and growth may affect size-specific metabolic rate, as well as the vertical elevation (metabolic level) and slope (exponent) of metabolic scaling relationships. Mechanistic causes of negative correlations between cell size and metabolic rate may involve reduced resource supply and/or demand in larger cells, related to decreased surface area per volume, larger intracellular resource-transport distances, lower metabolic costs of ionic regulation, slower cell multiplication and somatic growth, and larger intracellular deposits of metabolically inert materials in some tissues. A cell-size perspective helps to explain some (but not all) variation in metabolic rate and its body-mass scaling and thus should be included in any multi-mechanistic theory attempting to explain the full diversity of metabolic scaling. A cell-size approach may also help conceptually integrate studies of the biological regulation of cellular growth and metabolism with those concerning major transitions in ontogenetic development and associated shifts in metabolic scaling.

The purple acid phosphatase GmPAP17 predominantly enhances phosphorus use efficiency in soybean

Purple acid phosphatase (PAP) is an important plant acid phosphatase, which can secrete to the rhizosphere to decompose organophosphorus, promote phosphorus use efficiency, plant growth and development. However, little is known about the functions of intracellular PAP in plants, especially for soybean. Our previous study integrating QTL mapping and transcriptome analysis identified an promising low phosphorus (LP)-induced gene GmPAP17. Here, we determined that GmPAP17 was mainly expressed in roots and had a strong response to LP stress. Furthermore, and the relative expression in the root of LP tolerant genotypes NN94-156 was significantly greater than that of LP sensitive genotype Bogao after LP stress treatment. The overexpression of GmPAP17 significantly enhanced both acid phosphatase activity and growth performance of hairy roots under LP stress condition, it was vice versa for RNAi interference of GmPAP17, indicating that GmPAP17 plays an important role in P use efficiency. Moreover, yeast two-hybrid and bimolecular fluorescence complementation analysis showed that GmRAP2.2 was involved in the regulation network of GmPAP17. Taken together, our results suggest that GmPAP17 is a novel plant PAP that functions in the adaptation of soybean to LP stress, possibly through its involvement in P recycling in plants.

Comparative Transcriptomic, Anatomical and Phytohormone Analyses Provide New Insights Into Hormone-Mediated Tetraploid Dwarfing in Hybrid Sweetgum (Liquidambar styraciflua × L. formosana)

Polyploid breeding is an effective approach to improve plant biomass and quality. Both fast growth and dwarf types of in vitro or ex vitro plants are produced after polyploidization. However, little is known regarding the dwarf type mechanism in polyploids grown in vitro. In this study, the morphological and cytological characteristics were measured in tetraploid and diploid hybrid sweetgum (Liquidambar styraciflua × L. formosana) with the same genetic background. RNA sequencing (RNA-Seq) was used to analyse shoot and root variations between tetraploid and diploid plants; important metabolites were validated. The results showed that the shoot and root lengths were significantly shorter in tetraploids than in diploids after 25 d of culture. Most tetraploid root cells were wider and more irregular, and the length of the meristematic zone was shorter, while tetraploid cells were significantly larger than diploid cells. Differentially expressed genes (DEGs) were significantly enriched in the plant growth and organ elongation pathways, such as plant hormone biosynthesis and signal transduction, sugar and starch metabolism, and cell cycles. Hormone biosynthesis and signal transduction genes, such as YUCCA, TAA1, GH3, SAUR, CPS, KO, KAO, GA20ox, GA3ox, BAS1 and CYCD3, which help to regulate organ elongation, were generally downregulated. The auxin, gibberellin, and brassinolide (BL) contents in roots and stems were significantly lower in tetraploids than in diploids, which may greatly contribute to slow growth in the roots and stems of tetraploid regenerated plants. Exogenous gibberellic acid (GA₃) and indole-3-acetic acid (IAA), which induced plant cell elongation, could significantly promote growth in the stems and roots of tetraploids. In summary, comparative transcriptomics and metabolite analysis showed that the slow growth of regenerated tetraploid hybrid sweetgum was strongly related to auxin and gibberellin deficiency. Our findings provide insights into the molecular mechanisms that underlie dwarfism in allopolyploid hybrid sweetgum.

In vitro Induction and Phenotypic Variations of Autotetraploid Garlic (Allium sativum L.) With Dwarfism

Garlic (Allium sativum L.) is a compelling horticultural crop with high culinary and therapeutic values. Commercial garlic varieties are male-sterile and propagated asexually from individual cloves or bulbils. Consequently, its main breeding strategy has been confined to the time-consuming and inefficient selection approach from the existing germplasm. Polyploidy, meanwhile, plays a prominent role in conferring plants various changes in morphological, physiological, and ecological properties. Artificial polyploidy induction has gained pivotal attention to generate new genotype for further crop improvement as a mutational breeding method. In our study, efficient and reliable in vitro induction protocols of autotetraploid garlic were established by applying different antimitotic agents based on high-frequency direct shoot organogenesis initiated from inflorescence explant. The explants were cultured on solid medium containing various concentrations of colchicine or oryzalin for different duration days. Afterward, the ploidy levels of regenerated plantlets with stable and distinguished characters were confirmed by flow cytometry and chromosome counting. The colchicine concentration at 0.2% (w/v) combined with culture duration for 20 days was most efficient (the autotetraploid induction rate was 21.8%) compared to the induction rate of 4.3% using oryzalin at 60 μmol L-1 for 20 days. No polymorphic bands were detected by simple sequence repeat analysis between tetraploid and diploid plantlets. The tetraploids exhibited a stable and remarkable dwarfness effect rarely reported in artificial polyploidization among wide range of phenotypic variations. There are both morphological and cytological changes including extremely reduced plant height, thickening and broadening of leaves, disappearance of pseudostem, density reduction, and augmented width of stomatal. Furthermore, the level of phytohormones, including, indole propionic acid, gibberellin, brassinolide, zeatin, dihydrozeatin, and methyl jasmonate, was significantly lower in tetraploids than those in diploid controls, except indole acetic acid and abscisic acid, which could partly explain the dwarfness in hormonal regulation aspect. Moreover, as the typical secondary metabolites of garlic, organosulfur compounds including allicin, diallyl disulfide, and diallyl trisulfide accumulated a higher content significantly in tetraploids. The obtained dwarf genotype of autotetraploid garlic could bring new perspectives for the artificial polyploids breeding and be implemented as a new germplasm to facilitate investigation into whole-genome doubling consequences.

Elongating Effect of the Peptide AEDL on the Root of Nicotiana tabacum under Salinity

The overall survival of a plant depends on the development, growth, and functioning of the roots. Root development and growth are not only genetically programmed but are constantly influenced by environmental factors, with the roots adapting to such changes. The peptide AEDL (alanine–glutamine acid–asparagine acid–leucine) at a concentration of 10⁻⁷ M had an elongating effect on the root cells of Nicotiana tabacum seedlings. The action of this peptide at such a low concentration is similar to that of peptide phytohormones. In the presence of 150 mM NaCl, a strong distortion in the development and architecture of the tobacco roots was observed. However, the combined presence of AEDL and NaCl resulted in normal root development. In the presence of AEDL, reactive oxygen species (ROS) were detected in the elongation and root hair zones of the roots. The ROS marker fluorescence intensity in plant cells grown with AEDL was much lower than that of plant cells grown without the peptide. Thus, AEDL protected the root tissue from damage by oxidative stress caused by the toxic effects of NaCl. Localization and accumulation of AEDL at the root were tissue-specific. Fluorescence microscopy showed that FITC-AEDL predominantly localized in the zones of elongation and root hairs, with insignificant localization in the meristem zone. AEDL induced a change in the structural organization of chromatin. Structural changes in chromatin caused significant changes in the expression of numerous genes associated with the development and differentiation of the root system. In the roots of tobacco seedlings grown in the presence of AEDL, the expression of WOX family genes decreased, and differentiation of stem cells increased, which led to root elongation. However, in the presence of NaCl, elongation of the tobacco root occurred via a different mechanism involving genes of the expansin family that weaken the cell wall in the elongation zone. Root elongation of plants is of fundamental importance in biology and is especially relevant to crop production as it can affect crop yields.

Spatial control of cell division by GA-OsGRF7/8 module in a leaf explaining the leaf length variation between cultivated and wild rice

Cellular and genetic understanding of the rice leaf size regulation is limited, despite rice being the staple food of more than half of the global population. We investigated the mechanism controlling the rice leaf length using cultivated and wild rice accessions that remarkably differed for leaf size. Comparative transcriptomics, gibberellic acid (GA) quantification and leaf kinematics of the contrasting accessions suggested the involvement of GA, cell cycle and growth-regulating factors (GRFs) in the rice leaf size regulation. Zone-specific expression analysis and VIGS established the functions of specific GRFs in the process. The leaf length of the selected accessions was strongly correlated with GA levels. Higher GA content in wild rice accessions with longer leaves and GA-induced increase in the leaf length via an increase in cell division confirmed a GA-mediated regulation of division zone in rice. Downstream to GA, OsGRF7 and OsGRF8 function for controlling cell division to determine the rice leaf length. Spatial control of cell division to determine the division zone size mediated by GA and downstream OsGRF7 and OsGRF8 explains the leaf length differences between the cultivated and wild rice. This mechanism to control the rice leaf length might have contributed to optimizing leaf size during domestication.

Genome-Wide Expression Analysis of Root Tips in Contrasting Rice Genotypes Revealed Novel Candidate Genes for Water Stress Adaptation

Root system architecture (RSA) is an important agronomic trait with vital roles in plant productivity under water stress conditions. A deep and branched root system may help plants to avoid water stress by enabling them to acquire more water and nutrient resources. Nevertheless, our knowledge of the genetics and molecular control mechanisms of RSA is still relatively limited. In this study, we analyzed the transcriptome response of root tips to water stress in two well-known genotypes of rice: IR64, a high-yielding lowland genotype, which represents a drought-susceptible and shallow-rooting genotype; and Azucena, a traditional, upland, drought-tolerant and deep-rooting genotype. We collected samples from three zones (Z) of root tip: two consecutive 5 mm sections (Z1 and Z2) and the following next 10 mm section (Z3), which mainly includes meristematic and maturation regions. Our results showed that Z1 of Azucena was enriched for genes involved in cell cycle and division and root growth and development whereas in IR64 root, responses to oxidative stress were strongly enriched. While the expansion of the lateral root system was used as a strategy by both genotypes when facing water shortage, it was more pronounced in Azucena. Our results also suggested that by enhancing meristematic cell wall thickening for insulation purposes as a means of confronting stress, the sensitive IR64 genotype may have reduced its capacity for root elongation to extract water from deeper layers of the soil. Furthermore, several members of gene families such as NAC, AP2/ERF, AUX/IAA, EXPANSIN, WRKY, and MYB emerged as main players in RSA and drought adaptation. We also found that HSP and HSF gene families participated in oxidative stress inhibition in IR64 root tip. Meta-quantitative trait loci (QTL) analysis revealed that 288 differentially expressed genes were colocalized with RSA QTLs previously reported under drought and normal conditions. This finding warrants further research into their possible roles in drought adaptation. Overall, our analyses presented several major molecular differences between Azucena and IR64, which may partly explain their differential root growth responses to water stress. It appears that Azucena avoided water stress through enhancing growth and root exploration to access water, whereas IR64 might mainly rely on cell insulation to maintain water and antioxidant system to withstand stress. We identified a large number of novel RSA and drought associated candidate genes, which should encourage further exploration of their potential to enhance drought adaptation in rice.

Insights into the molecular basis of hypergravity-induced root growth phenotype in bread wheat (Triticum aestivum L.)

Hypergravity is a condition where the force of gravity exceeds that on the surface of the Earth and can be simulated by centrifugation. Previously, a significant increase in root growth phenotype was observed when wheat seeds were exposed to hypergravity (10 g for 12 h). In the present study, we investigated the molecular basis of this change through root transcriptome. The data revealed a total of 3765 up-regulated and 2102 down-regulated transcripts in response to hypergravity. GO enrichment analysis revealed hormonal responses, cell division, and cell-wall-related terms were significantly enriched in hypergravity. The increased isoform level expression of transcripts involved in auxin biosynthesis, transport, and signaling was observed. Further, enhanced expression of cell division transcripts and down-regulation of cell number regulator genes suggests rapid cell division. Overexpression of cellulose and hemicellulose biosynthesis transcripts suggests demand for cell-wall constituents. Collectively, this study identified candidate genes associated with hypergravity-induced enhanced root growth.

Combined Metabolome and Transcriptome Analyses of Young, Mature, and Old Rhizome Tissues of Zingiber officinale Roscoe

Ginger (Zingiber officinale Roscoe) is known for its unique pungent taste and useability in traditional Chinese medicine. The main compounds in ginger rhizome can be classified as gingerols, diarylheptanoids, and volatile oils. The composition and concentrations of the bioactive compounds in ginger rhizome might vary according to the age of the rhizome. In this regard, the knowledge on the transcriptomic signatures and accumulation of metabolites in young (Y), mature (M), and old (O) ginger rhizomes is scarce. This study used HiSeq Illumina Sequencing and UPLC-MS/MS analyses to delineate how the expression of key genes changes in Y, M, and O ginger rhizome tissues and how it affects the accumulation of metabolites in key pathways. The transcriptome sequencing identified 238,157 genes of which 13,976, 11,243, and 24,498 were differentially expressed (DEGs) in Y vs. M, M vs. O, and Y vs. O, respectively. These DEGs were significantly enriched in stilbenoid, diarylheptanoid, and gingerol biosynthesis, phenylpropanoid biosynthesis, plant-hormone signal transduction, starch and sucrose metabolism, linoleic acid metabolism, and α-linoleic acid metabolism pathways. The metabolome profiling identified 661 metabolites of which 311, 386, and 296 metabolites were differentially accumulated in Y vs. M, Y vs. O, and M vs. O, respectively. These metabolites were also enriched in the pathways mentioned above. The DEGs and DAMs enrichment showed that the gingerol content is higher in Y rhizome, whereas the Y, M, and O tissues differ in linoleic and α-linoleic acid accumulation. Similarly, the starch and sucrose metabolism pathway is variably regulated in Y, M, and O rhizome tissues. Our results showed that ginger rhizome growth slows down (Y > M > O) probably due to changes in phytohormone signaling. Young ginger rhizome is the most transcriptionally and metabolically active tissue as compared to M and O. The transitioning from Y to M and O affects the gingerol, sugars, linoleic acid, and α-linoleic acid concentrations and related gene expressions.

Molecular and Physiological Perspectives of Abscisic Acid Mediated Drought Adjustment Strategies

Drought is the most prevalent unfavorable condition that impairs plant growth and development by altering morphological, physiological, and biochemical functions, thereby impeding plant biomass production. To survive the adverse effects, water limiting condition triggers a sophisticated adjustment mechanism orchestrated mainly by hormones that directly protect plants via the stimulation of several signaling cascades. Predominantly, water deficit signals cause the increase in the level of endogenous ABA, which elicits signaling pathways involving transcription factors that enhance resistance mechanisms to combat drought-stimulated damage in plants. These responses mainly include stomatal closure, seed dormancy, cuticular wax deposition, leaf senescence, and alteration of the shoot and root growth. Unraveling how plants adjust to drought could provide valuable information, and a comprehensive understanding of the resistance mechanisms will help researchers design ways to improve crop performance under water limiting conditions. This review deals with the past and recent updates of ABA-mediated molecular mechanisms that plants can implement to cope with the challenges of drought stress.

Abscisic acid mediates the reduction of petunia flower size at elevated temperatures due to reduced cell division

Elevated temperatures suppress cell division in developing petunia buds leading to smaller flowers, mediated by ABA. Flower size is one of the most important showy traits in determining pollinator attraction, and a central factor determining the quality of floricultural products. Whereas the adverse effects of elevated temperatures on showy traits have been described in detail, its underlining mechanisms is poorly understood. Here, we investigated the physiological mechanism responsible for the reduction of flower size in petunia under elevated temperatures. We found that the early stages of flower-bud development were most sensitive to elevated temperatures, resulting in a drastic reduction of flower diameter that was almost independent of flower load. We demonstrated that the temperature-mediated flower size reduction occurred due to a shorter growth period, and a lower rate of corolla cell division. Consistently, local application of cytokinin, a phytohormone that promotes cell division, resulted in recovery of flower dimensions when grown under elevated temperatures. Hormone analysis of temperature-inhibited flower buds revealed no significant changes in levels of cytokinin, and a specific increase of abscisic acid (ABA) levels, known to inhibit cell division. Moreover, local application of ABA on flower buds caused a reduction of flower dimensions as a result of lower levels of cell division, suggesting that ABA mediates the reduction of flower size at elevated temperatures. Taken together, our results shed light on the mechanism by which elevated temperatures decrease petunia flower size, and show that temperature-mediated reduction of flower size can be alleviated by increasing the cytokinin/ABA ratio.

Role of Basal ABA in Plant Growth and Development

Abscisic acid (ABA) regulates various aspects of plant physiology, including promoting seed dormancy and adaptive responses to abiotic and biotic stresses. In addition, ABA plays an im-portant role in growth and development under non-stressed conditions. This review summarizes phenotypes of ABA biosynthesis and signaling mutants to clarify the roles of basal ABA in growth and development. The promotive and inhibitive actions of ABA in growth are characterized by stunted and enhanced growth of ABA-deficient and insensitive mutants, respectively. Growth regulation by ABA is both promotive and inhibitive, depending on the context, such as concentrations, tissues, and environmental conditions. Basal ABA regulates local growth including hyponastic growth, skotomorphogenesis and lateral root growth. At the cellular level, basal ABA is essential for proper chloroplast biogenesis, central metabolism, and expression of cell-cycle genes. Basal ABA also regulates epidermis development in the shoot, by inhibiting stomatal development, and deposition of hydrophobic polymers like a cuticular wax layer covering the leaf surface. In the root, basal ABA is involved in xylem differentiation and suberization of the endodermis. Hormone crosstalk plays key roles in growth and developmental processes regulated by ABA. Phenotypes of ABA-deficient and insensitive mutants indicate prominent functions of basal ABA in plant growth and development.

Phosphatidylserine Is Required for the Normal Progression of Cell Plate Formation in Arabidopsis Root Meristems

Phosphatidylserine (PS) is involved in various cellular processes in yeast and animals. However, PS functions in plants remain unclear. In Arabidopsis, PS is relatively enriched in flower and root tissues, and the genetic disturbance of PS biosynthesis in phosphatidylserine synthase1 (PSS1)/ pss1 heterozygotes induces sporophytic and gametophytic defects during pollen maturation. This study functionally characterized PS in Arabidopsis roots and observed that pss1 seedlings exhibited a short-root phenotype by reducing the meristem size and cell elongation capacity. Confocal microscopy imaging analyses of PS with GFP-LactC2 and the endocytic activity with FM 4-64 revealed that although GFP-LactC2 (or PS) was localized in the plasma membrane and endocytic membranes, the lack of PS in pss1 roots did not affect the constitutive endocytosis. Instead, a fluorescence imaging analysis of the cytokinetic phases in the dividing zone of pss1-2 roots revealed a significant delay in telophase progression, requiring active cargo vesicle trafficking for cell plate formation. Confocal microscopy imaging analysis of transgenic GFP-LactC2 root cells with developing cell plates indicated that GFP-LactC2 was localized at the cell plate. Moreover, confocal microscopy images of transgenic pss1-2 and PSS1 roots expressing the cell plate-specific syntaxin construct ProKNOLLE:eGFP-KNOLLE showed abnormal cell plate development in pss1-2ProKNOLLE:eGFP-KNOLLE roots. These results suggested that PS is required for root cytokinesis, possibly because it helps mediate the cargo vesicular trafficking required for cell plate formation.

Role of Auxin and Nitrate Signaling in the Development of Root System Architecture

The plant root is an important storage organ that stores indole-3-acetic acid (IAA) from the apical meristem, as well as nitrogen, which is obtained from the external environment. IAA and nitrogen act as signaling molecules that promote root growth to obtain further resources. Fluctuations in the distribution of nitrogen in the soil environment induce plants to develop a set of strategies that effectively improve nitrogen use efficiency. Auxin integrates the information regarding the nitrate status inside and outside the plant body to reasonably distribute resources and sustainably construct the plant root system. In this review, we focus on the main factors involved in the process of nitrate- and auxin-mediated regulation of root structure to better understand how the root system integrates the internal and external information and how this information is utilized to modify the root system architecture.

Shaping the root system: the interplay between miRNA regulatory hubs and phytohormones

The root system commonly lies underground, where it provides anchorage for the aerial organs, as well as nutrients and water. Both endogenous and environmental cues contribute to the establishment of the root system. Among the endogenous cues, microRNAs (miRNAs), transcription factors, and phytohormones modulate root architecture. miRNAs belong to a subset of endogenous hairpin-derived small RNAs that post-transcriptionally control target gene expression, mostly transcription factors, comprising the miRNA regulatory hubs. Phytohormones are signaling molecules involved in most developmental processes. Some miRNAs and targets participate in more than one hormonal pathway, thereby providing new bridges in plant hormonal crosstalk. Unraveling the intricate network of molecular mechanisms underlying the establishment of root systems is a central aspect in the development of novel strategies for plant breeding to increase yield and optimize agricultural land use. In this review, we summarize recent findings describing the molecular mechanisms associated with the interplay between miRNA regulatory hubs and phytohormones to ensure the establishment of a proper root system. We focus on post-embryonic growth and development of primary, lateral, and adventitious roots. In addition, we discuss novel insights for future research on the interaction between miRNAs and phytohormones in root architecture.

A perspective on cell proliferation kinetics in the root apical meristem

Organogenesis in plants is primarily postembryonic and relies on a strict balance between cell division and cell expansion. The root is a particularly well-suited model to study cell proliferation in detail since the two processes are spatially and temporally separated for all the different tissues. In addition, the root is amenable to detailed microscopic analysis to identify cells progressing through the cell cycle. While it is clear that cell proliferation activity is restricted to the root apical meristem (RAM), understanding cell proliferation kinetics and identifying its parameters have required much effort over many years. Here, we review the main concepts, experimental settings, and findings aimed at obtaining a detailed knowledge of how cells proliferate within the RAM. The combination of novel tools, experimental strategies, and mathematical models has contributed to our current view of cell proliferation in the RAM. We also discuss several lines of research that need to be explored in the future.

Hormonal orchestration of root apical meristem formation and maintenance in Arabidopsis

Plant hormones are key regulators of a number of developmental and adaptive responses in plants, integrating the control of intrinsic developmental regulatory circuits with environmental inputs. Here we provide an overview of the molecular mechanisms underlying hormonal regulation of root development. We focus on key events during both embryonic and post-embryonic development, including specification of the hypophysis as a future organizer of the root apical meristem (RAM), hypophysis asymmetric division, specification of the quiescent centre (QC) and the stem cell niche (SCN), RAM maturation and maintenance of QC/SCN activity, and RAM size. We address both well-established and newly proposed concepts, highlight potential ambiguities in recent terminology and classification criteria of longitudinal root zonation, and point to contrasting results and alternative scenarios for recent models. In the concluding remarks, we summarize the common principles of hormonal control during root development and the mechanisms potentially explaining often antagonistic outputs of hormone action, and propose possible future research directions on hormones in the root.

Genome Maintenance Mechanisms at the Chromatin Level

Genome integrity is constantly threatened by internal and external stressors, in both animals and plants. As plants are sessile, a variety of environment stressors can damage their DNA. In the nucleus, DNA twines around histone proteins to form the higher-order structure “chromatin”. Unraveling how chromatin transforms on sensing genotoxic stress is, thus, key to understanding plant strategies to cope with fluctuating environments. In recent years, accumulating evidence in plant research has suggested that chromatin plays a crucial role in protecting DNA from genotoxic stress in three ways: (1) changes in chromatin modifications around damaged sites enhance DNA repair by providing a scaffold and/or easy access to DNA repair machinery; (2) DNA damage triggers genome-wide alterations in chromatin modifications, globally modulating gene expression required for DNA damage response, such as stem cell death, cell-cycle arrest, and an early onset of endoreplication; and (3) condensed chromatin functions as a physical barrier against genotoxic stressors to protect DNA. In this review, we highlight the chromatin-level control of genome stability and compare the regulatory systems in plants and animals to find out unique mechanisms maintaining genome integrity under genotoxic stress.

Supraoptimal Brassinosteroid Levels Inhibit Root Growth by Reducing Root Meristem and Cell Elongation in Rice

Root growth depends on cell proliferation and cell elongation at the root meristem, which are controlled by plant hormones and nutrient availability. As a foraging strategy, rice (Oryza sativa L.) grows longer roots when nitrogen (N) is scarce. However, how the plant steroid hormone brassinosteroid (BR) regulates rice root meristem development and responses to N deficiency remains unclear. Here, we show that BR has a negative effect on meristem size and a dose-dependent effect on cell elongation in roots of rice seedlings treated with exogenous BR (24-epicastasterone, ECS) and the BR biosynthesis inhibitor propiconazole (PPZ). A genome-wide transcriptome analysis identified 4110 and 3076 differentially expressed genes in response to ECS and PPZ treatments, respectively. The gene ontology (GO) analysis shows that terms related to cell proliferation and cell elongation were enriched among the ECS-repressed genes. Furthermore, microscopic analysis of ECS- and PPZ-treated roots grown under N-sufficient and N-deficient conditions demonstrates that exogenous BR or PPZ application could not enhance N deficiency-mediated root elongation promotion as the treatments could not promote root meristem size and cell elongation simultaneously. Our study demonstrates that optimal levels of BR in the rice root meristem are crucial for optimal root growth and the foraging response to N deficiency.

Plant programmed cell death meets auxin signalling

Both auxin signalling and programmed cell death (PCD) are essential components of a normally functioning plant. Auxin underpins plant growth and development, as well as regulating plant defences against environmental stresses. PCD, a genetically controlled pathway for selective elimination of redundant, damaged or infected cells, is also a key element of many developmental processes and stress response mechanisms in plants. An increasing body of evidence suggests that auxin signalling and PCD regulation are often connected. While generally auxin appears to suppress cell death, it has also been shown to promote PCD events, most likely via stimulation of ethylene biosynthesis. Intriguingly, certain cells undergoing PCD have also been suggested to control the distribution of auxin in plant tissues, by either releasing a burst of auxin or creating an anatomical barrier to auxin transport and distribution. These recent findings indicate novel roles of localized PCD events in the context of plant development such as control of root architecture, or tissue regeneration following injury, and suggest exciting possibilities for incorporation of this knowledge into crop improvement strategies.

Identification and Characterization of Short Crown Root 8, a Temperature-Sensitive Mutant Associated with Crown Root Development in Rice

Crown roots are essential for plants to obtain water and nutrients, perceive environmental changes, and synthesize plant hormones. In this study, we identified and characterized short crown root 8 (scr8), which exhibited a defective phenotype of crown root and vegetative development. Temperature treatment showed that scr8 was sensitive to temperature and that the mutant phenotypes were rescued when grown under low temperature condition (20 °C). Histological and EdU staining analysis showed that the crown root formation was hampered and that the root meristem activity was decreased in scr8. With map-based cloning strategy, the SCR8 gene was fine-mapped to an interval of 126.4 kb on chromosome 8. Sequencing analysis revealed that the sequence variations were only found in LOC_Os08g14850, which encodes a CC-NBS-LRR protein. Expression and inoculation test analysis showed that the expression level of LOC_Os08g14850 was significantly decreased under low temperature (20 °C) and that the resistance to Xanthomonas oryzae pv. Oryzae (Xoo) was enhanced in scr8. These results indicated that LOC_Os08g14850 may be the candidate of SCR8 and that its mutation activated the plant defense response, resulting in a crown root growth defect.