Transcriptional changes during crown-root development and emergence in barley (Hordeum vulgare L.).

BACKGROUND: Roots play an important role during plant growth and development, ensuring water and nutrient uptake. Understanding the mechanisms regulating their initiation and development opens doors towards root system architecture engineering. RESULTS: Here, we investigated by RNA-seq analysis the changes in gene expression in the barley stem base of 1 day-after-germination (DAG) and 10DAG seedlings when crown roots are formed. We identified 2,333 genes whose expression was lower in the stem base of 10DAG seedlings compared to 1DAG seedlings. Those genes were mostly related to basal cellular activity such as cell cycle organization, protein biosynthesis, chromatin organization, cytoskeleton organization or nucleotide metabolism. In opposite, 2,932 genes showed up-regulation in the stem base of 10DAG seedlings compared to 1DAG seedlings, and their function was related to phytohormone action, solute transport, redox homeostasis, protein modification, secondary metabolism. Our results highlighted genes that are likely involved in the different steps of crown root formation from initiation to primordia differentiation and emergence, and revealed the activation of different hormonal pathways during this process. CONCLUSIONS: This whole transcriptomic study is the first study aiming at understanding the molecular mechanisms controlling crown root development in barley. The results shed light on crown root emergence that is likely associated with a strong cell wall modification, death of the cells covering the crown root primordium, and the production of defense molecules that might prevent pathogen infection at the site of root emergence.

Raman developmental markers in root cell walls are associated with lodging tendency in tef.

MAIN CONCLUSION: Using Raman micro-spectroscopy on tef roots, we could monitor cell wall maturation in lines with varied genetic lodging tendency. We describe the developing cell wall composition in root endodermis and cylinder tissue. Tef [Eragrostis tef (Zucc.) Trotter] is an important staple crop in Ethiopia and Eritrea, producing gluten-free and protein-rich grains. However, this crop is not adapted to modern farming practices due to high lodging susceptibility, which prevents the application of mechanical harvest. Lodging describes the displacement of roots (root lodging) or fracture of culms (stem lodging), forcing plants to bend or fall from their vertical position, causing significant yield losses. In this study, we aimed to understand the microstructural properties of crown roots, underlining tef tolerance/susceptibility to lodging. We analyzed plants at 5 and 10 weeks after emergence and compared trellised to lodged plants. Root cross sections from different tef genotypes were characterized by scanning electron microscopy, micro-computed tomography, and Raman micro-spectroscopy. Lodging susceptible genotypes exhibited early tissue maturation, including developed aerenchyma, intensive lignification, and lignin with high levels of crosslinks. A comparison between trellised and lodged plants suggested that lodging itself does not affect the histology of root tissue. Furthermore, cell wall composition along plant maturation was typical to each of the tested genotypes independently of trellising. Our results suggest that it is possible to select lines that exhibit slow maturation of crown roots. Such lines are predicted to show reduction in lodging and facilitate mechanical harvest.

Response of millet and sorghum to a varying water supply around the primary and nodal roots.

BACKGROUND AND AIMS: Cereals have two root systems. The primary system originates from the embryo when the seed germinates and can support the plant until it produces grain. The nodal system can emerge from stem nodes throughout the plant's life; its value for yield is unclear and depends on the environment. The aim of this study was to test the role of nodal roots of sorghum and millet in plant growth in response to variation in soil moisture. Sorghum and millet were chosen as both are adapted to dry conditions. METHODS: Sorghum and millet were grown in a split-pot system that allowed the primary and nodal roots to be watered separately. KEY RESULTS: When primary and nodal roots were watered (12 % soil water content; SWC), millet nodal roots were seven times longer than those of sorghum and six times longer than millet plants in dry treatments, mainly from an 8-fold increase in branch root length. When soil was allowed to dry in both compartments, millet nodal roots responded and grew 20 % longer branch roots than in the well-watered control. Sorghum nodal roots were unchanged. When only primary roots received water, nodal roots of both species emerged and elongated into extremely dry soil (0.6-1.5 % SWC), possibly with phloem-delivered water from the primary roots in the moist inner pot. Nodal roots were thick, short, branchless and vertical, indicating a tropism that was more pronounced in millet. Total nodal root length increased in both species when the dry soil was covered with plastic, suggesting that stubble retention or leaf mulching could facilitate nodal roots reaching deeper moist layers in dry climates. Greater nodal root length in millet than in sorghum was associated with increased shoot biomass, water uptake and water use efficiency (shoot mass per water). Millet had a more plastic response than sorghum to moisture around the nodal roots due to (1) faster growth and progression through ontogeny for earlier nodal root branch length and (2) partitioning to nodal root length from primary roots, independent of shoot size. CONCLUSIONS: Nodal and primary roots have distinct responses to soil moisture that depend on species. They can be selected independently in a breeding programme to shape root architecture. A rapid rate of plant development and enhanced responsiveness to local moisture may be traits that favour nodal roots and water use efficiency at no cost to shoot growth.

ROS-stimulated protein lysine acetylation is required for crown root development in rice.

INTRODUCTION: As signal molecules in aerobic organisms, locally accumulated ROS have been reported to balance cell division and differentiation in the root meristem. Protein posttranslational modifications such as lysine acetylation play critical roles in controlling a variety of cellular processes. However, the mechanism by which ROS regulate root development is unknown. In addition, how protein lysine acetylation is regulated and whether cellular ROS levels affect protein lysine acetylation remain unclear. OBJECTIVES: We aimed to elucidate the relationship between ROS and protein acetylation by exploring a rice mutant plant that displays a decreased level of ROS in postembryonic crown root (CR) cells and severe defects in CR development. METHODS: First, proteomic analysis was used to find candidate proteins responsible for the decrease of ROS detected in the wox11 mutant. Then, biochemical, molecular, and genetic analyses were used to study WOX11-regulated genes involved in ROS homeostasis. Finally, acetylproteomic analysis of wild type and wox11 roots treated with or without potassium iodide (KI) and hydrogen peroxide (H2O2) was used to study the effects of ROS on protein acetylation in rice CR cells. RESULTS: We demonstrated that WOX11 was required to maintain ROS homeostasis by upregulating peroxidase genes in the crown root meristem. Acetylproteomic analysis revealed that WOX11-dependent hydrogen peroxide (H2O2) levels in CR cells promoted lysine acetylation of many non-histone proteins enriched for nitrogen metabolism and peptide/protein synthesis pathways. Further analysis revealed that the redox state affected histone deacetylases (HDACs) activity, which was likely related to the high levels of protein lysine acetylation in CR cells. CONCLUSION: WOX11-controlled ROS level in CR meristem cells is required for protein lysine acetylation which represents a mechanism of ROS-promoted CR development in rice.

Understanding of Adventitious Root Formation: What Can We Learn From Comparative Genetics?

Adventitious root (AR) formation is a complex developmental process controlled by a plethora of endogenous and environmental factors. Based on fossil evidence and genomic phylogeny, AR formation might be considered the default state of plant roots, which likely evolved independently several times. The application of next-generation sequencing techniques and bioinformatics analyses to non-model plants provide novel approaches to identify genes putatively involved in AR formation in multiple species. Recent results uncovered that the regulation of shoot-borne AR formation in monocots is an adaptive response to nutrient and water deficiency that enhances topsoil foraging and improves plant performance. A hierarchy of transcription factors required for AR initiation has been identified from genetic studies, and recent results highlighted the key involvement of additional regulation through microRNAs. Here, we discuss our current understanding of AR formation in response to specific environmental stresses, such as nutrient deficiency, drought or waterlogging, aimed at providing evidence for the integration of the hormone crosstalk required for the activation of root competent cells within adult tissues from which the ARs develop.

Rice Genotype Differences in Tolerance of Zinc-Deficient Soils: Evidence for the Importance of Root-Induced Changes in the Rhizosphere.

Zinc (Zn) deficiency is a major constraint to rice production and Zn is also often deficient in humans with rice-based diets. Efforts to breed more Zn-efficient rice are constrained by poor understanding of the mechanisms of tolerance to deficiency. Here we assess the contributions of root growth and root Zn uptake efficiency, and we seek to explain the results in terms of specific mechanisms. We made a field experiment in a highly Zn-deficient rice soil in the Philippines with deficiency-tolerant and -sensitive genotypes, and measured growth, Zn uptake and root development. We also measured the effect of planting density. Tolerant genotypes produced more crown roots per plant and had greater uptake rates per unit root surface area; the latter was at least as important as root number to overall tolerance. Tolerant and sensitive genotypes took up more Zn per plant at greater planting densities. The greater uptake per unit root surface area, and the planting density effect can only be explained by root-induced changes in the rhizosphere, either solubilizing Zn, or neutralizing a toxin that impedes Zn uptake (possibly [Formula: see text] or Fe(2+)), or both. Traits for these and crown root number are potential breeding targets.

Influence of some environmental factors on populations of Pratylenchus minyus in wheat.

The distribution and density of Pratylenchus minyus and possible relationships of several environmental components, including ammonium nitrate, were investigated in a wheat field in South Australia. Seasonal variation as measured every 2-4 weeks was eliminated from the observations by periodic regression. Correlation and regression analyses were then used to investigate the association of host plant, rainfall, temperature, and the fungus Gaeumannomyces graminis with P. minyus. Other than seasonal effects, soil moisture and G. graminis were the only components associated with P. minyus. Ammonium nitrate usually was correlated with fewer P. minyus in wheat roots. Much higher numbers of P. minyus were observed in seminal than in crown roots of wheat.