Bioinformatic and experimental analyses revealed pathogen-derived pathoPEP candidates predicted to control plant miRNA expression and infection.

MicroRNAs (miRNAs) in plants and animals function as post-transcriptional regulators of target genes, many of which are involved in multicellular development. miRNAs guide effector complexes to target mRNAs through base-pair complementarity, facilitating site-specific cleavage or translational repression. Biogenesis of miRNAs involves nucleolytic processing of a precursor transcript with extensive foldback structure. Here, we provide evidence that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences. Several recently evolved genes encoding miRNAs in Arabidopsis thaliana and other small RNA-generating loci possess the hallmarks of inverted duplication events that formed the arms on each side of their respective foldback precursors. We propose a model for miRNA evolution that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities.

Plants exhibit daily rhythms in their growth, providing an ideal system for the study of interactions between environmental stimuli such as light and internal regulators such as the circadian clock. We previously found that two basic loop-helix-loop transcription factors, PHYTOCHROME-INTERACTING FACTOR4 (PIF4) and PIF5, integrate light and circadian clock signaling to generate rhythmic plant growth in Arabidopsis (Arabidopsis thaliana). Here, we use expression profiling and real-time growth assays to identify growth regulatory networks downstream of PIF4 and PIF5. Genome-wide analysis of light-, clock-, or growth-correlated genes showed significant overlap between the transcriptomes of clock-, light-, and growth-related pathways. Overrepresentation analysis of growth-correlated genes predicted that the auxin and gibberellic acid (GA) hormone pathways both contribute to diurnal growth control. Indeed, lesions of GA biosynthesis genes retarded rhythmic growth. Surprisingly, GA-responsive genes are not enriched among genes regulated by PIF4 and PIF5, whereas auxin pathway and response genes are. Consistent with this finding, the auxin response is more severely affected than the GA response in pif4 pif5 double mutants and in PIF5-overexpressing lines. We conclude that at least two downstream modules participate in diurnal rhythmic hypocotyl growth: PIF4 and/or PIF5 modulation of auxin-related pathways and PIF-independent regulation of the GA pathway.

Root architecture is key in determining how effective plants are at intercepting and absorbing nutrients and water. Previously, the wheat (Triticum aestivum) cultivars Spica and Maringa were shown to have contrasting root morphologies. These cultivars were crossed to generate an F6:1 population of recombinant inbred lines (RILs) which was genotyped using a 90 K single nucleotide polymorphisms (SNP) chip. A total of 227 recombinant inbred lines (RILs) were grown in soil for 21 days in replicated trials under controlled conditions. At harvest, the plants were scored for seven root traits and two shoot traits. An average of 7.5 quantitative trait loci (QTL) were associated with each trait and, for each of these, physical locations of the flanking markers were identified using the Chinese Spring reference genome. We also compiled a list of genes from wheat and other monocotyledons that have previously been associated with root growth and morphology to determine their physical locations on the Chinese Spring reference genome. This allowed us to determine whether the QTL discovered in our study encompassed genes previously associated with root morphology in wheat or other monocotyledons. Furthermore, it allowed us to establish if the QTL were co-located with the QTL identified from previously published studies. The parental lines together with the genetic markers generated here will enable specific root traits to be introgressed into elite wheat lines. Moreover, the comprehensive list of genes associated with root development, and their physical locations, will be a useful resource for researchers investigating the genetics of root morphology in cereals.

To understand the expansion of multicopy microRNA (miRNA) families in plants, we localized the reported miRNA genes from Arabidopsis and rice to their chromosomes, respectively, and observed that 37% of 117 miRNA genes from Arabidopsis and 35% of 173 miRNA genes from rice were segmental duplications in the genome. In order to characterize whether the expression diversification has occurred among plant multicopy miRNA family members, we designed PCR primers targeting 48 predicted miRNA precursors from 10 families in Arabidopsis and rice. Results from RT-PCR data suggest that the transcribed precursors of members within the same miRNA family were present at different expression levels. In addition, although miR160 and miR162 sequences were conserved in Arabidopsis and rice, we found that the expression patterns of these genes differed between the two species. These data suggested that expression diversification has occurred in multicopy miRNA families, increasing our understanding of the expression regulation of miRNAs in plants.

Roots function dually as a support system and as the nutrient uptake organ of plants. Root morphology changes in response to the soil environment to minimize the metabolic cost of maintaining the root system, while maximizing nutrient acquisition. In response to nutrient-limiting conditions, plants may increase root fineness or specific root length (root length per gram root weight), root/shoot ratio, or root hair length and number. Each of these adaptations involves a different metabolic cost to the plant, with root hair formation as the least costly change, buffering against more costly changes in root/shoot ratio. Mycorrhizal symbiosis is another alternative to such changes. Plants with high degrees of dependence on the symbiosis have coarser root systems, less plasticity in root/shoot ratio, and develop fewer root hairs in low-fertility soils. In nutrient-limited soils, plants highly dependent on mycorrhiza reduce metabolic cost by developing an even more coarse or magnolioid root system, which is less able to obtain nutrients and thus creates a greater dependence of the plant on the symbiosis. These subtle changes in root architecture may be induced by mycorrhizal fungi and can be quantified using topological analysis of rooting patterns. The ability of mycorrhizal fungi to elicit change in root architecture appears to be limited to plant species which are highly dependent upon mycorrhizal symbiosis.

The worldwide demand for vegetable oils is rising. Oilseed rape (Brassica napus) diversifies cereal dominated crop rotations but requires important nitrogen input. Yet, the root organ is offering an untapped opportunity to improve the nitrogen capture in soil. This study evaluates three culture systems in controlled environment, to observe root morphology and to identify root attributes for superior biomass production and nitrogen use. The phenotypic diversity in a panel of 55 modern winter oilseed rape cultivars was screened in response to two divergent nitrate supplies. Upon in vitro and hydroponic cultures, a large variability for root morphologies was observed. Root biomass and morphological traits positively correlated with shoot biomass or leaf area. The activities of high-affinity nitrate transport systems correlated negatively with the leaf area, while the combined high- and low-affinity systems positively with the total root length. The X-ray computed tomography permitted to visualize the root system in pipes filled with soil. The in vitro root phenotype at germination stage was indicative of lateral root deployment in soil-grown plants. This study highlights great genetic potential in oilseed rape, which could be manipulated to optimize crop root characteristics and nitrogen capture with substantial implications for agricultural production.

Circadian clocks synchronized with the environment allow plants to anticipate recurring daily changes and give a fitness advantage. Here, we mapped the dynamic growth phenotype of leaves and roots in two lines of Arabidopsis thaliana with a disrupted circadian clock: the CCA1 over-expressing line (CCA1ox) and the prr9 prr7 prr5 (prr975) mutant. We demonstrate leaf growth defects due to a disrupted circadian clock over a 24 h time scale. Both lines showed enhanced leaf growth compared with the wild-type during the diurnal period, suggesting increased partitioning of photosynthates for leaf growth. Nocturnal leaf growth was reduced and growth inhibition occurred by dawn, which may be explained by ineffective starch degradation in the leaves of the mutants. However, this growth inhibition was not caused by starch exhaustion. Overall, these results are consistent with the notion that the defective clock affects carbon and energy allocation, thereby reducing growth capacity during the night. Furthermore, rosette morphology and size as well as root architecture were strikingly altered by the defective clock control. Separate analysis of the primary root and lateral roots revealed strong suppression of lateral root formation in both CCA1ox and prr975, accompanied by unusual changes in lateral root growth direction under light-dark cycles and increased lateral extension of the root system. We conclude that growth of the whole plant is severely affected by improper clock regulation in A.thaliana, resulting not only in altered timing and capacity for growth but also aberrant development of shoot and root architecture.

Root architecture can be very important in plant productivity. The importance of studies on root morphology and development is discussed to improve seedling growth. Root systems of dicotyledonous species are reviewed, with emphasis on differences between growth of basal and lateral roots. The presence of different types of roots in plant species suggests possible differences in function as well. The architecture of a root system related to its functions is considered. Classical methods for studying root systems comprise excavation of root system, direct observation, and indirect analyses. While the first method is destructive and the third is effective in understanding root architecture only on a relatively gross scale, observation methods allow the scientist a complete a nondestructive architectural study of a root system. The three groups are reviewed related to their potential to give valuable information related to the root architecture and development of the seedling, with emphasis on the availability of a medium-transparent plant-growing system, enabling nondestructive daily observations and plant measurements under controlled environmental conditions. Effects of CO 2 enrichment on seedling growth is reviewed, emphasizing the effects of CO 2 on root growth.

AimsRoot characteristics are important for predicting plant and ecosystem responses to resource scarcity. Simple, categorical traits for roots could be broadly applied to ecosystem function and restoration experiments, but they need to be evaluated for their role and behaviour under various stresses, including water limitation. We hypothesised that more complex root architectures allow more plastic responses to limited water than do tap roots.MethodsWe carried out two greenhouse experiments: one with a range of grassland plant species; the other with only species of Asteraceae to test the responsiveness of root architectural classes to location of limited water in the soil column. Using trait screening techniques and X-ray tomography, we measured the plasticity of the roots in response to water location.ResultsPlasticity of root biomass was lowest in tap rooted species, while fibrous and rhizomatous roots allocated biomass preferentially to where the soil was wettest. X-ray tomography indicated that root morphology was least plastic in rhizomatous species.ConclusionsOur results provide a starting point to effective categorisation of plants in terms of rooting architecture that could aid in understanding drought tolerance of grassland species. They also demonstrate the utility of X-ray tomography in root analyses.

Effects of root temperature on the growth and morphology of roots were measured in oilseed rape (Brassica napus L.) and barley (Hordeum vulgare L.). Plants were grown in flowing solution culture and acclimatized over several weeks to a root temperature of 5°C prior to treatment at a range of root temperatures between 3 and 25°C, with common shoot temperature. Root temperature affected root extension, mean radius, root surface area, numbers and lengths of root hairs. Total root length of rape plants increased with temperature over the range 3–9°C, but was constant at higher temperatures. Root length of barley increased with temperature in the range 3–25°C, by a factor of 27 after 20 days. Root radii had a lognormal distribution and their means decreased with increasing temperature from 0.14 mm at 3°C to 0.08 mm at 25°C. The density of root hairs on the root surface increased by a factor of 4 in rape between 3 and 25°C, but in barley the highest density was at 9°C. The contribution of root hairs to total root surface area was relatively greater in rape than in barley. The changes in root system morphology may be interpreted as adaptive responses to temperature stress on nutrient uptake, providing greater surface area for absorption per unit root weight or length.

Annual Meeting, Winnipeg, Manitoba, 2009

A barley cDNA for the thaumatin-like protein Hv-TLP8 driven by the CaMV 35S promoter was introduced into oilseed rape (Brassica napus) via Agrobacterium-mediated transformation. Some transgenic lines were obtained which exhibited enhanced resistance to the clubroot pathogen (Plasmodiophora brassicae). To increase resistance, double haploid (DH) lines were generated from these transgenic plants. Of these, DH-line 189 showed stable inheritance of the transgenic trait and its associated resistance for at least three generations.

MicroRNAs (miRNAs) are a class of short and endogenously initiated non-coding RNAs that post-transcriptionally control gene expression via either translational repression or mRNA degradation. Mature miRNAs are reported to be highly conserved throughout the plant kingdom; therefore, comparative genomics approaches are used to predict the novel miRNA genes and their target genes. In this study, bioinformatics and laboratory approaches followed by the EST and miRNA sequences in the databases for chicory species were employed for the identification of potential miRNAs and their potential targets either in Cichorium intybus or Cichorium endivia. To identify the potential miRNAs in the C. intybus and C. endivia, all the publicly available EST sequences of the plant were blasted against the previously known Plant miRNAs. Ultimately, four novel miRNAs belonging to four different families of miR166, miR156, miR162 and miR393 were identified. Also, a large number of genes, such as TIR1, Squamusa promoter binding proteins genes were identified as target genes of these miRNAs. Furthermore, the results of Real Time PCR showed that the transcriptional activities of miR156 in the leaf tissue of C. endivia are extremely high, not only than those observed for flower tissue of the same species, but also as compared with the leaf and flower tissues of the another species of C. intybus.

We have limited understanding of architecture and morphology of fine root systems in large woody trees. This study investigated architecture, morphology, and biomass of different fine root branch orders of two temperate tree species from Northeastern China—Larix gmelinii Rupr and Fraxinus mandshurica Rupr —by sampling up to five fine root branch orders three times during the 2003 growing season from two soil depths (i.e., 0–10 and.10–20 cm). Branching ratio (R b) differed with the level of branching: R b values from the fifth to the second order of branching were approximately three in both species, but markedly higher for the first two orders of branching, reaching a value of 10.4 for L. gmelinii and 18.6 for F. mandshurica. Fine root diameter, length, SRL and root length density not only had systematic changes with root order, but also varied significantly with season and soil depth. Total biomass per order did not change systematically with branch order. Compared to the second, third and/or fourth order, the first order roots exhibited higher biomass throughout the growing season and soil depths, a pattern related to consistently higher R b values for the first two orders of branching than the other levels of branching. Moreover, the differences in architecture and morphology across order, season, and soil depth between the two species were consistent with the morphological disparity between gymnosperms and angiosperms reported previously. The results of this study suggest that root architecture and morphology, especially those of the first order roots, should be important for understanding the complexity and multi-functionality of tree fine roots with respect to root nutrient and water uptake, and fine root dynamics in forest ecosystems.

The main aims of this study were to evaluate the P uptake of Brazilian wheat cultivars and to identify the root traits involved in P uptake capacity. Two greenhouse studies were carried out. An isotopic dilution technique with 32P as a tracer was used in the first experiment. The root morphology and architecture was evaluated in the second experiment. The results indicated differences in P uptake between the cultivars. The cultivars with higher values of P uptake exhibited total root shallow, which enhances root proliferation in P-rich surface soil. Twenty-one cultivars showed potentially greater phosphorus uptake efficiency, and we observed the importance of root traits for improving the P uptake ability.