Genome-wide identification of nitrate-responsive microRNAs by small RNA sequencing in the rice restorer cultivar Nanhui 511

Rice productivity relies heavily on nitrogen fertilization, and improving nitrogen use efficiency (NUE) is important for hybrid rice breeding. Reducing nitrogen inputs is the key to achieving sustainable rice production and reducing environmental problems. Here, we analyzed the genome-wide transcriptomic changes in microRNAs (miRNAs) in the indica rice restorer cultivar Nanhui 511 (NH511) under high (HN) and low nitrogen (LN) conditions. The results showed that NH511 is sensitive to nitrogen supplies and HN conditions promoted the growth its lateral roots at the seedling stage. Furthermore, we identified 483 known miRNAs and 128 novel miRNAs by small RNA sequencing in response to nitrogen in NH511. We also detected 100 differentially expressed genes (DEGs), including 75 upregulated and 25 downregulated DEGs, under HN conditions. Among these DEGs, 43 miRNAs that exhibited a 2-fold change in their expression were identified in response to HN conditions, including 28 upregulated and 15 downregulated genes. Additionally, some differentially expressed miRNAs were further validated by qPCR analysis, which showed that miR443, miR1861b, and miR166k-3p were upregulated, whereas miR395v and miR444b.1 were downregulated under HN conditions. Moreover, the degradomes of possible target genes for miR166k-3p and miR444b.1 and expression variations were analyzed by qPCR at different time points under HN conditions. Our findings revealed comprehensive expression profiles of miRNAs responsive to HN treatments in an indica rice restorer cultivar, which advances our understanding of the regulation of nitrogen signaling mediated by miRNAs and provides novel data for high-NUE hybrid rice cultivation

A novel role for abscisic acid emerges from underground

The continuous formation of lateral roots is a vital part of establishing a root system and enables plants to react with developmental plasticity to changing soil conditions. Evidence is accumulating that abscisic acid (ABA), which is known to be involved in stress responses, has an important role in lateral root formation. An ABA receptor mutant, fca-1, shows an altered response to ABA during lateral root formation. Interestingly, ABA seems to have distinct roles at different stages in lateral root development. The emerging role of ABA in lateral root development fits well with its general functional properties as a stress hormone, including its role in dormancy

Dual pathways for regulation of root branching by nitrate.

Root development is extremely sensitive to variations in nutrient supply, but the mechanisms are poorly understood. We have investigated the processes by which nitrate (NO3), depending on its availability and distribution, can have both positive and negative effects on the development and growth of lateral roots. When Arabidopsis roots were exposed to a locally concentrated supply of NO3 there was no increase in lateral root numbers within the NO3-rich zone, but there was a localized 2-fold increase in the mean rate of lateral root elongation, which was attributable to a corresponding increase in the rate of cell production in the lateral root meristem. Localized applications of other N sources did not stimulate lateral root elongation, consistent with previous evidence that the NO3 ion is acting as a signal rather than a nutrient. The axr4 auxin-resistant mutant was insensitive to the stimulatory effect of NO3, suggesting an overlap between the NO3 and auxin response pathways. High rates of NO3 supply to the roots had a systemic inhibitory effect on lateral root development that acted specifically at the stage when the laterals had just emerged from the primary root, apparently delaying final activation of the lateral root meristem. A nitrate reductase-deficient mutant showed increased sensitivity to this systemic inhibitory effect, suggesting that tissue NO3 levels may play a role in generating the inhibitory signal. We present a model in which root branching is modulated by opposing signals from the plant's internal N status and the external supply of NO

Dissecting Arabidopsis lateral root development

Recent studies in the model plant Arabidopsis provide new insight into the regulation of root architecture, a key determinant of nutrient- and water-use efficiency in crops. Lateral root (LR) primordia originate from a subset of pericycle founder cells. Sophisticated massspectroscopy-based techniques have been used to map the sites of biosynthesis of auxin and its distribution in Arabidopsis seedlings, highlighting the importance of the phytohormone during LR initiation and emergence. Key components of the cell cycle and signal-transduction pathway(s) that promote and attenuate auxin-dependent LR initiation have recently been identified. Additional signals, such as abscisic acid and nitrate, also regulate LR emergence, raising intriguing questions about the cross-talk between their transduction pathways

Transcriptomic and Physiological Analyses of Two Rice Restorer Lines under Different Nitrogen Supplies Provide Novel Insights into Hybrid Rice Breeding

Improving plant nitrogen-use efficiency (NUE) has great significance for various crops, particularly in hybrid breeding. Reducing nitrogen inputs is key to achieving sustainable rice production and mitigating environmental problems. In this study, we analyzed the transcriptomic and physiological changes in two indica restorer lines (Nanhui511 [NH511] and Minghui23 [MH23]) under high nitrogen (HN) and low nitrogen (LN) conditions. Compared to MH23, NH511 was more sensitive to different nitrogen supplies and exhibited higher nitrogen uptake and NUE under HN conditions by increasing lateral root and tiller numbers in the seedling and maturation stages, respectively. NH511 also exhibited a lower survival rate than MH23 when planted in a chlorate-containing hydroponic solution, indicating its HN uptake ability under different nitrogen-supply conditions. Transcriptomic analysis showed that NH511 has 2456 differentially expressed genes, whereas MH23 had only 266. Furthermore, these genes related to nitrogen utilization showed differential expression in NH511 under HN conditions, while the opposite was observed in MH23. Our findings revealed that NH511 could be regarded as elite rice and used for breeding high-NUE restorer lines by regulating and integrating nitrogen-utilization genes, which provides novel insights for the cultivation of high-NUE hybrid rice

Diurnal expression of <i>F. vesca PIP</i> aquaporins.

<p>Diurnal expression pattern of <i>FvPIP</i> genes in leaves of <i>F. vesca</i> on two consecutive days. Grey columns – control plants, black columns – drought-stressed plants. Data are means+SE, <i>n</i> = 3 biological replicates. Different letters annotate statistically significant differences determined by LSD following repeated measurements ANOVA (<i>P</i><0.05). The difference between treatments was significant for (a), (b), (c), and (d).</p

<i>F. vesca</i> PIP isoform-specific and reference gene primers.

<p><i>F. vesca</i> PIP isoform-specific and reference gene primers.</p

Relative <i>PIP</i> expression in leaves and roots of <i>F. vesca</i> under different levels of drought stress.

<p>Expression of four <i>F. vesca PIP</i> aquaporin genes after six days of drought stress (a, c, e, g) and upon re-watering (b, d, f, h). C – control plants; D25– plants receiving 25% of the control irrigation; D0 − plants with no irrigation. Data are means+SE, <i>n</i> = 4 plants. Different letters denote statistically significant differences within each time point determined by LSD following one way ANOVA (<i>P</i><0.05).</p