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Prefrontal cortex (PFC) is the cognitive center that integrates and regulates global brain activity. However, the whole-brain organization of PFC axon projections remains poorly understood. Using single-neuron reconstruction of 6,357 mouse PFC projection neurons, we identified 64 projectome-defined subtypes. Each of four previously known major cortico-cortical subnetworks was targeted by a distinct group of PFC subtypes defined by their first-order axon collaterals. Further analysis unraveled topographic rules of soma distribution within PFC, first-order collateral branch point-dependent target selection and terminal arbor distribution-dependent target subdivision. Furthermore, we obtained a high-precision hierarchical map within PFC and three distinct functionally related PFC modules, each enriched with internal recurrent connectivity. Finally, we showed that each transcriptome subtype corresponds to multiple projectome subtypes found in different PFC subregions. Thus, whole-brain single-neuron projectome analysis reveals organization principles of axon projections within and outside PFC and provides the essential basis for elucidating neuronal connectivity underlying diverse PFC functions.The authors reconstructed the individual projectomes of 6,357 mouse prefrontal cortical projection neurons, revealing projectome-defined neuron subtypes and organizing principles of axon projections and correspondence with transcriptomes.

The indica and japonica rice ( Oryza sativa ) subspecies differ in nitrate (NO 3 − ) assimilation capacity and nitrogen (N) use efficiency (NUE). Here, we show that a major component of this difference is conferred by allelic variation at OsNR2 , a gene encoding a NADH/NADPH-dependent NO 3 − reductase (NR). Selection-driven allelic divergence has resulted in variant indica and japonica OsNR2 alleles encoding structurally distinct OsNR2 proteins, with indica OsNR2 exhibiting greater NR activity. Indica OsNR2 also promotes NO 3 − uptake via feed-forward interaction with OsNRT1.1B , a gene encoding a NO 3 − uptake transporter. These properties enable indica OsNR2 to confer increased effective tiller number, grain yield and NUE on japonica rice, effects enhanced by interaction with an additionally introgressed indica OsNRT1.1B allele. In consequence, indica OsNR2 provides an important breeding resource for the sustainable increases in japonica rice yields necessary for future global food security. Indica rice has higher nitrate assimilation and nitrogen use efficiency (NUE) than japonica rice, but the mechanism is unclear. Here, the authors reveal that the difference is partly due to allelic variation of a nitrate reductase encoding gene and this indica allele can increase yield potential and NUE.

Field experiments were conducted over two years to evaluate the effects of planting density and nitrogen input rate on grain yield and nitrogen use efficiency (NUE) of inbred and hybrid rice varieties. A significant interaction effect was observed between nitrogen input and planting density on grain yield. Higher number of panicles per square meter and spikelets per panicle largely accounted for the observed advantage in performance of inbred, relative to hybrid varieties. Compared with high nitrogen input rate, nitrogen absorption efficiency, nitrogen recovery efficiency, and partial factor productivity increased by 24.6%, 28.0%, and 33.3% in inbred varieties, and by 32.2%, 29.3%, and 35.0% in hybrids under low nitrogen input, respectively. Inbred varieties showed higher nitrogen absorption efficiency, nitrogen recovery efficiency, and partial factor productivity than hybrids, regardless of nitrogen input level. Nitrogen correlated positively with panicle number, spikelets per panicle, biomass production at flowering, and after flowering in inbred varieties but only with panicle number and biomass production at flowering in hybrids. Inbred varieties are more suitable for high planting density at reduced nitrogen input regarding higher grain yield and NUE. These findings bear important implications for achieving high yield and high efficiency in nutrient uptake and utilization in modern rice-production systems.

Rhizosphere microbiomes and metabolomes are influenced by host genotype and developmental stage. However, there has been limited research that simultaneously profiles the rhizosphere microbiome and metabolism of rice across different genotypes and developmental stages. Furthermore, the interactions between rhizosphere microbiomes and metabolism in various plant genotypes and developmental stages are not well understood. Here, we investigated the diversity and composition of rhizosphere microbial community and metabolism across three hybrid rice varieties and their respective parent lines during three developmental stages (tillering, heading, and mature) using amplicon sequencing and untargeted metabolomics analyses. Plant developmental stages and genotypes significantly influence the rhizosphere microbiome and metabolome, with the impact of developmental stages being more pronounced. The composition of microbial communities and metabolites in the rhizosphere exhibited significant differences between the tillering stage and other developmental stages, with these differences becoming less distinct as the growth period continued. Hybrid rice displayed heterosis characteristics in their rhizosphere microorganisms compared to their parent varieties, as reflected by the significant enrichment of microbial species and the enhanced potential for microbial interactions within the co-occurrence network. Moreover, the differential microorganisms between the tillering and heading stages showed significant correlations with differential metabolites and soil chemical properties, including total phosphorus (TP), available phosphorus (AP), and nitrate nitrogen (NN). Taken together, this study contributes to our understanding of plant-microbiota-metabolome associations and provides a foundation for developing beneficial plant microbiomes and compounds to promote sustainable agricultural production.