Significance: Phosphate (Pi) is a primary nutrient for plant growth. Because of the low availability of soil Pi, the Pi starvation signaling in plants is gaining great interest. Arabidopsis AtPHR1 and its rice homologue OsPHR2 are known to be central transcription factors in Pi homeostasis; however, the mechanism of how plants sense external Pi fluctuation to regulate the activity of AtPHR1/OsPHR2 has been elusive. Here, we identify rice SPX1 and SPX2 as Pi-dependent inhibitors of PHR2, implicating SPX1 and SPX2 in the Pi-sensing mechanism. We also show that the SPX domain of SPX1 and SPX2 is critical for repressing PHR2 binding to cis elements by protein interaction. The discovery of cellular nutrient concentration-dependent fine-tuning sheds light on a novel mechanism of plant adaption to environmental cues.

Roots are fundamentally important for growth and development, anchoring the plant to its growth substrate, facilitating water and nutrient uptake from the soil, and sensing and responding to environmental signals such as biotic and abiotic stresses. Understanding the molecular mechanisms controlling root architecture is essential for improving nutrient uptake efficiency and crop yields. In this review, we describe the progress being made in the identification of genes and regulatory pathways involved in the development of root systems in rice (Oryza sativa L.), including crown roots, lateral roots, root hairs, and root length. Genes involved in the adaptation of roots to the environmental nutrient status are reviewed, and strategies for further study and agricultural applications are discussed. The growth and development of rice roots are controlled by both genetic factors and environmental cues. Plant hormones, especially auxin and cytokinin, play important roles in root growth and development. Understanding the molecular mechanisms regulating root architecture and response to environmental signals can contribute to the genetic improvement of crop root systems, enhancing their adaptation to stressful environmental conditions.

Phosphorus (P), an essential macronutrient for all living cells, is indispensable for agricultural production. Although Arabidopsis (Arabidopsis thaliana) PHOSPHATE RESPONSE1 (PHR1) and its orthologs in other species have been shown to function in transcriptional regulation of phosphate (Pi) signaling and Pi homeostasis, an integrative comparison of PHR1-related proteins in rice (Oryza sativa) has not previously been reported. Here, we identified functional redundancy among three PHR1 orthologs in rice (OsPHR1, OsPHR2, and OsPHR3) using phylogenetic and mutation analysis. OsPHR3 in conjunction with OsPHR1 and OsPHR2 function in transcriptional activation of most Pi starvation-induced genes. Loss-of-function mutations in any one of these transcription factors (TFs) impaired root hair growth (primarily root hair elongation). However, these three TFs showed differences in DNA binding affinities and messenger RNA expression patterns in different tissues and growth stages, and transcriptomic analysis revealed differential effects on Pi starvation-induced gene expression of single mutants of the three TFs, indicating some degree of functional diversification. Overexpression of genes encoding any of these TFs resulted in partial constitutive activation of Pi starvation response and led to Pi accumulation in the shoot. Furthermore, unlike OsPHR2-overexpressing lines, which exhibited growth retardation under normal or Pi-deficient conditions, OsPHR3-overexpressing plants exhibited significant tolerance to low-Pi stress but normal growth rates under normal Pi conditions, suggesting that OsPHR3 would be useful for molecular breeding to improve Pi uptake/use efficiency under Pi-deficient conditions. We propose that OsPHR1, OsPHR2, and OsPHR3 form a network and play diverse roles in regulating Pi signaling and homeostasis in rice.

Summary: Nitrogen (N) is one of the key essential macronutrients that affects rice growth and yield. Inorganic N fertilizers are excessively used to boost yield and generate serious collateral environmental pollution. Therefore, improving crop N use efficiency (NUE) is highly desirable and has been a major endeavour in crop improvement. However, only a few regulators have been identified that can be used to improve NUE in rice to date. Here we show that the rice NIN‐like protein 4 (OsNLP4) significantly improves the rice NUE and yield. Field trials consistently showed that loss‐of‐OsNLP4 dramatically reduced yield and NUE compared with wild type under different N regimes. In contrast, the OsNLP4 overexpression lines remarkably increased yield by 30% and NUE by 47% under moderate N level compared with wild type. Transcriptomic analyses revealed that OsNLP4 orchestrates the expression of a majority of known N uptake, assimilation and signalling genes by directly binding to the nitrate‐responsive cis‐element in their promoters to regulate their expression. Moreover, overexpression of OsNLP4 can recover the phenotype of Arabidopsis nlp7 mutant and enhance its biomass. Our results demonstrate that OsNLP4 plays a pivotal role in rice NUE and sheds light on crop NUE improvement.

The major root system of cereals consists of crown roots (or adventitious roots), which are important for anchoring plants in the soil and for water and nutrient uptake. However, the molecular basis of crown root formation is largely unknown. Here, we isolated a rice (Oryza sativa) mutant with fewer crown roots, named lower crown root number1 (lcrn1). Map-based cloning revealed that lcrn1 is caused by a mutation of a putative transcription factor–coding gene, O. sativa SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 (OsSPL3). We demonstrate that the point mutation in lcrn1 perturbs theO. sativa microRNA156 (OsmiR156)-directed cleavage of OsSPL3 transcripts, resulting in the mutant phenotype. Chromatin immunoprecipitation sequencing assays of OsSPL3 binding sites and RNA sequencing of differentially expressed transcripts in lcrn1 further identified potential direct targets of OsSPL3 in basal nodes, including a MADS-box transcription factor, OsMADS50. OsMADS50-overexpressing plants produced fewer crown roots, phenocopying lcrn1, while knocking out OsMADS50 in the lcrn1 background reversed this phenotype. We also show that OsSPL12, another OsmiR156 target gene, regulates OsMADS50 and crown root development. Taken together, our findings suggest a novel regulatory pathway in which the OsmiR156-OsSPL3/OsSPL12 module directly activates OsMADS50 in the node to regulate crown root development in rice.