Rice foot rot disease caused by the pathogen Dickeya zeae (formerly known as Erwinia chrysanthemi pv. zeae), is a newly emerging damaging bacterial disease in China and the southeast of Asia, resulting in the loss of yield and grain quality. However, the genetic resistance mechanisms mediated by miRNAs to D. zeae are unclear in rice. In the present study, 652 miRNAs including osa-miR396f predicted to be involved in multiple defense responses to D. zeae were identified with RNA sequencing. A total of 79 differentially expressed miRNAs were detected under the criterion of normalized reads ≥10, including 51 known and 28 novel miRNAs. Degradome sequencing identified 799 targets predicted to be cleaved by 168 identified miRNAs. Among them, 29 differentially expressed miRNA and target pairs including miRNA396f-OsGRFs were identified by co-expression analysis. Overexpression of the osa-miR396f precursor in a susceptible rice variety showed enhanced resistance to D. zeae, coupled with significant accumulation of transcripts of osa-miR396f and reduction of its target the Growth-Regulating Factors (OsGRFs). Taken together, these findings suggest that miRNA and targets including miR396f-OsGRFs have a role in resisting the infections by bacteria D. zeae.

• The darker the colour of purple rice grain, the stronger the total antioxidant capacity. • The total antioxidant capacity at the early filling stage was lower than that at the middle and late filling stages. • Flavonoid synthesis in purple rice grains increased significantly 21 days after grain filling. • Phlorizin, myricetin 3-galactoside and trilobatin are metabolite biomarkers of antioxidant properties of purple rice grains.

Rice black-streaked dwarf virus (RBSDV) belongs to the genus Fijivirus in the family of Reoviridae and causes severe yield loss in rice-producing areas in Asia. RNA silencing, as a natural defence mechanism against plant viruses, has been successfully exploited for engineering virus resistance in plants, including rice. In this study, we generated transgenic rice lines harbouring a hairpin RNA (hpRNA) construct targeting four RBSDV genes, S1, S2, S6 and S10, encoding the RNA-dependent RNA polymerase, the putative core protein, the RNA silencing suppressor and the outer capsid protein, respectively. Both field nursery and artificial inoculation assays of three generations of the transgenic lines showed that they had strong resistance to RBSDV infection. The RBSDV resistance in the segregating transgenic populations correlated perfectly with the presence of the hpRNA transgene. Furthermore, the hpRNA transgene was expressed in the highly resistant transgenic lines, giving rise to abundant levels of 21–24 nt small interfering RNA (siRNA). By small RNA deep sequencing, the RBSDV-resistant transgenic lines detected siRNAs from all four viral gene sequences in the hpRNA transgene, indicating that the whole chimeric fusion sequence can be efficiently processed by Dicer into siRNAs. Taken together, our results suggest that long hpRNA targeting multiple viral genes can be used to generate stable and durable virus resistance in rice, as well as other plant species.

Cooking can lead to varying degrees of nutrient loss in purple rice. For this investigation, two varieties of purple rice (YZN1 and YZ6) were chosen as the focal points to explore the metabolites associated with rice nutrition post cooking using nontargeted and targeted metabolomics techniques. The results showed that after cooking the two purple rice varieties, the contents of the flavonoids; OPC; TP; total antioxidant capacity; and K, Na, Fe, Mn, Zn, Cu, Ca, and Mg significantly decreased. Compared with YZN1U (YZN1 uncooked), the amino acid and mineral element contents in YZN1C (YZN1 cooked) decreased to varying degrees. After cooking YZ6, the contents of seven amino acids significantly decreased. Following the preparation of purple rice, the metabolites primarily engaged in the pathways of flavonoid synthesis and flavone and flavonol synthesis. Flavonoids, total antioxidant capacity, mineral elements, and amino acids showed a strong correlation with delphinidin and luteolin. The ROC analysis demonstrated that the value of the area under the curve for delphinidin and luteolin was 1 when comparing YZ6C (YZ6 cooked) and YZ6U (YZ6 uncooked), as well as YZN1C and YZN1U. Delphinidin and luteolin can be used as potential biomarkers of nutrient loss after cooking purple rice. This study holds significant implications for the balanced nutrition and healthy development of human dietary grains.

This study investigated the impact of nitrogen (N) fertilization on the yield and grain filling (GF) characteristics of two conventional japonica rice varieties with distinct panicle types: Yangchan 3501 (large-panicle: spikelets per panicle $> 150$) and Nangeng 46 (medium-panicle: $100 <$ spikelets per panicle $< 150$). Field experiments were conducted over two growing seasons (2022–2023) with three N application rates (T1: 225 kg ha⁻¹, T2: 270 kg ha⁻¹, T3: 315 kg ha⁻¹). Key measurements included tiller dynamics, panicle composition, GF parameters modeled using the Richards equation, and enzyme activities related to nitrogen metabolism (Fd-GOGAT, NR) and carbohydrate transport (α-amylase, SPS). Results showed that the yield increased with higher N levels for both varieties, with Yangchan 3501 achieving higher yields primarily through increased grains per panicle (15.65% rise under T3 vs. T1), while Nangeng 46 relied on panicle number (8.83% increase under T3 vs. T1). Nitrogen application enhanced Fd-GOGAT and NR activities, prolonging photosynthesis and improving GF rates, particularly in the inferior grains of Yangchan 3501 during middle and late stages. However, a high N reduced seed-setting rates and 1000-grain weight, with larger panicle types exhibiting a greater sensitivity to N-induced changes in branch structure and assimilate allocation. This study highlights that optimizing N management can improve nitrogen-metabolism enzyme activity and GF efficiency, especially in large-panicle rice, while medium-panicle types require higher N inputs to maximize panicle number. These findings provide actionable insights for achieving high yields and efficient nutrient use in conventional rice cultivation.