Reducing nitrogen (N) input is a key measure to achieve a sustainable rice production in China, especially in Jiangsu Province. Tiller is the basis for achieving panicle number that plays as a major factor in the yield determination. In actual production, excessive N is often applied in order to produce enough tillers in the early stages. Understanding how N regulates tillering in rice plants is critical to generate an integrative management to reduce N use and reaching tiller number target. Aiming at this objective, we utilized RNA sequencing and weighted gene co-expression network analysis (WGCNA) to compare the transcriptomes surrounding the shoot apical meristem of indica (Yangdao6, YD6) and japonica (Nipponbare, NPB) rice subspecies. Our results showed that N rate influenced tiller number in a different pattern between the two varieties, with NPB being more sensitive to N enrichment, and YD6 being more tolerant to high N rate. Tiller number was positively related to N content in leaf, culm and root tissue, but negatively related to the soluble carbohydrate content, regardless of variety. Transcriptomic comparisons revealed that for YD6 when N rate enrichment from low (LN) to medium (MN), it caused 115 DEGs (LN vs. MN), from MN to high level (HN) triggered 162 DEGs (MN vs. HN), but direct comparison of low with high N rate showed a 511 DEGs (LN vs. HN). These numbers of DEG in NPB were 87 (LN vs. MN), 40 (MN vs. HN), and 148 (LN vs. HN). These differences indicate that continual N enrichment led to a bumpy change at the transcription level. For the reported sixty-five genes which affect tillering, thirty-six showed decent expression in SAM at tiller starting phase, among them only nineteen being significantly influenced by N level, and two genes showed significant interaction between N rate and variety. Gene ontology analysis revealed that the majority of the common DEGs are involved in general stress responses, stimulus responses, and hormonal signaling process. WGCNA network identified twenty-two co-expressing gene modules and ten candidate hubgenes for each module. Several genes associated with tillering and N rate fall on the related modules. These indicate that there are more genes participating in tillering regulation in response to N enrichment.

Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice.

Reverse transcription quantitative real-time PCR (RT-qPCR) is arguably the most prevalent and accurate quantitative gene expression analysis. However, selection of reliable reference genes for RT-qPCR in rice (Oryza sativa) is still limited, especially for a specific tissue type or growth condition. In this study, we took the advantage of our RNA-seq datasets encompassing data from five rice varieties with diverse treatment conditions, identified 12 novel candidate reference genes, and conducted rigorous evaluations of their suitability across typical rice tissues. Comprehensive analysis of the leaves, shoots, and roots of two rice seedlings subjected to salt (30 mmol/L NaCl) and drought (air-dry) stresses have revealed that OsMED7, OsACT1, and OsOS-9 were the robust reference genes for leaf samples, while OsACT1, OsZOS3-23, and OsGDCP were recommended for shoots and OsMED7, OsOS-9, and OsGDCP were the most reliable reference genes for roots. Comparison results produced by different sets of reference genes revealed that all these newly recommended reference genes displayed less variation than previous commonly used references genes under the experiment conditions. Thus, selecting appropriate reference genes from RNA-seq datasets leads to identification of reference genes suitable for respective rice tissues under drought and salt stress. The findings offer valuable insights for refining the screening of candidate reference genes under diverse conditions through the RNA-seq database. This refinement serves to improve the accuracy of gene expression in rice under similar conditions.

The composition and distribution of storage substances in rice endosperm directly affect grain quality. A floury endosperm mutant, wcr (white-core rice), was identified, exhibiting a loose arrangement of starch granules with a floury opaque appearance in the inner layer of mature grains, resulting in reduced grain weight. The total starch and amylose content remained unchanged, but the levels of the four component proteins in the mutant brown rice significantly decreased. Additionally, the milled rice (inner endosperm) showed a significant decrease in total starch and amylose content, accompanied by a nearly threefold increase in albumin content. The swelling capacity of mutant starch was reduced, and its chain length distribution was altered. The target gene was mapped on chromosome 5 within a 65 kb region. A frameshift mutation occurred due to an insertion of an extra C base in the second exon of the cyOsPPDKB gene, which encodes pyruvate phosphate dikinase. Expression analysis revealed that wcr not only affected genes involved in starch metabolism but also downregulated expression levels of genes associated with storage protein synthesis. Overall, wcr plays a crucial role as a regulator factor influencing protein synthesis and starch metabolism in rice grains.

Maintaining rice yield and reducing nitrogen (N) input are two important targets in sustainable agriculture practices. The adoption of a nitrogen-saving variety (NSV) provides a unique opportunity to achieve this. However, limited options in NSV japonica rice and a lack of information on their responses to N reduction make management decisions difficult. This study aims to explore the responses of yield and nitrogen use efficiency (NUE) in NSV to N reduction. Two newly released NSVs and two popular general varieties (GVs) of japonica rice were field tested in Yangzhou, located at the lower reaches of Yangtze River of China, in two consecutive years. The results showed that for NSVs, with a 40–60% reduction in common practice N rate (300 Kg ha⁻¹), the rice yield could maintain a record average level (p < 0.05), whereas the yield for the GV would drop 20–30% (p < 0.05). This indicates that combining the practices of adoption of NSV and N reduction to 120–180 Kg N ha⁻¹ could balance the yield and N consumption. Moderate N reduction promotes the N accumulation and NUE, and it increases the number of tillers, the productive tiller percentage and the total amount of spikelets in the population, and increases the carbon and N metabolism of the population in the NSV. Compared with GV, NSV showed higher NUE and non-structural carbohydrate re-mobilization in the reduced N rate. The results showed that the practice of N reduction has to adopt NSV at the same time in order to maintain the grain yield level in rice.

Uneven seed placement in nursery trays reduces seedling uniformity and can reduce the reliability of mechanical transplanting in hybrid rice, but the optimum printed seeding density remains unclear. This study evaluated the effects of printed seeding density on seed distribution, seedling quality, transplanting performance, canopy productivity and yield formation in machine-transplanted hybrid indica rice. A two-year split-plot field experiment was conducted in Xuzhou, China, using Runliangyou 313 and Yangxianyou 903. Five printed seeding densities (1400–2600 printed points tray⁻¹) were compared with two local weight-based broadcasting controls, representing practical establishment systems rather than seed-number-matched contrasts. Moderate printed densities improved seed distribution uniformity, strengthened the seedling mat, reduced transplanting defects and supported productive tiller formation. T3 and T4 produced the highest harvested yields, increasing yield by 13.3–15.5% over the standard broadcasting control. These gains were associated with higher panicle number, greater post-anthesis dry matter accumulation and higher harvest index. The results indicate that moderate-density printed seeding can improve establishment quality and grain yield under wheat-rice rotation conditions.