Background: Low temperature (LT) often occurs at the seedling stage in the early rice-growing season, especially for direct seeded early-season indica rice, and using flooding irrigation can mitigate LT damage in rice seedlings. The molecular mechanism by which flooding mitigates the damage induced by LT stress has not been fully elucidated. Thus, LT stress at 8 °C, LT accompanied by flooding (LTF) and CK (control) treatments were established for 3 days to determine the transcriptomic, proteomic and physiological response in direct seeded rice seedlings at the seedling stage. Results: LT damaged chloroplasts, and thylakoid lamellae, and increased osmiophilic bodies and starch grains compared to CK, but LTF alleviated the damage to chloroplast structure caused by LT. The physiological characteristics of treated plants showed that compared with LT, LTF significantly increased the contents of rubisco, chlorophyll, PEPCK, ATP and GA₃ but significantly decreased soluble protein, MDA and ABA contents. 4D-label-free quantitative proteomic profiling showed that photosynthesis-responsive proteins, such as phytochrome, as well as chlorophyll and the tricarboxylic acid cycle were significantly downregulated in LT/CK and LTF/CK comparison groups. However, compared with LT, phytochrome, chlorophyllide oxygenase activity and the glucan branching enzyme in LTF were significantly upregulated in rice leaves. Transcriptomic and proteomic studies identified 72,818 transcripts and 5639 proteins, and 4983 genes that were identified at both the transcriptome and proteome levels. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were significantly enriched in glycine, serine and threonine metabolism, biosynthesis of secondary metabolites, glycolysis/gluconeogenesis and metabolic pathways. Conclusion: Through transcriptomic, proteomic and physiological analyses, we determined that a variety of metabolic pathway changes were induced by LT and LTF. GO and KEGG enrichment analyses demonstrated that DEGs and DEPs were associated with photosynthesis pathways, antioxidant enzymes and energy metabolism pathway-related proteins. Our study provided new insights for efforts to reduce the damage to direct seeded rice caused by low-temperature stress and provided a breeding target for low temperature flooding-resistant cultivars. Further analysis of translational regulation and metabolites may help to elucidate the molecular mechanisms by which flooding mitigates low-temperature stress in direct seeded early indica rice at the seedling stage.

Phosphorus (P) is one of the essential macronutrients for rice. In this study, we used 120 rice backcross recombinant inbred lines (BRILs) derived from a cross indica cv. Changhui 891 and japonica cv. 02428. To elucidate the genetic control of P deficiency tolerance in rice, we have used high quality SNPs bin markers to identify some important loci underlying phosphorus deficiency. The bin map was generated which includes 3057 bins covering distance of 1266.5 cM with an average of 0.41 cM between markers. Based on this map, 50 loci, including four novel loci, qSL-3, qRL-11, qSDW-1, qRDW-1 with phenotypic variance 23.26%, 12.06%, 9.89% associated with P deficiency-related seedling traits were identified. No significant QTLs was found for root length under P+, shoot fresh weight P− and root length, shoot fresh weight for P+, P− and their ratio respectively. Root fresh weight, and root dry weight were strongly correlated to each other, and QTLs for these variables were located on the same chromosome 1 at the same region. Notably, 3 pleiotropic regions is the pioneer of our study, and these regions would facilitate map-based cloning to expedite the MAS selection for developing low phosphorous tolerant varieties. This study not only improves our knowledge about molecular processes associated with P deficiency, but also provides useful information to understand the genetic architecture of low phosphorous tolerance.

Xanthine dehydrogenase (XDH) is a crucial enzyme involved in purine metabolism. Although the essential role of XDH is well studied in leguminous plants and Arabidopsis, the importance of this enzyme...

An increased planting density and decreased nitrogen (N) rate combination may obtain a stable yield and enhance N utilization. However, the effects of an increased planting density and decreased N rate combination on the yield and nutrient utilization in different ecological regions are unclear. The aim of this research was to assess the interactive impacts of the N rates and planting densities on double cropping rice yields and nutrient utilization in two ecological regions in field experiments during 2018 and 2019. The results showed that, at Shanggao, increased planting densities of 67% and 200% compensated for the biomass, nutrient uptake and yield losses from N application reductions of 20% and 27% and increased the nutrient utilization of the early and late seasons. However, at Xingguo, compared with the N₂D₁ treatment (165 kg ha⁻¹ with 57 plants per m²), the late rice yield under the N₁D₂ treatment (120 kg ha⁻¹ with 114 plants per m²) decreased by 6.71% and 5.02% in 2018 and 2019, respectively. The photosynthetic rate and nutrient uptake were likely related to the positive interaction on the double cropping rice yield in the two ecological regions. Our results indicate that dense planting is a feasible cultivation strategy to decrease N inputs for double cropping rice, but the low soil nutrient supplies negatively affect stable yields in different ecological regions.