The biological characteristics of crop roots are closely related to the efficient utilization of nitrogen and have become a research hotspot in agricultural cultivation and breeding in recent years. The root system and root microbiota play a crucial role in both the basic and the plastic growth and development of plants in response to external environmental changes. Nitrogen is an indispensable nutrient element for crop growth, and the efficient utilization of nitrogen is the key to achieving the high yield and quality of crops and establishing environmentally friendly agricultural production. The nitrogen absorbed and utilized by rice mainly enters the aboveground part of the plant through the root system from within the soil. This process is explored from the perspective of root biology (root morphology, physiological and biochemical characteristics, root growth and development process and regulation, rhizosphere microorganisms, and their symbiotic systems), which is in line with the directions of “less investment, increased production, environmental protection, and sustainable development” in China. Based on the research status in this field at present, this article explored the interaction mechanism between crop root biology and nitrogen absorption and utilization, and looks forward to the future research directions for root biology. This study provides a theoretical basis for reducing nitrogen fertilizer application, optimizing nitrogen-efficient cultivation management techniques, and selecting nitrogen-efficient varieties.

The aim of this study was to explore the differences in metabolites related to rice quality formation under different nitrogen (N) fertilizers and planting densities. In this study, Yangnongxiang 28 was used as the experimental material with the following conditions: high nitrogen and low density (HNLD; high nitrogen: 360 kg·hm⁻², low density: the row spacing of rice plants was 16 cm × 30 cm), medium nitrogen and medium density (MNMD; medium nitrogen: 270 kg·hm⁻², medium density: the row spacing of rice plants was 13 cm × 30 cm), and low nitrogen and high density (LNHD; low nitrogen: 270 kg·hm⁻², high density: the row spacing of rice plants was 10 cm × 30 cm). The rice quality indexes, including the processing quality, amylose content, and taste value, were compared under different treatments, and we analyzed their relationship with the metabolites. The results show that the milled rice rate of HNLD was 13.85% and was 1.89% higher than that of LNHD and MNMD, respectively. The head milled rice rate of HNLD was 32.45% and 6.39% higher than that of LNHD and MNMD, respectively. The milled rice rate and head milled rice rate of HNLD and MNMD were significantly higher than those of LNHD. This study identified 22 differential metabolites (DMs) in HNLD and LNHD, 38 DMs in HNLD and MNMD, and 23 DMs in LNHD and MNMD. Most of the identified differential metabolites were lipid metabolites, which were mainly enriched in the lipid metabolic pathways and amino acid metabolic pathways. The correlation analysis showed that the lipid metabolite physapubescin was significantly negatively correlated with the taste value. The lipid metabolites 2-undecen-1-ol, lucidenic acid F, and 8-deoxy-11,13-dihydroxygrosheimin were significantly positively correlated with the taste value. Lipids may be important substances that lead to differences in taste under different nitrogen fertilizer and density treatments.

To understand differences in the quality of different conventional japonica rice varieties and variations in metabolites related to rice quality, the quality of three conventional japonica varieties was determined, and the metabolites of the milled rice were investigated using nontargeted metabolomics technology. The results showed that the taste value (TV) of Yangda 4Hao (YD4) was significantly higher than that of Yangda 3Hao (YD3) and Huaidao 5Hao (HD5). The protein content (PC) of HD5 was significantly higher than that of YD3 and YD4. PC was significantly negatively correlated with TV. Ninety-one differential metabolites (59 increased and 32 decreased) were identified between YD3 and HD5. A total of 144 differential metabolites (96 upregulated and 48 downregulated) were identified between YD4 and HD5. A total of 114 differential metabolites (40 increased and 74 decreased) were identified between YD3 and YD4. The metabolites with a high correlation to rice quality were mostly involved in the amino acid metabolism pathway. Amino acid metabolites play an important role in the formation of rice quality. The key metabolites in the synthesis and regulation of metabolic pathways are sucrose, levan, and amylose, which are carbohydrates, and L-glutamine, L-aspartic acid, and L-asparagine, which are amino acid metabolites. It can be seen from this study that the metabolites of sucrose, levan, amylose, L-glutamine, L-aspartic acid, and L-asparagine may be the key metabolites in the quality formation of high-quality rice varieties.

We explored the related metabolites produced by different quality semi-glutinous japonica rice varieties and the modulatory role of key metabolites in metabolic mechanisms. In this study, three high-quality edible semi-glutinous rice varieties were employed as investigational materials, the metabolites of the three varieties were detected using LC–MS metabolomics technology, and the rice quality traits of the three rice varieties were determined. The taste value (TV) of Yangnongxiang 28 (YNX28H) was substantially higher than that of Hongyang 5 hao (HY5H) and Nanjing 5718 (NJ5718), and the hardness (HA) of YNX28H was significantly lower than that of HY5H and NJ5718. The HA was significantly negatively correlated with the TV. The highest chalkiness rate (CR) and chalkiness degree (CD) were observed for NJ5718, and the lowest CR and CD were observed for HY5H. HY5H had a substantially lower protein content (PC) than YNX28H and NJ5718 and a markedly higher amylose content (AC) than those two varieties. Overall, 188 differential metabolites (DMs) were recognized between HY5H and NJ5718. A total of 136 DMs were detected between YNX28H and NJ5718, and 198 DMs were recognized between HY5H and YNX28H. The metabolites with a strong correlation with rice quality were mainly associated with amino acid metabolism, lipid metabolism and the citrate cycle. The key metabolites in the metabolic pathway include lipid metabolites (sagittariol, glycerophosphocholine, gamma-eudesmol rhamnoside, goshonoside F1, diosbulbinoside F, and corchorifatty acid F), amino acid metabolites (pantothenic acid, L-serine, L-proline, L-aspartic acid, L-glutamate, L-asparagine, and glutathione) and carbohydrate metabolites (sucrose, levan, D-maltose, and amylose). These key metabolites play important regulatory roles in metabolic mechanisms, providing a theoretical basis for breeding new high-quality edible rice varieties.

Heterosis is a common biological phenomenon that is useful for breeding superior lines. Using heterosis to increase the yield and quality of crops is one of the main achievements of modern agricultural science. In this study, we analysed the transcriptome and metabolome of two three-line hybrid rice varieties, Taiyou 871 (TY871), and Taiyou 398 (TY398) and the parental grain endosperm using RNA-seq (three biological repeats per variety) and untargeted metabolomic (six biological repeats per variety) methods. TY871 and TY398 showed specific heterosis in yield and quality. Transcriptome analysis of the hybrids revealed 638 to 4059 differentially expressed genes in the grain when compared to the parents. Metabolome analysis of the hybrids revealed 657 to 3714 differential grain metabolites when compared to the parents. The honeydew1 and grey60 module core genes Os04g0350700 and Os05g0154700 are involved in the regulation of awn development, grain size, and grain number, as well as the regulation of grain length and plant height, respectively. Rice grain length may be an important indicator for improving the quality of three-line hybrid rice. In addition, the rice quality-related metabolite NEG_M341T662 was highly connected to the module core genes Os06g0254300 and Os03g0168100. The functions of Os06g0254300 and Os03g0168100 are EF-hand calcium binding protein and late embroideries absolute protein repeat containing protein, respectively. These genes may play a role in the formation of rice quality. We constructed a gene and metabolite coexpression network, which provides a scientific basis for the utilization of heterosis in producing high-yield and high-quality hybrid rice.

Under the same nitrogen fertilizer and cultivation conditions, the nutrients of rice are strongly affected during the processing of brown rice to polished rice, especially in special rice varieties. In this study, twenty-two amino acids in brown and polished rice of two purple rice varieties were quantified using targeted metabolomics, and the relationships among the main nutrients, mineral elements and metabolites were analysed. The results showed that the amino acid levels in YZN1_H (polished rice of Yangzinuo No. 1) and YZN2_H (polished rice of Yangzinuo No. 2) decreased to different degrees compared with those in YZN1_B (brown rice of Yangzinuo No. 1) and YZN2_B (brown rice of Yangzinuo No. 2). Citric acid is closely associated with amino acids. The total sugar (TS), ATP, and soluble dietary fiber (SDF) levels in YZN1_B decreased by 9.37%, 53.85%, and 75.71%, respectively, compared with those in YZN1_H. The TS, ATP, and SDF levels in YZN2_B decreased significantly by 6.92%, 21.03%, and 76.78%, respectively, compared with those in YZN2_H. Citric acid was significantly negatively correlated with ATP and SDF but significantly positively correlated with carotenoids. The Se content in YZN1_H was significantly higher than that in YZN1_B by 87.02%. The Se content in YZN2_H was significantly higher than that in YZN2_B by 72.02%. Citric acid was significantly positively correlated with Fe, Mn, Ca, and Mg. Citric acid was identified as a candidate key metabolite that affects changes in the main nutrients in purple rice during processing.