Search Results (33)

Cooked-rice aroma strongly affects consumer choice, yet the chemical traits distinguishing glutinous rice from normal-amylose japonica rice remain underexplored because earlier studies targeted only a few dozen volatiles using one-dimensional gas chromatography–mass spectrometry (GC-MS). In this study, four glutinous and seven normal Japanese cultivars were cooked under identical conditions, their headspace volatiles trapped with MonoTrap and qualitatively profiled by comprehensive GC × GC-TOFMS. The two-dimensional platform resolved 1924 peaks—about ten-fold previous coverage—and, together with hierarchical clustering, PCA, heatmap visualization and volcano plots, cleanly separated the starch classes (78.3% cumulative PCA variance; Euclidean distance >140). Volcano plots highlighted 277 compounds enriched in the glutinous cultivars and 295 in Koshihikari, including 270 compounds that were not previously documented in rice. Normal cultivars were dominated by ethers, aldehydes, amines and other nitrogenous volatiles associated with grainy, grassy and toasty notes. Glutinous cultivars showed abundant ketones, furans, carboxylic acids, thiols, steroids, nitro compounds, pyrroles and diverse hydrocarbons and aromatics, yielding sweeter, fruitier and floral accents. These results expand the volatile library for japonica rice, provide molecular markers for flavor-oriented breeding and demonstrate the power of GC × GC-TOFMS coupled with chemometrics for grain aroma research. Full article

Mycorrhizal-mediated seedling establishment may reduce dependency on chemical fertilizers, but the effectiveness of infection for growth may differ depending on species with different eco-physiological adaptations. The infection of arbuscular mycorrhizal fungi (AMF) and P uptake were compared between rice (Oryza sativa L.) (Koshihikari (rice_k), Togo4 (rice_t)), and pearl millet (Pennisetum glaucum (L.) R. Br.) (ICMB89111 (millet₈₉₁), ICMB95444 (millet₉₅₄)) seedlings (i) in response to three different commercial AMF inoculants of Rhizoglomus irregulare (popular inoculant Dr. Kinkon (I₁); two new inoculants Rootella P (I₂) and Rootella F (I₃)) in comparison with indigenous AMF from Andosol upland and paddy topsoils (Exp. 1–2 as the inoculant experiments) and (ii) across different water regimes from upland to flooded lowland conditions for I₁ inoculant (Exp. 3–4 as the water regime experiments). The new inoculants I₂ and I₃ with higher propagule numbers showed a higher infection rate than the control seedlings in both rice and pearl millet, with a tendency for slower leaf development and no seedling growth enhancement. I₁ inoculant had more significant positive effects on the root transversal area and shoot growth parameters than the control. The infection rates of all three inoculants were lower than the indigenous AMF from upland Andosol in rice and pearl millet, in which a higher infection rate led to higher P uptake found in millet₉₅₄. I₁ inoculant increased the infection rate in pearl millet and rice but had no clear indication of interaction with water regimes. A higher infection rate led to higher P uptake and shoot dry weight in pearl millet but not in rice with higher root length density. This study provided the significance of inoculants for seedling establishment and highlighted more mycorrhizal-mediated P uptake in pearl millet than in rice. Full article

The whiteness of rice grains (WRG) is a key indicator of appearance quality, directly impacting its commercial value. The trait is quantitative, influenced by multiple factors, and no specific genes have been cloned to date. In this study, we first examined the correlation between the whiteness of polished rice, cooked rice, and rice flour, finding that the whiteness of rice flour significantly correlated with both polished and cooked rice. Thus, the whiteness of rice flour was chosen as the indicator of WRG in our QTL analysis. Using a set of chromosome segment substitution lines (CSSL) with japonica rice Koshihikari as the recipient and indica rice Nona Bokra as the donor, we analyzed QTLs for WRG across two growth environments and identified six WRG QTLs. Notably, qWRG9 on chromosome 9 displayed stable genetic effects in both environments. Through chromosomal segment overlapping mapping, qWRG9 was narrowed to a 1.2 Mb region. Additionally, a BC₄F₂ segregating population confirmed that low WRG was a dominant trait governed by the major QTL qWRG9, with a segregation ratio of low to high WRG approximating 3:1, consistent with Mendelian inheritance. Further grain quality analysis on the BC₄F₂ population revealed that rice grains carrying the Indica-type qWRG9 allele not only exhibited lower WRG but also had significantly higher protein content. These findings support the fine mapping of the candidate gene and provide an important QTL for improving rice grain quality through genetic improvement. Full article

Abscisic acid (ABA) is a well-known phytohormone that initiates seed dormancy. This is the first study elucidating the variability and relationship in the accumulation of phenolics, melatonin, and momilactones A (MA) and B (MB) during a rice (Oryza sativa L. var. Koshihikari, Akisakari, and Akiroman) seed dormancy process treated by ABA with concentrations of 0 (control), 10, 50, and 100 µM over 8 days. Accordingly, increased concentrations of ABA resulted in an extended dormancy period of rice seeds, along with reducing fresh weight while maintaining stable dry weight in all varieties. ABA treatment elevated total phenolic (TPC) and flavonoid (TFC) contents. Particularly, quantities of ferulic and cinnamic acids were enhanced, in line with the promoted antioxidant capacities of ABA-treated rice seeds. Momilactone contents were increased (3.8% to 32.6% for MA and 16.3% to 31.3% for MB) during the extension of rice seed dormancy regulated by ABA. Notably, the accumulation tendency of MA and MB under ABA effects was consistent with that of melatonin, a phytohormone associated with seed dormancy prolongation. The finding implies that MA and MB may play a role alongside melatonin in signaling the extended dormancy of rice seeds through the ABA pathway. Future research should delve into the molecular mechanisms underlying these observations. Full article

The tiller angle, which is an important agronomic trait, determines plant architecture and greatly influences the grain yield of rice. In this study, a population of chromosome segment substitution lines derived from a cross between a japonica variety with a compact plant architecture—Koshihikari—and an indica variety with a spread-out plant architecture—Nona Bokra—was used to investigate the genetic basis of the tiller angle. Five quantitative trait loci (qTA1, qTA5, qTA9-1, qTA9-2, and qTA11) for the tiller angle were detected on chromosomes 1, 5, 9, 9, and 11 in two different environments. The phenotypic variation in these QTLs ranged from 3.78% to 8.22%. Two pairs of digenic epistatic QTLs were detected in Lingshui. The epistatic interaction explained 15.19% and 13.60% of the phenotypic variance, respectively. Among the five QTLs, qTA9-2 was detected in both environments. An F₂ mapping population containing the qTA9-2 QTL was established. The location of qTA9-2 was narrowed down to a 187 kb region between InDel markers M9 and M10 on chromosome 9. Thirty open reading frames (ORFs), including TAC1, a gene known to regulate the tiller angle, were identified in this region. The gene sequencing results suggested that a base substitution from G to A at position 1557 in the 3′-untranslated region led to a difference in the expression of qTA9-2 in Koshihikari and Nona Bokra. These findings provide a potential gene resource for the improvement of rice plant architecture. Full article

This is the first study aiming to enrich momilactones A (MA) and B (MB) and phenolic compounds in germinated brown rice (GBR) and non-GBR var. Koshihikari and Milky Queen through the cooking process. Extraction methods for these compounds were optimized by applying various conditions, including solvents (80% methanol and 80% ethanol), heat (80 °C), and sonication (2 h). Momilactone and phenolic quantities were determined by ultra-performance liquid chromatography–electrospray ionization mass spectrometry (UPLC–ESI-MS) and high-performance liquid chromatography (HPLC), respectively. Accordingly, cooked Koshihikari GBR extract using 80% methanol and sonication (GKB4) revealed the highest amounts of tricin, caffeic, ρ-hydroxybenzoic, ρ-coumaric, ferulic, salicylic, and cinnamic acids (1.71, 1.01, 0.62, 0.45, 0.94, 2.50, and 0.37 mg/g DW, respectively), consistent with the strongest antiradical activities in DPPH and ABTS assays (IC₅₀ = 1.47 and 1.70 mg/mL, respectively). Non-cooked GBR Koshihikari extract using 80% ethanol and sonication (GKB9) exhibited the highest MA and MB contents (147.73 and 118.8 μg/g DW, respectively). Notably, GKB9 showed potent inhibition of α-amylase and α-glucosidase (IC₅₀ = 0.48 and 0.15 mg/mL, respectively), compared with the anti-diabetic drug acarbose (IC₅₀ = 0.26 and 2.48 mg/mL, respectively). The findings hold significant implications for developing phenolic- and momilactone-enriched brown rice with health-beneficial properties. Full article

Greenhouse gas (GHG) emissions from paddy fields depend on water management practices and rice varieties. Lysimeter experiments were conducted to determine the effect of rice varieties (lowland; Koshihikari (KH) and upland; Dourado Precoce (DP)) on GHG emissions under two water management practices: alternate wetting and drying (AWD) and continuous flooding (CF). A repeated cycle of drying and wetting in AWD irrigation was performed by drying the soil to −40 kPa soil matric potential and then rewetting. Consequently, the closed chamber method was used to measure direct emissions of methane (CH₄), nitrous oxide (N₂O), and carbon dioxide (CO₂). The result revealed that water management significantly affected CH₄ and N₂O emissions (p < 0.05), while no significant effect was observed between different rice varieties. Although, AWD irrigation reduced CH₄ emissions, it increased N₂O emissions compared to CF irrigation, likely due to increased oxygen supply. AWD irrigation decreased GWP by 55.6% and 59.6% in KH and DP, respectively, compared to CF irrigation. Furthermore, CH₄ and N₂O emissions significantly correlated with soil redox potential and volumetric water content. These results suggest that AWD irrigation might be an effective water management method for mitigating GHG emissions from rice fields in central Japan. Full article

This study exploits quantitative algorithms of Raman spectroscopy to assess, at the molecular scale, the nutritional quality of individual kernels of the Japanese short-grain rice cultivar Koshihikari in terms of amylose-to-amylopectin ratio, fractions of phenylalanine and tryptophan aromatic amino acid residues, protein-to-carbohydrate ratio, and fractions of protein secondary structures. Statistical assessments on a large number of rice kernels reveal wide distributions of the above nutritional parameters over nominally homogeneous kernel batches. This demonstrates that genetic classifications cannot catch omic fluctuations, which are strongly influenced by a number of extrinsic factors, including the location of individual grass plants within the same rice field and the level of kernel maturation. The possibility of collecting nearly real-time Raman “multi-omic snapshots” of individual rice kernels allows for the automatic (low-cost) differentiation of groups of kernels with restricted nutritional characteristics that could be used in the formulation of functional foods for specific diseases and in positively modulating the intestinal microbiota for protection against bacterial infection and cancer prevention. Full article

Rice lodging causes a loss of yield and leads to lower-quality rice. In Japan, Koshihikari is the most popular rice variety, and it has been widely cultivated for many years despite its susceptibility to lodging. Reducing basal fertilizer is recommended when the available nitrogen in soil (SAN) exceeds the optimum level (80–200 mg N kg⁻¹). However, many commercial farmers prefer to simultaneously apply one-shot basal fertilizer at transplant time. This study investigated the relationship between the rice lodging and SAN content by assessing their spatial distributions from unmanned aircraft system (UAS) images in a Koshihikari paddy field where one-shot basal fertilizer was applied. We analyzed the severity of lodging using the canopy height model and spatially clarified a heavily lodged area and a non-lodged area. For the SAN assessment, we selected green and red band pixel digital numbers from multispectral images and developed a SAN estimating equation by regression analysis. The estimated SAN values were rasterized and compiled into a 1 m mesh to create a soil fertility map. The heavily lodged area roughly coincided with the higher SAN area. A negative correlation was observed between the rice inclination angle and the estimated SAN, and rice lodging occurred even within the optimum SAN level. These results show that the amount of one-shot basal fertilizer applied to Koshihikari should be reduced when absorbable nitrogen (SAN + fertilizer nitrogen) exceeds 200 mg N kg⁻¹. Full article

This is the first investigation, conducted in a completely randomized design (CRD), to determine the effects of different salinity levels (75 and 150 mM) and germination periods (3, 4, and 5 days) on momilactone and phenolic accumulations in germinated brown rice (GBR) var. Koshihikari. Particularly, the identification of bioactive compounds was confirmed using electrospray ionization-mass spectrometry (ESI-MS) and nuclear magnetic resonance (NMR) spectroscopy (¹H and ¹³C). Momilactone A (MA) and momilactone B (MB) amounts were determined by ultra-performance liquid chromatography–electrospray ionization-mass spectrometry (UPLC–ESI-MS), whereas other compounds were quantified by spectrophotometry and high-performance liquid chromatography (HPLC). Accordingly, GBR under B2 treatment (75 mM salinity for 4 days) showed the greatest total phenolic and flavonoid contents (14.50 mg gallic acid and 11.06 mg rutin equivalents, respectively, per g dry weight). GBR treated with B2 also accumulated the highest quantities of MA, MB, ρ-coumaric, ferulic, cinnamic, salicylic acids, and tricin (18.94, 41.00, 93.77, 139.03, 46.05, 596.26, and 107.63 µg/g DW, respectively), which were consistent with the strongest antiradical activities in DPPH and ABTS assays (IC₅₀ = 1.58 and 1.78 mg/mL, respectively). These findings have implications for promoting the value of GBR consumption and rice-based products that benefit human health. Full article

Salinity is a severe stress that causes serious losses in rice production worldwide. This study, for the first time, investigated the effects of fulvic acid (FA) with various concentrations of 0.125, 0.25, 0.5, and 1.0 mL/L on the ability of three rice varieties, Koshihikari, Nipponbare, and Akitakomachi, to cope with a 10 dS/m salinity level. The results show that the T3 treatment (0.25 mL/L FA) is the most effective in stimulating the salinity tolerance of all three varieties by enhancing their growth performance. T3 also promotes phenolic accumulation in all three varieties. In particular, salicylic acid, a well-known salt-stress-resistant substance, is found to increase during salinity stress in Nipponbare and Akitakomachi treated with T3 by 88% and 60%, respectively, compared to crops receiving salinity treatment alone. Noticeably, the levels of momilactones A (MA) and B (MB) fall in salt-affected rice. However, their levels markedly rise in rice treated with T3 (by 50.49% and 32.20%, respectively, in Nipponbare, and by 67.76% and 47.27%, respectively, in Akitakomachi), compared to crops receiving salinity treatment alone. This implies that momilactone levels are proportional to rice tolerance against salinity. Our findings suggest that FA (0.25 mL/L) can effectively improve the salinity tolerance of rice seedlings even in the presence of a strong salt stress of 10 dS/m. Further studies on FA application in salt-affected rice fields should be conducted to confirm its practical implications. Full article

Brown rice traits are critical to both grain yield and quality. In the present study, the chromosome segment substitution lines (CSSLs) population derived from a cross between japonica Koshihikari and indica Nona Bokra was used to analyze the brown rice length (BRL), brown rice width (BRW), length–width ratio of brown rice (BLWR), brown rice thickness (BRT), brown rice perimeter (BRP), brown rice area (BRA), thousand-grain weight of brown rice (BRGW), brown rice ratio (BRR), taste value of brown rice (BTV), and water content of brown rice (BWC). Correlations analysis showed that most of the brown rice traits had significant correlations with each other, except for BRR, BTV, and BWC. A total of sixty-one QTLs for these traits were identified under three environments, which mapped to chromosomes 1, 2, 3, 5, 6, 7, 8, 10, 11, and 12, with the LOD ranging from 2.52 to 16.68 and accounting for 2.60 to 25.38% of the total phenotypic variations. Moreover, thirty pairs of epistatic interactions for BRL, BRW, BLWR, BRP, and BRA were estimated and distributed on all chromosomes except 10. These findings will provide a further understanding of the genetic basis of brown rice traits and facilitate the genetic improvement of rice yield and quality through breeding. Full article

Plants have evolved various mechanisms for low P tolerance, one of which is changing their membrane lipid composition by remodeling phospholipids with non-phospholipids. The objective of this study was to investigate the remodeling of membrane lipids among rice cultivars under P deficiency. Rice (Oryza sativa L.) cultivars (Akamai, Kiyonishiki, Akitakomachi, Norin No. 1, Hiyadateine, Koshihikari, and Netaro) were grown in 0 (−P) and 8 (+P) mg P L⁻¹ solution cultures. Shoots and roots were collected 5 and 10 days after transplanting (DAT) in solution culture and subjected to lipidome profiling using liquid chromatography-mass spectrometry. Phosphatidylcholine (PC)34, PC36, phosphatidylethanolamine (PE)34, PE36, phosphatidylglycerol (PG)34, phosphatidylinositol (PI)34 were the major phospholipids and digalactosyldiacylglycerol (DGDG)34, DGDG36, 1,2-diacyl-3-O-alpha-glucuronosylglycerol (GlcADG)34, GlcADG36, monogalactosyldiacylglycerol (MGDG)34, MGDG36, sulfoquinovosyldiacylglycerol (SQDG)34 and SQDG36 were the major non-phospholipids. Phospholipids were lower in the plants that were grown under −P conditions than that in the plants that were grown under +P for all cultivars at 5 and 10 DAT. The levels of non-phospholipids were higher in −P plants than that in +P plants of all cultivars at 5 and 10 DAT. Decomposition of phospholipids in roots at 5 DAT correlated with low P tolerance. These results suggest that rice cultivars remodel membrane lipids under P deficiency, and the ability of remodeling partly contributes to low P tolerance. Full article

The global cultivation area of rice is equivalent to 4% of the world’s forest area and may be an important sink and source of trace gases. To produce a precise terpenoid emission inventory, it is essential to obtain reliable data of terpenoid emission from rice plants. In the present study, terpenoid emissions from various rice species were measured using flow-through chamber and tower flux measurement methods. In the flow-through chamber measurement, linalool was emitted from the above-ground parts of the three rice cultivars “Koshihikari”, “Nipponbare” and “IR72”. The emission rates gradually decreased (<0.1 µg gDW⁻¹ h⁻¹) within two days during the measurement periods. As the touching stimulus might have enhanced linalool emission, a non-contact measurement method, i.e., the tower flux measurement method, was applied to a “Koshihikari” paddy. Linalool was not detected, but α-pinene was detected in the atmosphere above the rice paddy. The α-pinene flux (mean ± 95% confidence interval) was 0.006 ± 0.004 nmol m⁻² s⁻¹ on a land-area basis. The flux was 1/200 of the previously reported monoterpene emission rate of the rice plants measured in a commercial chamber, but was not largely different from three other reports. We provide terpenoid flux data above a rice paddy for the first time, which is more reliable because the tower flux measurement method can avoid stimuli to rice leaves and stems. Although the obtained terpenoid emission rate is very low, the obtained values can contribute to the establishment of a precise BVOC inventory in Asia. Full article

The genetic dissection of agronomically important traits in closely related Japanese rice cultivars is still in its infancy mainly because of the narrow genetic diversity within japonica rice cultivars. In an attempt to unveil potential polymorphism between closely related Japanese rice cultivars, we used a next-generation-sequencing-based genotyping method: genotyping by random amplicon sequencing-direct (GRAS-Di) to develop genetic linkage maps. In this study, four recombinant inbred line (RIL) populations and their parents were used. A final RIL number of 190 for RIL71, 96 for RIL98, 95 for RIL16, and 94 for RIL91 derived from crosses between a common leading Japanese rice cultivar Koshihikari and Yamadanishiki, Taichung 65, Fujisaka 5, and Futaba, respectively, and the parent plants were subjected to GRAS-Di library construction and sequencing. Approximately 438.7 Mbp, 440 Mbp, 403.1 Mbp, and 392 Mbp called bases covering 97.5%, 97.3%, 98.3%, and 96.1%, respectively, of the estimated rice genome sequence at average depth of 1× were generated. Analysis of genotypic data identified 1050, 1285, 1708, and 1704 markers for each of the above RIL populations, respectively. Markers generated by GRAS-Di were organized into linkage maps and compared with those generated by GoldenGate SNP assay of the same RIL populations; the average genetic distance between markers showed a clear decrease in the four RIL populations when we integrated markers of both linkage maps. Genetic studies using these markers successfully localized five QTLs associated with heading date on chromosomes 3, 6, and 7 and which previously were identified as Hd1, Hd2, Hd6, Hd16, and Hd17. Therefore, GRAS-Di technology provided a low cost and efficient genotyping to overcome the narrow genetic diversity in closely related Japanese rice cultivars and enabled us to generate a high density linkage map in this germplasm. Full article