Indica-japonica Hybrid Research Articles

Effects of Storage Temperature on Indica-Japonica Hybrid Rice Metabolites, Analyzed Using Liquid Chromatography and Mass Spectrometry.

The Yongyou series of indica-japonica hybrid rice has excellent production potential and storage performance. However, little is known about the underlying mechanism of its storage resistance. In this study, Yongyou 1540 rice (Oryza sativa cv. yongyou 1540) was stored at different temperatures, and the storability was validated though measuring nutritional components and apparent change. In addition, a broad-targeted metabolomic approach coupled with liquid chromatography-mass spectrometry was applied to analyze the metabolite changes. The study found that under high temperature storage conditions (35 °C), Yongyou 1540 was not significantly worse in terms of fatty acid value, whiteness value, and changes in electron microscope profile. A total of 19 key differential metabolites were screened, and lipid metabolites related to palmitoleic acid were found to affect the aging of rice. At the same time, two substances, guanosine 3′,5′-cyclophosphate and pipecolic acid, were beneficial to enhance the resistance of rice under harsh storage conditions, thereby delaying the deterioration of its quality and maintaining its quality. Significant regulation of galactose metabolism, alanine, aspartate and glutamate metabolism, butyrate metabolism, and arginine and proline metabolism pathways were probably responsible for the good storage capacity of Yongyou 1540.

Understanding the Palatability, Flavor, Starch Functional Properties and Storability of Indica-Japonica Hybrid Rice.

The rice quality and starch functional properties, as well as the storability of three YY-IJHR cultivars, which included YY12 (biased japonica type YY-IJHR), YY1540 (intermedius type YY-IJHR) and YY15 (biased indica type YY-IJHR), were studied and compared to N84 (conventional japonica rice). The study results suggested that the three YY-IJHR varieties all had greater cooking and eating quality than N84, as they had lower amylose and protein content. The starch of YY-IJHR has a higher pasting viscosity and digestibility, and there was a significant difference among the three YY-IJHR cultivars. Rice aroma components were revealed by GC-IMS, which indicated that the content of alcohols vola-tile components of YY-IJHR were generally lower, whereas the content of some aldehydes and esters were higher than N84. In addition, YY-IJHR cultivars’ FFA and MDA contents were lower, which demonstrated that YY-IJHR had a higher palatability and storability than those of N84 in fresh rice and rice stored for 12 months. In conclusion, this study suggested that YY-IJHR had better rice quality and storability than N84. PCA indicated that the grain quality and storability of YY12 and YY15 were similar and performed better than YY1540, while the aroma components and starch functional properties of YY-IJHR cultivars all had significant differences.

Vascular Bundle Characteristics of Different Rice Variety Treated with Nitrogen Fertilizers and Its Relation to Stem Assimilates Allocation and Grain Yield

The vascular bundle plays a vital role in photoassimilates transportation in rice. However, the vascular bundle characteristics of basal internode and its relationship with stem assimilates allocation and yield remain unclear. In this study, experiments with four different types of rice varieties subjected to three nitrogen application levels were conducted. The results showed that large vascular bundles (LVB) and small vascular bundles (SVB)-related traits of basal internode exhibited genotypic differences. Indica-japonica hybrid varieties had the highest number of cross sectional areas and phloem areas of LVB and SVB, thus the highest stem nonstructural carbohydrates (NSC) translocation, grain filling percentage and grain yield, followed by indica hybrid varieties and indica conventional varieties, and those were the lowest in japonica conventional varieties. The LVB and SVB related traits were significantly and positively correlated with stem NSC translocation, grain filling percentage and grain yield, respectively These results suggested that improving the characteristics of basal internodes was beneficial to enhance stem NSC translocation and consequently increase grain yield. Nitrogen application increased LVB and SVB related traits. Therefore, varieties with developed vascular bundles of basal internodes and cultivation techniques for improving vascular bundle related traits should be considered as the effective route for increasing grain yield.

Development of Wide-Compatible Indica Lines by Pyramiding Multiple Neutral Alleles of Indica-Japonica Hybrid Sterility Loci.

Since the development of indica hybrid rice in the 1970s, great success has been achieved in hybrid rice production in China and around the world. The utilization of inter-subspecific indica–japonica hybrid rice has always been considered due to its stronger heterosis characteristics. However, indica–japonica hybrids face a serious problem of sterility, which hinders the exploitation of their heterosis. In the past decades, the genetic basis of indica–japonica hybrid sterility has been well studied. It was found that in sterile indica–japonica hybrids, female sterility was mainly controlled by the S5 locus and male sterility by the Sa, Sb, Sc, Sd, and Se loci. In this study, we developed wide-compatible indica lines (WCILs) by pyramiding multiple neutral (n) alleles of the hybrid sterility loci. First, we identified Sn alleles of the loci in single-segment substitution lines (SSSLs) in the genetic background of indica Huajingxian 74 (HJX74). Then, the Sn alleles of S5, Sb, Sc, Sd, and Se loci in SSSLs were pyramided in the HJX74 genetic background. The WCILs carrying Sn alleles at the S5, Sb, Sc, Sd, and Se loci showed wide compatibility with indica and japonica rice varieties. Therefore, the WCILs will be used to develop inter-subspecific indica–japonica hybrid rice with normal fertility.

The Next Generation of Rice: Inter-Subspecific Indica-Japonica Hybrid Rice.

Rice (Oryza sativa) is an important food crop and has two subspecies, indica and japonica. Since the last century, four generations of rice varieties have been applied to rice production. Semi-dwarf rice, intra-subspecific hybrid rice, and inter-subspecific introgression rice were developed successively by genetic modification based on the first generation of tall rice. Each generation of rice has greater yield potential than the previous generation. Due to the stronger heterosis of indica-japonica hybrids, utilization of the inter-subspecific heterosis has long been of interest. However, indica-japonica hybrid sterility hinders the utilization of heterosis. In the past decades, indica-japonica hybrid sterility has been well understood. It is found that indica-japonica hybrid sterility is mainly controlled by six loci, S5, Sa, Sb, Sc, Sd, and Se. The indica-japonica hybrid sterility can be overcome by developing indica-compatible japonica lines (ICJLs) or wide-compatible indica lines (WCILs) using genes at the loci. With the understanding of the genetic and molecular basis of indica-japonica hybrid sterility and the development of molecular breeding technology, the development of indica-japonica hybrid rice has become possible. Recently, great progress has been made in breeding indica-japonica hybrid rice. Therefore, the indica-japonica hybrid rice will be the next generation of rice. It is expected that the indica-japonica hybrid rice will be widely applied in rice production in the near future.

Higher Radiation Use Efficiency and Photosynthetic Characteristics After Flowering Could Alleviate the Yield Loss of Indica-Japonica Hybrid Rice Under Shading Stress

Higher Radiation Use Efficiency and Photosynthetic Characteristics After Flowering Could Alleviate the Yield Loss of Indica-Japonica Hybrid Rice Under Shading Stress

Bin mapping-based QTL analyses using three genetic populations derived from indica-japonica crosses uncover multiple grain shape heterosis-related loci in rice.

Exploitation of heterosis between indica and japonica has important significance in scientific research and agriculture application. However, the molecular mechanism of grain shape heterosis in indica-japonica hybrid remains unknown in rice (Oryza sativa L.). To reveal the genetic mechanism of grain shape in indica--japonica hybrid, we constructed a high-generation recombinant inbred line (RIL) population and two testcross hybrid populations derived from the cross of RILs and two cytoplasmic male sterile material (YTA and Z7A) and then performed a bin mapping-based quantitative trait locus (QTL) mapping of multiple grain shape traits, such as grain length (GL), grain width (GW), and grain length-to-width ratio (GLWR). A total of sixteen QTLs and 30 heterosis-related QTLs of grain shape traits were detected. We found that GS3, GS5, and OsPPKL2 were also correlated with grain shape both in RILs and two testcross hybrid populations. Homologous gene analysis emphasized two candidate grain shape-associated genes (LOC_Os06g14260 and LOC_Os04g51950). Our findings uncover multiple grain shape heterosis-related loci and provides a new insight into heterosis mechanism of grain shape in rice.

The difference in the starch properties related to eating and cooking quality among six indica-japonica rice hybrids

The difference in the starch properties related to eating and cooking quality among six indica-japonica rice hybrids

Transcriptome and metabolome profiling reveal the regulatory mechanism of protein accumulation in inferior grains of indica-japonica rice hybrids

Protein content in the inferior grains (IG) has a great impact on eating quality of indica-japonica rice hybrids. However, the mechanisms of the difference in protein accumulation between IG and superior grains (SG) remains unclear. A field experiment was carried out using an indica-japonica hybrid Yongyou17 and two nitrogen levels. The result showed that prolamin concentration was significantly higher in IG than SG, while there was no significant difference in glutelin concentration between the two types of grains. Totally, 465 metabolites were identified, and 26 “core metabolites” differentially accumulated in IG could be divided into three types. Asparagine and 1-aminocyclopropanecarboxylic acid were markedly increased in IG, while flavonoid compounds were obviously reduced, in comparison with those in SG. Weighted gene co-expression network analysis indicated that bisque4 and darkorange2 modules for type 1 and type 3 of the “core metabolites” were closely associated with the synthesis of ribosomal protein and stress response, respectively. Eight hub genes, i.e. rpL32_8.1, novel.907, RPS15a and RPL13a.4 in bisque4 and OsSAP5, OsHSP20, PRX12 and DUF3741 were identified in darkorange2. In addition, genes WDR, R2R3-MYB and bHLHs were significantly down-regulated in IG, companied by reduced synthesis of flavonoid compounds. IG had higher ethylene and N levels, resulting more protein accumulation. The current study provides a new insight into the regulation network of protein synthesis in IG of indica-japonica rice hybrids.

Grain yield and nitrogen use efficiency response to polymer coated urea for two indica-japonica hybrid rice varieties

To meet the food demand of an increasing population, hybrid rice varieties with high yields were selected, including indica-japonica hybrids. However, information about growth characteristics under the utilization of coated urea was limited. In this study, growth performance and yield of two indica-japonica hybrid varieties under five coated urea rates (0, 150, 225, 300 and 375 kg N ha−1) were investigated, while two conventional late japonica were used as controls. Consequently, yield of indica-japonica hybrids was obviously higher than that of late japonica under a single application of coated urea, due to larger grain number per panicle. The relationship of yield and N rate was an open downward conic curve, while polymer coated urea for the maximum yield of the four varieties was about 225 kg N ha−1. The dry matter accumulation of indica-japonica hybrids was significantly higher than that of the late japonica. Nitrogen use efficiencies were higher under lower nitrogen rate.

Effects of submergence stress at the vegetative growth stage on hybrid rice growth and grain yield in China

Submergence stress can greatly limit grain yield of inbred rice (Oryza sativa L.), but the effects of submergence on hybrid rice are unclear. A pot experiment was conducted to clarify the effects of submergence that happens at the vegetative growth stage on two Chinese hybrid rice cultivars. The rice cultivars Zheyou-18, an indica-japonica hybrid, and Yliangyou-689, an indica hybrid, were planted under two treatments, submergence (43 cm depth of tap water for about 2 wk) and control (no submergence). Results showed that the grain yield of submerged ‘Yliangyou-689’ was 539.0 g m-2 in 2018 and 614.2 g m-2 in 2019; submergence significantly reduced grain yield by 49.6% and 44.2% of that of the control. The lower level of grain yield was attributed to reduced survival rate, numbers of tillers and spikelets, plant dry weight, and crop growth rate, and excessive elongation of stems due to submergence of plants. The grain yield of submerged ‘Zheyou-18’ was 466.8 g m-2 in 2018 and 376.4 g m-2 in 2019 and neither of which were significantly different from that of the control, indicating higher submergence tolerance in ‘Zheyou-18’ than in ‘Yliangyou-689’. Submergence did not affect plant N and K contents, but it reduced plant N uptake rates by 47.8% to 88.7% and it reduced K uptake rates by 53.9% to 89.5% of that of the control in these two hybrid cultivars. Furthermore, nonsignificant differences were observed in all of the parameters related to rice starch viscosity between control and submergence treatment.

Effect of ozone stress on yield characteristics of indica-japonica hybrid rice Yongyou 538 in two consecutive growing seasons

The hybrid rice cultivar Yongyou 538 (Y538) was exposed to 100 ppb ozone (O3) and control conditions throughout the cropping seasons in 2016–2017 in Yangzhou, China. The average daily maximum temperature during reproductive the growth stage (mid-August) of Y538 in 2016 was 3.6 °C higher than that in 2017. The heading stage of Y538 was reached 6.5 days earlier in the control than in the high-O3 treatments. Ozone stress decreased plant height and tiller number at all growth stages, and the O3–induced reductions in these two parameters were gradually increased with plant development. Compared to the control, O3 stress significantly decreased yield by an average of 29.9 %, and by 35.2 and 24.0 % in 2016 and 2017, respectively. Averaged across 2 years, O3 stress caused slight reductions in both panicle number (PN) and filled grain weight (FGW). However, spikelet number per panicle (-9.6 %, SNP) and filled grain percentage (-17.5 %, FGP) showed significant reductions due to O3 exposure, while O3 stress increased empty grain percentage (EGP) and incompletely-filled grain percentage (IGP) by 72.9 and 80.0 %, respectively, when averaged across 2 years. A significant interaction of O3 by year or grain position in a panicle was observed on yield, FGP, EGP, and IGP, as the changes in 2016 were more significantly affected than those in 2017; grains at lower parts of the panicle were more affected than those at upper parts. Ozone stress significantly reduced the above ground dry weight of rice at maturity in 2 years by an average of 18.3 %, which was mainly related to the decrease in stem (-19.3 %) and panicle weight (-22.9 %), while no O3 effect was detected for leaf weight. Ozone stress significantly increased the ratio of leaf to aboveground dry weight by 23.4 % when averaged across 2 years, while the ratio of stem or panicle showed a declining trend. Correlation and path analysis showed that yield loss due to O3 exposure was closely related to the decreases in FGP (especially the middle and lower parts of the panicle) and SNP. Ozone treatment of 100 ppb significantly decreased the productivity of Y538, and the high temperature in the reproductive growth period would further exacerbate the damage caused by O3, leading to substantial yield losses.

Assisted selection of eating quality progeny of indica (O. sativa L. ssp. indica) and japonica (O. sativa L. ssp. japonica) hybrids using rice starch properties

Eating quality (EQ) of rice is mainly determined by sensory evaluation using tasting, which is affected by the taster’s geographic residential area, gender, and age. The sensory evaluation protocol also requires rice samples (usually > 500 g) larger than the amount harvested from the early generations of breeding in many cases, thereby hindering the sensory tasting practices. The characteristics of rice starch have a significant impact on EQ; however, information on starch assisted-selection of EQ is insufficient. In this study, the recombinant inbred lines and backcross recombinant inbred lines constructed by the hybridization of japonica (O. sativa L. ssp. japonica) rice (cv. Toyonishiki) and indica (O. sativa L. ssp. indica) rice (cv. Qishanzhan) were used as test materials to analyze and explore the relationships between the amylose content (AC), rapid visco analyzer (RVA) profile characteristics, and the EQ score obtained from sensory tasting assessment. We provided a feasible solution to use rice starch properties to assist in selection of EQ. The results indicated that AC and RVA profile characteristics including trough viscosity (TV), final viscosity (FV), breakdown (BD), and setback (SB) were closely related to the EQ values. Furthermore, an integrated indicator—i.e., starch properties quality (SPQ)—that represented a more comprehensive characterization of rice starch, was derived based on the EQ evaluation hierarchy and weighted AC, TV, FV, BD, and SB values. The correlation between SPQ and EQ was significant (p < 0.001), and was significantly higher compared with using individual indicators. Moreover, the SPQ method requires less rice samples (i.e., 3 g of milled rice flour) and can be applied to assisted-selection for EQ in early generations of breeding. This study provid esessential technical support for the rapid and accurate identification of the EQ of progeny of indica–japonica hybrids.

Compact plant type rice has higher lodging and N resistance under machine transplanting

To identify the major factors that contribute to the difference in lodging among different rice varieties under machine transplanting and their responses to nitrogen (N), field experiments were conducted at Danyang County (a representative eco-site of the Lower Yangtze River) in Jiangsu Province, China in 2017 and 2018, 22 hybrid indica varieties (HIs), 22 inbred japonica varieties (IJs) and two indica japonica hybrid varieties (IJHs) were transplanted by machine with three N rates (N0, N150 and N300, 0, 150 and 300 kg ha–1, respectively). Lodging-related physical parameters, morphological characteristics and apparent transport rates of dry matter were examined. Significant difference in yield was observed among different types of rice, and followed by IJs<HIs<IJHs. The average lodging index (LI) of hybrid varieties (HIs and IJHs) was higher than that of the inbred varieties (IJs) with higher plant height; moreover, lower apparent export rate of dry matter resulted lower LI in IJHs than in HIs. The HIs had a large difference in the LI, which came from the difference in bending stress (BS) induced by the difference in the apparent export rate of dry matter, varieties with lower leaf angle of upper three leaves possess strong lodging resistance capacity; however, the gap among the IJs was due to the difference in the cross section modulus (Z). The LI in the IJs or IJHs increased slightly with the increased N application, and there was no lodging incidence under the high N level, which was due to the low leaf angle and barely changed under high N; there was a significant interaction between varieties (HIs) and N rates in lodging rate and LI, varieties with lower leaf angle of upper three leaves were resistant to high N. These results suggest that compact plant type rice has higher lodging and N resistance at machine-transplanting method.

The Influence of Nitrogen Application Level on Eating Quality of the Two Indica-Japonica Hybrid Rice Cultivars.

Indica-japonica hybrid rice cultivars show great yield potential but poor eating quality and require more nitrogen (N) input relative to japonica rice. However, the effect of N levels on the eating quality of indica-japonica hybrid rice is little known. A field experiment was carried out to investigate the effects of four N levels on two indica-japonica hybrid rice cultivars (Yongyou12 and Yongyou17) differing in eating quality. The results showed that the contents of amylose chains and water-insoluble storage proteins, especially prolamin, increased largely under a high N level, leading to deterioration of the rice-eating quality, although a low N level (100 N kg/ha) had a less negative effect on the eating quality. Moreover, both of the indica-japonica hybrids had high ratios of inferior grains (IG), and the ratio of IG increased with the N level. Grain weight and the immature ratio of IG were reduced and increased with the N level, respectively, which are also factors for deterioration of the eating quality. The two cultivars differed greatly in the responses of eating quality to the N level, with Yongyou17 being more sensitive than Yongyou12. The current results indicated that a high N level deteriorates the eating quality of indica-japonica hybrid rice mainly due to a large increase of IG.

Development and evaluation of improved lines based on an elite rice variety 9311 for overcoming hybrid sterility in rice

Hybrid sterility is a major obstacle to the development of superior inter-subspecific hybrids between indica and japonica subspecies of Asian-cultivated rice. To overcome hybrid sterility, we introduced four japonica alleles (S-j) at Sa, Sc, f5, and S32 loci from Nipponbare into 9311 through marker-assisted backcross breeding, and four improved lines were obtained. Three wide-compatibility lines 9311(S5-n), 9311(f5-n), and 9311(S5-n+f5-n) previously constructed were used as control and parental line of hybridization. By crossing with 9311(S5-n+f5-n), two pyramiding lines 9311(Sa+S5-n+f5-n) and 9311(S32+Sa+S5-n+f5-n) were obtained. To evaluate the gene effect of pollen fertility and spikelet fertility, the near-isogenic lines (NILs) harboring S5-n, f5-n, Sa, Sc, f5, or S32 and three pyramiding lines with S5-n+f5-n, Sa+S5-n+f5-n, or S32+Sa+S5-n+f5-n were testcrossed to six japonica varieties. The results showed that single-gene f5, f5-n, S32, and S5-n could significantly improve spikelet fertility in majority of indica-japonica hybrids. Single-gene Sa and Sc could significantly improve spikelet fertility in part of indica-japonica hybrids. Moreover, the pyramiding lines exhibited significantly higher spikelet fertility than the control in indica-japonica hybrids. A significant increase in spikelet fertility (31.4–55%) was observed in three- or four-gene pyramiding lines. Our results provide an effective approach to exploiting heterosis between indica and japonica subspecies, which had a profound implication in rice breeding.

Agronomic and physiological performance of an indica–japonica rice variety with a high yield and high nitrogen use efficiency

AbstractHybrid rice (Oryza sativa L.) varieties usually need more N application to produce a higher grain yield and exhibit lower N use efficiency (NUE) than inbreds. However, little information is available about the mechanism underlying an indica–japonica rice variety with high yield and high NUE under low N rates. This study investigated this issue. The indica–japonica hybrid rice variety Yongyou 2640 (Y‐2640) and the japonica inbred rice variety Lianjing 7 (L‐7) were grown in a paddy field at N rates of 0 and 200 kg N ha−1. The results showed that the grain yield and internal NUE (grain yield/total N uptake of plants) of Y‐2640 were 16–23% and 9–10%, respectively, higher than those of L‐7. A higher grain yield for Y‐2640 was mainly attributed to the greater spikelet number per unit area that resulted from greater root oxidation activity at panicle initiation and its higher crop growth rate and net assimilation rate before heading. A higher leaf area index and greater root length, root, and shoot biomass were the important agronomic traits of Y‐2640. Higher cytokinin content and the expression of genes involved in the amino acid transporters OsAAP1 and OsLHT1 in the roots and leaves, a higher photosynthetic NUE, and a greater N harvest index were the main physiological traits of Y‐2640. The results suggest that improved agronomic and physiological performance accounts for the high yield and high NUE for the indica–japonica hybrid rice variety.

Comparative analysis on grain quality and yield of different panicle weight indica-japonica hybrid rice (Oryza sativa L.) cultivars

Indica-japonica hybrid rice (Oryza sativa L.) cultivars showed high yield potential and poor tasting quality when compared with common japonica rice cultivars. Large panicle is a prominent factor of high yield for indica-japonica hybrid rice cultivars, and the panicle weight varies greatly among different indica-japonica hybrid rice cultivars. It is important to research on yield and grain quality of different panicle weight indica-japonica hybrid rice cultivars. In this study, two different panicle types indica-japonica hybrid cultivars were used to research on the relation of yield and grain quality. The yields of two heavy panicle weights indica-japonica hybrid cultivars were significantly higher than that of two medium panicle weight rice cultivars. The cooking and eating quality and starch properties of different panicle type cultivars were evaluated. Yongyou 6715 (medium panicle) and Yongyou 1852 (heavy panicle) got the relatively higher cooking and eating quality. Rice cultivars with medium panicle weight had more large starch granules and higher relative crystallinity than cultivars with heavy panicle weight. Transition temperature and retrogradation enthalpy (ΔHret) of medium panicle type cultivars were significantly higher than that of heavy panicle type cultivars. There was no significant difference in amylose content among different panicle type cultivars. Protein content of heavy panicle type cultivar was higher than that of medium panicle type cultivar, and protein content is the main factor affect cooking and eating quality in this study. The cultivar Yongyou 6715 got the highest taste value with the lowest protein content. Thus, it is suggested that the emphasis on improving rice cooking and eating quality of indica-japonica hybrid rice cultivars is how to reduce the protein content in rice grain. According to the results of this study, medium panicle type with high grain weight is the desired panicle type for high quality indica-japonica hybrid rice breeding.

Artificial Selection in Domestication and Breeding Prevents Speciation in Rice

Speciation has long been regarded as an irreversible process once the reproductive barriers had been established. However, unlike in natural populations, artificial selection might either accelerate or prevent speciation processes in domesticated species. Asian cultivated rice is a target crop for both domestication and artificial breeding; it contains two subspecies of indica and japonica, which usually produce sterile inter-subspecific hybrids due to reproductive barriers. In this study, we constructed the evolutionary trajectory of a reproductive isolation system S5, which regulates fertility in indica–japonica hybrids via three adjacent genes, based on the data of 606 accessions including two cultivated and 11 wild rice species. Although hybrid sterility haplotypes at S5 lead to establishment of a killer-protector reproductive barrier, origin of wide-compatibility haplotypes by complex hybridization and recombination provides an opposing force to reproductive isolation and thus prevents speciation during domestication. Analysis in a diallel set of 209 crosses involving 21 parents showed that the wide-compatibility genotypes largely rescued fertility of indica–japonica hybrids, indicating that the wide-compatibility gene would enable gene flow to maintain species coherence. This counteracting system indicates that combined effects of natural evolution and artificial selection may result in reversible processes of speciation in rice, which may also have implications for genetic improvement of rice.

Optimizing integrative cultivation management improves grain quality while increasing yield and nitrogen use efficiency in rice

A major challenge in rice (Oryza sativa L.) production is to cope with increasing grain yield and fertilizer use efficiency without compromising grain quality. This study was designed to determine if optimizing integrative cultivation management in rice could improve grain quality while increase yield and nitrogen use efficiency (NUE). An indica-japonica hybrid rice cultivar and a japonica rice cultivar were grown in the field, with five cultivation managements including no N application (0 N), local farmer's practice (LFP), and three optimizing integrative cultivation managements, reducing N rate and increasing plant density (ND), ND+alternate wetting and moderate soil drying irrigation (NDW), and NDW+applying rapeseed cake fertilizer (NDWR). The results showed that the optimizing integrative cultivation managements could not only increase grain yield, but also enhance NUE compared to LFP. Compared to LFP, NDWR significantly increased brown, milled, head milled rice rate, ratio of the kernel length to breadth and breakdown value of starch, whereas decreased amylose content, gel consistency, prolamin content, setback value, percentage of chalky kernels, and chalkiness. The three optimizing integrative cultivation managements increased contents of total proteins, albumin and glutelin, activities of the key enzymes involved in the sucrose-starch conversion in grains, root oxidation activity, and malic and succinic acid concentrations in root exudates during the grain-filling period. The results suggested that optimizing integrative cultivation managements could improve grain quality meanwhile increase grain yield and NUE by enhancing physiological activities of rice plants.