Japonica Type Rice Research Articles

Late Bronze Age agriculture and the early westward transmission of rice at Luanzagangzi, Northern Xinjiang, China

The Dzungar Basin of northern Xinjiang has previously been considered a marginal environment with little evidence for the development of prehistoric agriculture. Recent archaeobotanical studies have indicated the region as being a route for the transmission of domesticated plants, technologies and ideas between East and West Eurasia during prehistory, as early as 5000 BP. These interactions are still poorly understood and most evidence for early plant food production and consumption in the region comes from limited mortuary contexts. In this study we present plant macrofossil analysis from the settlement site of Luanzagangzi on the southern side of the Dzungar Basin. From ca. 3130 BP an agricultural package of east and west Asian cereals and chaff is present, comprising wheat, barley, foxtail millet, broomcorn millet, and significantly a single grain of japonica type rice. AMS dating indicates this is the oldest directly dated rice in Xinjiang and the broader region, ranging 3069–2881 cal. BP. Cereal morphometrics and material culture from the site further indicate a connection with the Gansu region to the east. The spread of agriculture into the site environment may be linked to the onset of wetter conditions relating to strengthened westerly systems across arid Central Asia in the Late-Holocene. A declining abundance of West Asian cultivars over the period of the site’s occupation possibly reflect a shift away from intensive agriculture to low-level management of millets.

Assessing the factors impacting the bioaccessibility of mercury (Hg) in rice consumption by an in-vitro method

Mercury (Hg) in rice is drawing mounting concern since methylmercury (MeHg) was found capable of accumulating in rice. In-vitro bioaccessibility is a feasible and reliable method to assess the health effects of Hg in rice and has been utilized in a number of studies. This study was done to investigate the impact of cultivar, planting location, and cooking on the total mercury (THg) and MeHg bioaccessibility of rice, for which multiple statistical analysis methods were used to analyze the significance of their effects. The THg concentrations of rice samples taken from non-Hg contaminated areas of China were all below 15 ng/g and their MeHg concentrations were below 2 ng/g. Cooking could significantly reduce the MeHg bioaccessibility of rice because the MeHg was mainly combined with protein and the protein will be denatured during the cooking process, and then the denatured MeHg is difficult to be dissolved into the liquid phase. Indica- and japonica-type rice cultivars did not show significant differentiation in either the concentration of Hg or its bioaccessibility. However, the glutinous rice type differed significantly from the above rice types, and it showed greater bioaccessibility of THg and MeHg due to its distinct protein contents and starch properties. Planting location can affect the Hg concentration in rice and THg bioaccessibility but has a limited impact on MeHg bioaccessibility. Based on these results, two macro factors (rice cultivar, planting location) are presumed to impact Hg bioaccessibility by how they affect micro factors (i.e., Hg forms).

Effect of Types of Cooking Water on the Palatability and Physicochemical Properties of Chinese Japonica–Type Rice Cultivars

Effect of Types of Cooking Water on the Palatability and Physicochemical Properties of Chinese Japonica–Type Rice Cultivars

Reliability of Sensory Test for Japonica Type Rice Cultivars in China

It is of great theoretical and practical significance to construct a scientific taste sensory evaluation method to obtain accurate and reliable data, so as to provide theoretical basis and technical support for the breeding and cultivation technology development of taste japonica rice varieties. In this study, sensory evaluation experiments were carried out based on statistical analysis. Through the analysis of variance of the evaluation results, the identification ability and hobbies of the evaluators were analyzed, and the correlation between them was discussed. The results show that there are significant differences between appraisers and varieties between the two repetitions of the comprehensive evaluation items investigated in this experiment, which verifies the repeatability of sensory evaluation and reveals the feasibility of taste sensory evaluation method. Among the 20 taste tasters participating in the taste evaluation experiment, 16 (80% of all) have low recognition ability for the taste comprehensive evaluation items, of which 6 (30% of all) have different hobbies from the overall tendency of all tasters, so they are considered not suitable to carry out taste evaluation as taste tasters. However, the results also show that the number of evaluators participating in this experiment who have both high recognition ability and high consistency with all hobbies is less. Therefore, in order to obtain more reliable results, it is very necessary to strengthen the training of appraisers and cultivate appraisers with high discrimination ability.

Effects of BEIIb-Deficiency on the Cluster Structure of Amylopectin and the Internal Structure of Starch Granules in Endosperm and Culm of Japonica-Type Rice.

It is known that one of starch branching enzyme (BE) isoforms, BEIIb, plays a specific role not only in the synthesis of distinct amylopectin cluster structure, but also in the formation of the internal structure of starch granules in rice endosperm because in its absence the starch crystalline polymorph changes to the B-type from the typical A-type found in the wild-type (WT) cereal endosperm starch granules. In the present study, to examine the contribution of BEIIb to the amylopectin cluster structure, the chain-length distributions of amylopectin and its phosphorylase-limit dextrins (Φ-LD) from endosperm and culm of a null be2b mutant called amylose-extender (ae) mutant line, EM10, were compared with those of its WT cultivar, Kinmaze, of japonica rice. The results strongly suggest that BEIIb specifically formed new short chains whose branch points were localized in the basal part of the crystalline lamellae and presumably in the intermediate between the crystalline and amorphous lamellae of amylopectin clusters in the WT endosperm, whereas in its absence branch points which were mainly formed by BEI were only located in the amorphous lamellae of amylopectin. These differences in the cluster structure of amylopectin between Kinmaze and EM10 endosperm were considered to be responsible for the differences in the A-type and B-type crystalline structures of starch granules between Kinmaze and EM10, respectively. The changes in internal structure of starch granules caused by BEIIb were analyzed by wide angle X-ray diffraction, small-angle X-ray scattering, solid state 13C NMR, and optical sum frequency generation spectroscopy. It was noted that the size the amylopectin cluster in ae endosperm (approximately 8.24 nm) was significantly smaller than that in WT endosperm (approximately 8.81 nm). Based on the present results, we proposed a model for the cluster structure of amylopectin in WT and ae mutant of rice endosperm. We also hypothesized the role of BEIIa in amylopectin biosynthesis in culm where BEIIb was not expressed and instead BEIIa was the major BE component in WT of rice.

Thermotolerance evaluation of Taiwan Japonica type rice cultivars at the seedling stage

BackgroundThe subtropical rice varieties grown in Taiwan are mainly Japonica-type rice varieties, which are grown in the southernmost- and lowest-latitude Japonica type rice cultivation area in the world. In Taiwan, seedlings that are planted either by transplanting or direct seeding in the second crop will face the season with the highest temperatures during the year. High-temperature stress severely influences early rice growth and causes yield losses. With global warming deteriorating, this problem is becoming increasingly severe. This study attempted to establish a high-efficiency and time-saving screening tool for rice varieties that exhibit thermotolerance during the early growth stages and further identify good donors with better tolerance for high temperature stress from Taiwan Japonica type rice germplasm.ResultsDuring the initial germination stage, there were significantly different responses to heat stress among the different rice varieties. After the temperature induction response technique (TIR) treatment, the seedling survival rate and relative growth rate of the rice varieties under high temperature stress were significantly improved. In addition, the seedlings of the thermotolerant varieties demonstrated greater thermotolerance performance in the pot experiment as well as cell membrane stability (CMS) and cell activity (2,3,5-triphenyl-tetrazolium chloride; TTC) test results. However, the correlation between the thermotolerance of the seedlings and seeds was low. A phylogenetic dendrogram was plotted and revealed that thermotolerant genes did not concentrate in specific clusters. Furthermore, there was a non-significant correlation between the thermotolerance of the varieties and the years in which they were released.ConclusionsThe temperature induction screening tool established by this study could determine the potential of each variety to adapt to high temperature stress. Additionally, thermotolerance during different growth stages (i.e., the germination, seedling, and grain maturation stages) exhibited low correlations. In this study, the varieties obtained through preliminary screening (i.e., TK14, HC56, TT30, TNG70, and TK8) exhibited outstanding thermotolerance. The screen tools and thermotolerance varieties could be valuable resources for the countries that grow Japonica type rice to apply when breeding thermotolerant varieties in the future.

Identification of quantitative trait loci for panicle structure and grain filling using a cross between indica- and japonica-type high-yielding rice cultivars

ABSTRACTTo enhance the yield potential of rice by breeding, it is important to reveal the genetic factors affecting yield components in high-yielding cultivars. Quantitative trait loci (QTL) analysis for panicle structure and spikelet weight as an index of grain filling was conducted using recombinant inbred lines (RILs) derived from a cross between an indica-dominant high-yielding cultivar, Takanari, and a japonica-dominant high-yielding cultivar, Momiroman in 2012 and 2013 in eastern Japan. The grain-filling ability of Takanari is reported to be better than that of Momiroman. Since grain filling is generally better near the tip of the panicle and decreases as the number of branches from the rachis increases, we classified whole panicles into upper and lower side panicles and spikelets into primary, secondary, and tertiary spikelets according to the number of branches from the rachis. On chromosomes 1, 4, and 6, QTLs regulating the number of spikelets per panicle and panicle structure were detected and were most likely identical to GN1a, SPIKE, and APO1, respectively, which has been previously reported as QTLs regulating the number of spikelets per panicle. Takanari produced much heavier secondary and tertiary spikelets than Momiroman on the lower side panicle. On chromosome 5, novel QTLs regulating spikelet weight were detected. The Takanari allele enhanced secondary and tertiary spikelet weight on the lower side panicle. These results indicate that it may be possible to enhance sink capacity and translocation of source with a combination of novel QTLs detected on chromosome 5 and GN1, APO1, and SPIKE.

다수성 통일형을 포함한 벼 품종이 쌀미음 품질특성에 미치는 영향

This study was carried out to compare the physiochemical properties and quality characteristics of porridge made from different Korean rice varieties, including high yield tongil-type rice. The rice varieties used in this study were 4 tongil-type (Areum, Namcheon, Hanareum3, Hanareum4) and 5 japonica-type rices (Unkwang, Daebo, Goami4, Dodamssal and Hwaseonchal). The protein and amylose contents of the varieties ranged from 6.0% (Namcheon) to 7.3% (Hanareum3) and from 5.0% (Hwaseonchal) to 42.8% (Dodamssal). Compared to the other varieties, Hwaseonchal and Dodamssal had low final and setback viscosity values in the rapid-visco analyzer test. The color value of the porridge ranged between 52.90 and 71.12 for the L value, -2.06 and -1.01 for the a value, and -5.59 and -2.62 for the b value. SEM images revealed distinct differences in the endosperm structure of rice varieties as well as the porridge. Furthermore, porridge made from Hwaseonchal rice had the highest spreadability, followed by porridge made from others non-glutinous rice varieties, Goami4 rice, and Dodamssal rice. The results of this study suggested that rice varieties with different amylose contents could be effectively used to control the viscosity of rice porridge. In laboratory experiments, the sensory test did not indicate significant differences except for the mouthfeel. The mouthfeel of the porridge depended on the amylose content of rice. This study suggested that tongil-type rice variety such as Hanareum4 could be substituted with Japonica type rice for making porridge.

Knocking Out the Gene RLS1 Induces Hypersensitivity to Oxidative Stress and Premature Leaf Senescence in Rice

Improving a plant’s level of tolerance to oxidative stress can frequently also enhance its tolerance to several other abiotic stresses. Here, a screen of a japonica type rice T-DNA insertion mutant library identified a highly oxidative stress-sensitive mutant. The line exhibited premature leaf senescence, starting at the three-leaf stage, and the symptoms were particularly severe from the five-leaf stage onwards. The leaves progressively lost chlorophyll, suffered protein degradation and were compromised with respect to their photosynthetic activity; their leaf mesophyll and bulliform cells became shrunken, and several senescence-associated genes (SAGs), senescence-associated transcription factor genes (SATFs) and autophagy-related genes (ATGs) were progressively up-regulated. The product of the gene inactivated by the mutation, identified via positional cloning, was putatively a ubiquitin-conjugating enzyme. The gene was denoted here as RLS1 (reactive oxygen species-sensitive leaf senescence1). The phenotype of plants in which RLS1 was knocked down using RNA interference was comparable to that of the rls1 mutant. A comparative analysis of the knock-out line and the wild type leaves showed that the former accumulated more hydrogen peroxide and more malondialdehyde, expressed a heightened level of superoxide dismutase activity and a decreased level of catalase activity, and exhibited an altered transcriptional profile with respect to several SAGs, SATFs and ATGs, and that these effects were magnified when the plants were exposed to oxidative stress. The product of RLS1 is presumed to be a critical component of the rice oxidative stress response and is involved in ROS (reactive oxygen species)-mediated leaf senescence.

Progress Toward Rice Seed OMICS in Low-Level Gamma Radiation Environment in Iitate Village, Fukushima.

Here, we present an update on the next level of experiments studying the impact of the gamma radiation environment, created post-March, 2011 nuclear accident at Fukushima Daiichi nuclear power plant, on rice plant and its next generation-the seed. Japonica-type rice (Oryza sativa L. cv. Koshihikari) plant was exposed to low-level gamma radiation (~4 μSv/h) in the contaminated Iitate Farm field in Iitate village (Fukushima). Seeds were harvested from these plants at maturity, and serve as the treated group. For control group, seeds (cv. Koshihikari) were harvested from rice grown in clean soil in Soma city, adjacent to Iitate village, in Fukushima. Focusing on the multi-omics approach, we have investigated the dry mature rice seed transcriptome, proteome, and metabolome following cultivation of rice in the radionuclide contaminated soil and compared it with the control group seed (non-radioactive field-soil environment). This update article presents an overview of both the multi-omics approach/technologies and the first findings on how rice seed has changed or adapted its biology to the low-level radioactive environment.

Quantitative trait loci responsible for the difference in γ-oryzanol content in brown rice between japonica-type and indica-type rice cultivars

γ-Oryzanol is a main oleophilic component in rice bran oil and has been well recognized as a good dietary supplement for human health, as well as having uses in industrial materials. japonica-type rice cultivars generally showed significantly higher contents of total γ-oryzanol in brown rice compared with indica-type cultivars, although within-group variation was significant. The objective of this study was to explore quantitative trait loci (QTLs) responsible for the difference in the γ-oryzanol content between japonica-type and indica-type rice cultivars, using recombinant inbred lines (RILs), backcross inbred lines (BILs), and corresponding chromosome segment substitution lines (CSSLs) derived from crosses between japonica-type and indica-type. Results from RILs and BILs showed that eight QTLs were detected with R2 from .09 to .16. Nine candidate regions for QTL were also suggested from corresponding CSSLs. These QTLs from RILs and BILs and the candidate regions from CSSLs were not overlapped, although one QTLs was mapped near the boundaries of the respective candidate region. At four QTLs and three candidate regions, alleles or segments from japonica-type caused higher contents than those from indica-type. On the other hand, at the other four QTLs and six candidate regions, alleles or segments from indica-type caused higher contents than those from japonica-type, which is a reverse result to the parental differences. This result strongly suggested that alleles with increasing effects on γ-oryzanol content could be accumulated not only from japonica-type but also from indica-type, leading to a potential for increase in γ-oryzanol content in future breeding programs.

Effect of Amount of Nitrogen Application on Physicochemical Properties, Taste value and Yield of Chinese japonica–type Rice Varieties

Effect of Amount of Nitrogen Application on Physicochemical Properties, Taste value and Yield of Chinese japonica–type Rice Varieties

Comparison of Physicochemical Properties of Chinese and Japanese Japonica–Type Rice Varieties

Comparison of Physicochemical Properties of Chinese and Japanese Japonica–Type Rice Varieties

Physicochemical Properties Related to Palatability of Chinese japonica–type Rice

Physicochemical Properties Related to Palatability of Chinese japonica–type Rice

Correlation between Evaluation of Palatability by Sensory Test and Physicochemical Properties in Chinese japonica–type Rice

Correlation between Evaluation of Palatability by Sensory Test and Physicochemical Properties in Chinese japonica–type Rice

Effects of field high temperature on grain yield and quality of a subtropical type japonica rice—Pon-Lai rice

Typical japonica type rice is sensitive to high temperature. Pon-Lai rice is a special japonica type with adaptation to the subtropical climate in Taiwan. Facing climate change, rising temperatures would damage the yield and quality of rice production. This research was conducted using Pon-Lai rice in the field of a subtropical climate. We conducted 2 experiments, including a year-round experiment and collection of samples from different districts for building different temperature conditions. We analyzed the correlation between rising temperature and rice yield or quality. In our results, the critical period of temperature effect is 0–15 days after heading (H15). The threshold of high temperature damage in yield and appearance quality was 25–27 °C. Grain weight decreased about 2–6%, while the temperature of H15 was raised 1 °C above the thresholds. Perfect grain ratio and chalky grain ratio decreased and increased, respectively, while the temperature of H15 was raised above the thresholds. However, the high temperature in H15 affected the physicochemical characteristics. In addition, we found positive correlation between grain length to width ratio and perfect grain ratio. Grain length to width ratio could be an index of temperature effects for grain quality. In our study, when the temperature was below 30 °C, a rising temperature of H15 could damage rice yield and appearance quality, and change grain shape. Our results could provide reference for dealing with the warming future in other temperate rice-cultivated countries.

Genetic Mapping of a Rice Loose Upper Panicle Mutant

We identified a loose upper panicle mutant (lup) from a japonica-type rice variety, Hwacheongbyeo, treated by Ethyl Methane Sulfonate (EMS). The lup mutant displayed an increased distance between spikelets particularly in the first primary branches, and the number of spikelet was reduced. In addition, aborted spikelets in the tip of first primary branches were observed. Besides these morphological changes in the panicle, the lup mutant also displayed overall reduction in culm length, panicle length, grain weight, and tiller number. On the contrary, the chlorophyll content was relatively high in lup mutant in comparison to wild-type plants, and displayed a stay-green phenotype even after physiological maturity. Genetic analysis (using F2 population of lup/M.23) revealed that a single recessive gene is involved in the above-mentioned morphological changes in the lup mutant. A candidate genomic region was fine-mapped at an interval of 1.04 Mb flanked by two molecular markers, 18170 and D0052, on the long arm of chromosome 8. In this region, we found a total of 348 mutation points using a slightly modified MutMap method. Based on these results, we expect the candidate genomic region containing a putative LUP gene will provide an important clue in developmental regulation of spikelets and panicle in rice.

Agro‐climate changes over Northeast Asia in RCP scenarios simulated by WRF

Dynamically downscaled agro-climates for present (1981–2010) and future (2071–2100) climates under Representative Concentration Pathways (Historical, RCP4.5, and RCP8.5) in Northeast Asia (118°–138°E, 30°–45°N) are analysed in terms of the indices, such as vegetable and crop periods, frost days, and the climatic yield potential (CYP) for Japonica type rice (hereafter, rice). The model employed for dynamical downscaling is the Weather Research and Forecasting (WRF), with a 12.5-km horizontal grid spacing in the domain. According to our results, the CYP for rice, one of the major crops presently cultivated in the area, is expected to decrease throughout most of the region, despite a projected expansion of both vegetable and crop periods. This is projected to occur particularly in South Korea, Japan, and Southeast and Northeast China. Such a change is related to the projected rise in temperature within these regions, which will exceed the grain-filling optimum temperature of rice. In contrast, the climate projection of the RCPs is that the CYP will increase over northeastern parts of the Korean Peninsula and the Russian Far Eastern region (Primorsky), because temperatures in these regions are expected to rise and approach the grain-filling optimum temperature. For the RCPs, the optimum heading date, on which the domain averaged CYP is the highest, is expected to be later than that of the Historical by approximately 17–24 days. In addition, the maximum CYP in the RCPs is projected to decrease compared with that of the historical, and the possible period of rice ripening (period in which the CYP is greater than 0) is also expected to decrease.

OsCML4 improves drought tolerance through scavenging of reactive oxygen species in rice

Calmodulin-like (CML) genes function in regulating plant responses to different abiotic stresses, such as high salt and drought. Using japonica type rice seedlings (‘Nipponbare’), we induced the expression of OsCML4 (Accession No. NM_001057768), which encodes a rice CML protein. Under drought conditions, transgenic plants over-expressing that gene exhibited obviously improved growth performance and higher survival rates than the wild type (WT). Activity by reactive oxygen species (ROS)- scavenging enzymes superoxide dismutase (SOD) and catalase (CAT), as well as proline concentrations, were significantly increased in transgenic plants. Expression by ROS scavenging-related genes APXI and Cat-B and the stress-related gene OsP5CS1 was also enhanced in the transgenics under drought conditions. However, the sensitivity to abscisic acid (ABA) was similar between over-expressing and WT plants. These results suggest that OsCML4 confers drought tolerance partially through ROS-scavenging and also by inducing other stress-related genes in an ABAindependent manner.

Genotyping and development of single-nucleotide polymorphism (SNP) markers associated with blast resistance genes in rice using GoldenGate assay

Development and large-scale genotyping of single-nucleotide polymorphism (SNP) is required to use identified sequence variation in the alleles of different genes to determine their functional relevance to the candidate gene(s). In the present study, Illumina GoldenGate assay was used to validate and genotype SNPs in a set of six major rice blast resistance genes, viz. Pi-ta, Piz(t), Pi54, Pi9, Pi5(1) and Pib, distributed over five chromosomes, to understand their functional relevance and study the population structure in rice. All the selected SNPs loci (96) of six blast (Magnaporthe oryzae) resistance genes were genotyped successfully in 92 rice lines with an overall genotype call rate of 92.0 % and minimum GenTrain cutoff score of ≥0.448. The highest genotyped SNPs were found in japonica type (97.1 %) rice lines, followed by indica (92.12 %), indica basmati (91.84 %) and minimum in case of wild species (82.0 %). Among the genotyped loci, the highest score (98.68 %) was observed in case of Piz(t), followed by Pi-ta, Pi5(1), Pib, Pi54 and Pi9. Polymorphism was obtained in 87.5 % SNPs loci producing 7,728 genotype calls. Minor allele frequency ranged from 0.01 to 0.49 and has good differentiating power for distinguishing different rice accessions. Population structure analysis revealed that a set of genotypes from four rice subpopulations had “admix” ancestry (>26 %) with more than one genetic background of indica, japonica and wild types. SNPs markers were validated in a set of 92 rice lines and converted into CAPS markers which can be used in blast resistance breeding programme.