Japanese Rice Varieties Research Articles

Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding.

Direct seeding is employed to circumvent the labor-intensive process of rice (Oryza sativa) transplantation, but this approach requires varieties with vigorous low-temperature germination (LTG) when sown in cold climates. To investigate the genetic basis of LTG, we identified the quantitative trait locus (QTL) qLTG11 from rice variety Arroz da Terra, which shows rapid seed germination at lower temperatures, using QTL-seq. We delineated the candidate region to a 52-kb interval containing GENERAL REGULATORY FACTOR14h (GF14h) gene, which is expressed during seed germination. The Arroz da Terra GF14h allele encodes functional GF14h, whereas Japanese rice variety Hitomebore harbors a 4-bp deletion in the coding region. Knocking out functional GF14h in a near-isogenic line (NIL) carrying the Arroz da Terra allele decreased LTG, whereas overexpressing functional GF14h in Hitomebore increased LTG, indicating that GF14h is the causal gene behind qLTG11. Analysis of numerous Japanese rice accessions revealed that the functional GF14h allele was lost from popular varieties during modern breeding. We generated a NIL in the Hitomebore background carrying a 172-kb genomic fragment from Arroz da Terra including GF14h. The NIL showed superior LTG compared to Hitomebore, with otherwise comparable agronomic traits. The functional GF14h allele from Arroz da Terra represents a valuable resource for direct seeding in cold regions.

Investigating the Mechanisms Underlying the Durability and Sustainable Use of Pb1 Gene-Mediated High Field Resistance to Rice Panicle Blast

Rice blast, caused by Magnaporthe oryzae, poses a significant threat to rice production. Rice blast susceptibility has been observed in Japanese rice varieties with excellent eating quality. Enhancing blast resistance is essential to ensure minimal use of agricultural chemicals. Two types of blast resistance are observed: True resistance, which is a type of qualitative resistance expressed by a major gene, and field resistance, which is a type of quantitative resistance expressed by multiple micro-acting genes. ‘Resistance collapse’, in which a variety with a true resistance gene becomes diseased by blast fungus races compatible with the resistance gene, has been observed. Varieties carrying blast-resistance genes, such as Pb1 (panicle blast resistance 1), have been developed through DNA marker-assisted selection. In this review, we focus on the Pb1, which expresses strong quantitative resistance to panicle blast and has been widely used in Japan without showing ‘resistance collapse’ for 40 years. Pb1 is an ‘adult plant resistance gene’ that does not exert strong selection pressure on the blast population during the leaf blast stage, thus preventing the selective multiplication of Pb1-compatible blast strains. This epidemiological mechanism prevents ‘resistance collapse’. Interdisciplinary research and breeding are required to sustainably use genes that induce high field resistance.

Rice blast resistance gene profiling of Thai, Japanese and international rice varieties using gene-specific markers

AbstractRice blast disease, caused by Magnaporthe oryzae, is one of the most damaging diseases of rice worldwide. Cultivation of rice varieties carrying resistance genes is the most economic and successful strategy to control the disease. In this study, 451 rice varieties from around the world including 363 Thai landrace rice varieties, 21 Thai improved rice varieties, 43 Japanese rice varieties and 24 worldwide rice varieties were screened by PCR technique using gene-specific markers for 10 rice blast resistance genes: Pi9, Piz-t, Pi50, Pigm(t), Pid2, Pid3, Pia, Pik, Pi54 and Pita. The results showed that 382 (99.48%) Thai rice varieties have at least one resistance gene and two rice varieties, ‘Hom’ and ‘Bak muay’, contained eight out of ten screened rice blast resistance genes. 320 rice varieties (83.33%) contained three or more rice blast resistance genes. The frequency of the rice blast resistance gene ranges from 87.76–9.64 per cent, of which the Pid3 gene has the highest frequency and the Pi54 gene has the lowest frequency. Two major resistance genes, found in Japanese rice varieties, are the Pik gene (76.74%) and the Pi9 gene (72.09%). While two major resistance genes, found in the international rice varieties are the Pi9 gene (66.67%) and the Pi54 gene (62.50%). The disease resistance gene profile of each rice variety obtained from this study will benefit the rice blast resistant breeding programme in the future.

Genotype and phenotype variability of BC1F1 progenies from backcross of C3 and Koshihikari

Improvement of local rice variety could be conducted by crossing it with superior varieties. C3 is improved line of Acehnese rice ‘Cantik Manis’ by crossing it with the introduced Chinese rice variety Yin Zhan to make their progenies have shorter lifespan and good productivity. Although C3 line has been improved, this variety still has lifespan for about ± 135 days. Koshihikari is Japanese rice variety with its lifespan about 80-90 days. It is though that Koshihikari has various semidwarf gene such as sd-1 or other semidwarf genes. The strategy that can be used to decrease harvesting period of C3 is by crossing this variety with Koshihikari to insert semi-dwarf gene such as sd-1. The research was conducted to analyse the existing of sd-1 gen and phenotypic performance of their progenies specially in BC1F1. The seed of BC1F1 were found by crossing 2 prospective F1 plants (T8 and T10) with C3 parent. Molecular analysis showed that the whole progenies BC1F1-T8 inherit sd-1 gene (100%). Phenotypic observation showed the whole progenies had similar architecture as their parents with average heights at 45 DAP ranged from 74-91 cm, and number of tiller range from 3-9 tillers. Whereas in BC1F1-T10 progenies, there were 11 plant from 12 plants inherit sd-1 gene (91.7%). These progenies had average heights at 45 DAP ranged from 75-88 cm, and number of tiller range from 6-13 tillers.

Differences in the Sterility of Japanese Rice Varieties under Short-day Conditions and Seasonal Changes

Differences in the Sterility of Japanese Rice Varieties under Short-day Conditions and Seasonal Changes

Sterility of Japanese Rice Variety “Shinrei” Grown under Short-day Conditions

Sterility of Japanese Rice Variety “Shinrei” Grown under Short-day Conditions

The Selection of Gamma-Ray Irradiated Higher Yield Rice Mutants by Directed Evolution Method.

We have succeeded in selecting four higher yield mutants from five gamma-ray irradiated high-yielding Japanese rice varieties using a novel approach. A total of 464 M2 plants which had heavier total panicle weights per plant were first selected from 9801 irradiated M2 plants. Their higher yields were confirmed by yield trials conducted for three years with a six to ten-pairwise replicated plot design. FukuhibikiH6 and FukuhibikiH8 were selected from an irradiated high-yielding variety Fukuhibiki and showed 1.2% to 22.5% higher yield than their original significantly. YamadawaraH3 was selected from an irradiated high-yielding variety Yamadawara and its yield advantages were 2.7% to 3.9%. However, there was no difference in the genotypes of the 96 SNP (single nucleotide polymorphism) markers between the higher yield mutants and their respective original varieties. The differences in the measured phenotypical traits between each mutant and its original variety were not constant and the actual differences were marginal. Therefore, the higher yields of the selected mutants were likely to have been caused by physiological traits rather than phenotypical traits. The selection method used in this study is an application of the directed evolution method which has long been commonly used in the substantial improvements of microorganisms and their proteins.

Partial Sterility of Japanese Rice Varieties Grown Using Rapid Generation Advancement Techniques on Ishigaki Island

Partial Sterility of Japanese Rice Varieties Grown Using Rapid Generation Advancement Techniques on Ishigaki Island

Description of grain weight distribution leading to genomic selection for grain-filling characteristics in rice.

Grain-filling ability is one of the factors that controls grain yield in rice (Oryza sativa L.). We developed a method for describing grain weight distribution, which is the probability density function of single grain weight in a panicle, using 128 Japanese rice varieties. With this method, we quantitively analyzed genotypic differences in grain-filling ability and used the grain weight distribution parameters for genomic prediction subject to genetic improvement in grain yield in rice. The novel description method could represent the observed grain weight distribution with five genotype-specific parameters of a mixture of two gamma distributions. The estimated genotype-specific parameters representing the proportion of filled grains had applicability to explain the grain filling ability of genotypes comparable to that of sink-filling rate and the conventionally measured proportion of filled grains, which suggested the efficiency and flexibility of grain weight distribution parameters to handle several genotypes. We revealed that perfectly filled grains have to be prioritized over partially filled grains for the optimum allocation of the source of yield in a panicle, from the analysis for obtaining an ideal shape of grain weight distribution. We conducted genomic prediction of grain weight distribution considering five genotype-specific parameters of the distribution as phenotypes relating to grain filling ability. The proportion of filled grains, average weight of filled grains, and variance of filled grain weight, which were considered to control grain yield to a certain degree, were predicted with accuracies of 0.30, 0.28, and 0.53, respectively. The proposed description method of grain weight distribution facilitated not only the investigation of the optimum allocation of nutrients in a panicle for realizing high grain-filling ability, but also allowed genomic selection of grain weight distribution.

Production efficiency and effect of water management on rice yield in Japan: two-stage DEA model on 110 paddy fields of a large-scale farm

Water management is increasingly important for rice productivity to maintain soil temperature and fertility with the presence of global warming. Meanwhile, rice production in Japan is in urgent need to reduce the costs through improving the efficiency and market competitiveness. This paper aims to measure effect of water depth and water temperature on rice yield of individual paddy fields and improve the practice of water management for them. In the first stage, we measure the production efficiency of rice yield through the adoption of data envelopment analysis. The results indicate that enlarged scale of the paddy fields increases the efficiency, and rice quality can be improved more than quantity. Moreover, the most inefficiently used inputs include the amount of fertilizer nitrogen and the soil capacity, which is a compound measurement of 21 soil chemical properties. In the second stage, after comparing the 20 paddy fields with highest and lowest technical efficiency, an observation shows that the rice yield is much more affected by water temperature than by water depth. The data of all the variables used in this study were sampled in 2015 and comprised of 110 paddy fields of Koshihikari, one of the most popular Japanese rice varieties, from a large-scale farm located in Kanto Region of Japan. In the analysis, the outputs include yields of raw paddy, paddy with 15% moisture, unsorted brown rice, sorted brown rice, milled grain rice, and perfect grain rice. The inputs include the field area, air temperature, solar radiation, fertilizer nitrogen, soil capacity, and farming conditions.

Methane Emission Trend based on the Water Management during Rice Growing and Non-growing Seasons

Paddy fields are thought to be a major greenhouse gases emitter. Several studies have investigated the reduction of greenhouse gases emission from paddy fields by applying AWD irrigation (alternative wetting and drying), a method of water management practiced during rice growing seasons. However, few studies have conducted lysimeter experiments in which the irrigation, fertilizers, and drainage system are controlled to reduce the emission. Therefore, this study was conducted in a small scale lysimeter (500×160) cm2 on the rooftop of the Environmental Studies Building in the Kashiwa campus of the University of Tokyo from May to December 2013 to investigate methane emission patterns by observing depth-wise physicochemical properties of the soil. Soil pH, ORP (Oxidation Reduction Potential), temperature, and water content were also recorded at different soil depths of 5 cm, 10 cm, 15 cm and 20 cm. Japanese rice variety Koshihikari was transplanted, and the plant was irrigated depending on rainfall events throughout the experiment. Gas sampling was performed based on the ponding condition of the lysimeter. The results showed that methane flux occurred when the ORP dropped to -150 mV at a level 5 to 15 cm deep from the upper soil surface. The methane flux was higher during the rapid development of rice plants in vegetative phase. Methane flux also showed a positive correlation with soil water content and temperature at different soil depths. The global warming potential during rice growing and non-growing seasons from total methane emission was 0.72 and -0.21 g CO2 m-2 respectively. The results suggest that avoiding water stress for plants by a proper water management during vegetative phase is effective for the mitigation of methane release.

Production of Japanese Rice through Contract Farming System in Wiang Pa Pao District, Chiang Rai Province, Thailand

Many companies in Thailand have encouraged farmers especially the northern regions to cultivate DOA 1 and DOA 2 Japanese rice varieties (scientific name: Oryza sativa var. Japonica) through contract farming system in which each company may have different model and management approaches. Therefore, this study explored the currently prevailing contract farming of Japanese rice in Thailand especially in Wiang Pa Pao district, Chiang Rai province, to identify the advantageous and disadvantageous points of Japanese rice production, and to examine the important role of each stakeholder in Japanese rice production. The data of this study were collected from two state agencies, two rice millers, six collectors and thirty contract farmers who were selected for in-depth interviews by using questionnaires and interview forms. The contract farming model and management details were different in each rice mill such as signing a contract, purchase price, commission fee, specifications of rice quality, and so on. Lack of financial liquidity and fluctuation of contract price may influence the confidence of Japanese rice growers in the future. Moreover, lack of quality seeds was another obstacle of Japanese rice production in Thailand. The contract farming of Japanese rice involved many parties as follows: rice mill, collector, contract farmer, and state agency namely Chiang Rai Rice Research Center (CRI) while each stakeholder had different significant roles for the example; CRI produced rice seed to distribute to rice mills, and has developed varieties of this rice. Moreover, it established the Japanese rice community center to produce more rice seeds, and has encouraged farmers to raise the standards of production for the competitive domestic and international markets.

Studies of Japanese Rice Variety with New Properties on Suitable Preparation to Keep Functional Ingredients, Optimal Fermenting Methods, and Optimal Processing Methods.

Studies of Japanese Rice Variety with New Properties on Suitable Preparation to Keep Functional Ingredients, Optimal Fermenting Methods, and Optimal Processing Methods.

Identification of two phytotoxins, blumenol A and grasshopper ketone, in the allelopathic Japanese rice variety Awaakamai

Aqueous methanol extracts of the traditional rice (Oryza sativa) variety Awaakamai, which is known to have the greatest allelopathic activity among Japanese traditional rice varieties, inhibited the growth of roots and shoots of cress (Lepidium sativum), lettuce (Lactuca sativa), timothy (Phleum pratense), Digitaria sanguinalis, Lolium multiflorum and Echinochloa crus-galli. Increasing the extract concentration increased the inhibition, suggesting that the extract of Awaakamai contains growth inhibitory substances. The extract of Awaakamai was purified and two main growth inhibitory substances were isolated and determined by spectral data as blumenol A and grasshopper ketone. Blumenol A and grasshopper ketone, respectively, inhibited the growth of cress shoots and roots at concentrations greater than 10 and 30μmol/L. The concentrations required for 50% growth inhibition on cress roots and shoots were 84 and 27μmol/L, respectively, for blumenol A, and 185 and 76μmol/L, respectively, for grasshopper ketone. These results suggest that blumenol A and grasshopper ketone may contribute to the growth inhibitory effect of Awaakamai and may play an important role in the allelopathy of Awaakamai.

Transferring Translucent Endosperm Mutant Gene Wx-mq and Rice Stripe Disease Resistance Gene Stv-b i by Marker-Assisted Selection in Rice ( Oryza sativa)

A high-yielding japonica rice variety, Wuyunjing 7, bred in Jiangsu Province, China as a female parent was crossed with a Japanese rice variety Kantou 194, which carries a rice stripe disease resistance gene Stv-b i and a translucent endosperm mutant gene Wx-mq. From F 2 generations, a sequence characterized amplified region (SCAR) marker tightly linked with Stv-b i and a cleaved amplified polymorphic sequence (CAPS) marker for Wx-mq were used for marker-assisted selection. Finally, a new japonica rice line, Ning 9108, with excellent agronomic traits was obtained by multi-generational selection on stripe disease resistance and endosperm appearance. The utilization of the markers from genes related to rice quality and disease resistance was helpful not only for establishing a marker-assisted selection system of high-quality and disease resistance for rice but also for providing important intermediate materials and rapid selection method for good quality, disease resistance and high yield in rice breeding.

Rice archaeological remains and the possibility of DNA archaeology: examples from Yayoi and Heian periods of Northern Japan

Japanese rice cultivation in paddy fields has 2,400∼3,000 years of history. Most of modern Japanese rice varieties are classified as Temperate-japonica (Tm-J). Few landraces are recognized as Tropical-japonica (Tr-J) only in southwestern Japan. However, ancient DNA studies and phytolith analysis suggest that Tr-J strains were more popular in the past than now. Maekawa is a complex archaeological site composed of paddies dated from the Yayoi (2,100 years BP) to the Heian (1,100 years BP) periods. Phytolith analysis indicates that intensive rice cultivation was practiced in both periods, but there was no cultivation in the intervening period. Morphological features of bulliform phytoliths suggest that Tr-J was cultivated during both periods. Locally, rice cultivation during the Heian period was brought to a close by a flood event, in which immature rice plants were pulled down and buried in silt to be preserved in a quasi-carbonized/ waterlogged state. Ancient DNA (aDNA) analysis of the carbonized plant culm from Heian Maekawa recovered chloroplast DNA sequences of the 6C7A plastid subtype, which is common to both Tr-J and Tm-J, whereas two plastid subtypes, such as 6C7A and also 7C6A, were found in aDNA of carbonized grains from the Tareyanagi site of the Yayoi period. The latter plastid subtype was specific only to Tr-J. In order to better characterize the past rice populations, modern landraces collected in the local area were classified with morphophysiological traits. Some of the landraces were found to carry several traits of Tr-J, including bulliform phytolith types, but mixed with Tm-J traits. Based on the discontinuous distribution of rice phytoliths between the Yayoi and the Heian period, the early introduction of rice cultivation may have been discontinuous and locally reintroduced after a ∼1,000-year hiatus, but with a genetically different rice population. Such populations were composed from Tr-J like strains as shown by landraces but with reduced diversity in plastid types. Through such changes, since the Yayoi era, Tr-J was largely replaced by Tm-J, although ancient Tr-J continued to participate in the genetic makeup of later rice populations and may have aided the local adaptation of introduced Tm-J.

2D-DIGE analysis of rice proteins from different cultivars

The 2D-DIGE (2-Dimensional Fluorescence Difference Gel Electrophoresis) method was applied to proteomic phenotyping of natural variants in 10 varieties of rice (Nipponbare, Koshihikari, Sasanishiki, Akitakomachi, Hitomebore, Hinohikari, Kasalath, Rexark, Bleiyo, Cho-ko) from the world rice collection (WRC) in the GenBank of the National Institute of Agrobiological Sciences (NIAS), Japan. Salt-soluble protein extracts of Nipponbare brown rice were labeled with Cy2 fluorochrome and used as an internal standard. Protein extracts from nine other rice varieties were labeled with Cy3 or Cy5 fluorochrome and applied to 2D-PAGE (13 cm gel length) analysis. Approximately 700 spots of rice proteins were observed. Fluorescence intensities of each of these spots for the nine rice varieties were expressed as relative ratios to that of Nipponbare. Statistical analysis revealed the spot numbers of five Japanese rice varieties above threshold five (relative ratio of each variety to Nipponbare exceeded 5-fold or was less than 1/5) to be less than three, while those of four varieties from other countries were more than five (especially, Kasalath which was 29 and Bleiyo which was 23). The 2D-DIGE method seems to be useful for analyzing natural varieties of different cultivars and also for comparing the expression of allergen proteins.

Conception of Rice among Japanese Expatriates in Kentucky

Recent scholarship has recognized the relationship between food and ethnic identity and rice has been associated with Japanese identity in Japan. In this paper, we looked at how rice is conceived among Japanese expatriates in Kentucky. Japanese expatriates experience three stages of finding out the best rice in Kentucky. The stages are: (1) try substitutes and feel dissatisfied, (2) find a better variety, and finally (3) feel satisfied with rice made in California. Although they appreciate the availability of Japanese rice variety in Kentucky, the symbolic meaning of rice has been somewhat disrupted among Japanese expatriates. In Japan, close spatial/social distance between consumers and producers on rice was a source of imagination for paddy field as Japanese landscape and for farmer's hard work. Yet, in Kentucky, they have difficulty to provoke such images.

Low ovicidal response to the whitebacked planthopper in the Japanese rice variety 'Asahinoyume' and its progenitorial varieties

愛知県では水稲品種「あさひの夢」においてセジロウンカの多発が確認されてきた．本研究はその要因を解明するために，愛知県の奨励品種である「あさひの夢」，「コシヒカリ」，「祭り晴」のセジロウンカに対する殺卵反応を調査した．その結果，「あさひの夢」は殺卵率が有意に低く，セジロウンカの多発は殺卵反応の弱さに起因していることが示唆された．次に，殺卵反応の弱さの由来を明らかにするために，「あさひの夢」の系譜上を中心とした25品種・系統の殺卵反応を調査するとともに，殺卵反応の発現に必須である殺卵遺伝子 Ovcに近接するRFLPマーカー分析を行った．その結果，インド型稲品種「Modan」と，その戻し交雑反復親「農林8号」から「愛知37号（青い空）」まで続く系譜上のグループと，「京都旭」から「あさひの夢」まで続く系譜上のグループの殺卵反応が弱いことが明らかとなった．特に後者は殺卵反応の弱い品種・系統が連続しており，そのほとんどが殺卵遺伝子 Ovcを有しない「IR24」と同じRFLPマーカー分析結果を示した．これらのことから「あさひの夢」の殺卵反応が弱いのは殺卵遺伝子 Ovcを有さないためであると考えられ，それが「京都旭」由来である可能性が示唆された．

Application of FAO-56 for evaluating evapotranspiration in simulation of pollutant runoff from paddy rice field in Japan

Applicability of FAO-56 method in estimation of evapotranspiration for the simulation of pollutant runoff from rice paddy field in Japan was investigated. Crop evapotranspiration and crop coefficient recommended by FAO-56 method relative to those values obtained in the field monitoring for three Japanese rice varieties, namely, Nihonbare, Mangetsumochi and Koganemochi during first three growing stages were compared. Also, the pesticide fate model, PCPF-1, which incorporates the FAO-56 method was evaluated for the applicability of the FAO-56 method towards the accurate prediction of herbicide concentration in paddy water. The estimation of cumulative ET c in paddy rice by FAO-56 method using the recommended K c value resulted in estimation error of up to 17% from the observed values. The recommended values of K c-ini in FAO-56 method are appropriate if reliable atmospheric data are available. However, the K c-mid was found to be a sensitive parameter affecting ET c estimation and the careful calibration according to the regional conditions and varieties seemed to be required for the accurate prediction. Considering the effect of random errors, FAO-56 method is more reliable when calculating cumulative ET c longer than 7 days of period. Despite the relatively large error in cumulative ET c resulted from the FAO-56 method with the recommended K c value, the maximum error expected to have on the prediction of the herbicide concentration in paddy field is 5.6%, and that of herbicide runoff loss can be 3.2%. Therefore, it can be concluded that application of FAO-56 method with the recommended K c value is acceptable in the simulation of pesticide fate and transport.