Journal articles on the topic 'Japonica ric'
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1
Székely, Árpád, Tímea Szalóki, János Pauk, Csaba Lantos, Marks Ibadzade, and Mihály Jancsó. "Salinity Tolerance Characteristics of Marginally Located Rice Varieties in the Northernmost Rice-Growing Area in Europe." Agronomy 12, no. 3 (March 8, 2022): 652. http://dx.doi.org/10.3390/agronomy12030652.
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Detailed experiments were performed to investigate the effects of the marginal cultivation of temperate japonica rice on salinity tolerance in different developmental stages and to detect new genetic resources for further research and breeding projects. Eight rice varieties were screened for salinity tolerance in a greenhouse at two developmental stages. During seedling-stage screening, stress was induced with a 12 dS m−1 NaCl solution. For reproductive-stage analysis, we applied continuous salinity stress (8.39 dS m−1 of soil extract at 25 °C (EC25)). We compared the marginal rice genotypes (japonica_1) to widely grown controls (those being Mediterranean japonica genotypes, referred as the japonica_2 group, which also included one indica genotype). Without stress, marginally cultivated genotypes had significantly higher potassium storage capacity (406 µmol g−1) in flag leaves than did japonica_2 (347) or indica (267). Moreover, the seeds contained twice as much sodium (5.27) as did the others (2.19 and 2.00). Based on root-to-grain allocation, we identified two sodium excluders (‘Dular’ and ‘Dáma’) and six includers under constant salinity stress. Among the includers, we found that ‘M488’ had extremely high sodium concentration in both the flag leaves (250.54 µmol g−1) and the grains (13.57 µmol g−1). Rice varieties bred for the edge of their habitat show special physiological patterns. The differences are mainly manifested as lower levels of antioxidant pigments, higher amounts of potassium in flag leaves, and higher sodium levels in grains under normal conditions. With the onset of stress, higher tillering ability, enhanced antioxidant pigment synthesis, and rapid potassium translocation from the root are the key mechanisms which help the plants to avoid serious damage caused by salinity.
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Courtois, Brigitte, Raffaella Greco, Gianluca Bruschi, Julien Frouin, Nourollah Ahmadi, Gaëtan Droc, Chantal Hamelin, et al. "Molecular characterization of the European rice collection in view of association mapping." Plant Genetic Resources 9, no. 2 (June 15, 2011): 233–35. http://dx.doi.org/10.1017/s147926211100027x.
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In South Europe, rice is grown as an irrigated crop in river deltas where it plays an important role in soil desalinization. Specific varieties are needed for these tough conditions. We analyzed the genetic structure of a set of 305 varieties coming from the European Rice Germplasm Collection (ERGC) with 90 single nucleotide polymorphisms and compared it with a reference set representative of the diversity of Oryza sativa (mini-Germplasm Bank (GB)). These accessions had been characterized for their grain type and growth cycle duration. The polymorphism information contents of the ERGC were lower than those of the mini-GB, indicating a narrower genetic basis. Indeed, almost all ERGC accessions belong to the japonica group. Within the japonica group, both a dendrogram and a Bayesian clustering identified two major clusters. The first cluster encompassed tropical japonicas and American varieties from USA and Argentina characterized by long and narrow grains and medium to long duration. On a finer level, tropical japonicas appear separated from the other accessions. The second cluster is composed of European varieties mostly early or medium in duration and Asian temperate accessions, with a subgrouping based on grain format. A set of 200 accessions was composed for association mapping studies on traits such as salt tolerance.
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Hairmansis, A., Hajrial Aswidinnoor, Trikoesoemaningtyas Trikoesoemaningtyas, and Suwarno Suwarno. "IDENTIFICATION OF WIDE COMPATIBILITY VARIETIES IN SOME TROPICAL JAPONICA RICE." Indonesian Journal of Agricultural Science 6, no. 1 (July 23, 2013): 28. http://dx.doi.org/10.21082/ijas.v6n1.2005.28-31.
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The F1 hybrid sterility in indica/japonica crosses is the major barrier in developing hybrid rice varieties between these two diverse germplasm. The sterility problem in japonica/indica hybrids can be overcome by using wide compatibility genes. The objective of this study was to identify wide compatibility varieties (WCVs) in some tropical japonica rice. Twenty five tropical japonica varieties as male parents were crossed with indica (IR64) and japonica (Akitakomachi) testers as female parents. The crosses were planted following a randomized complete block design with three replications. Varieties having average spikelet fertility of more than 70% with both the indica and japonica testers were rated as WCVs. Result from this study showed that six tropical japonica varieties were classified as WCVs, i.e., Cabacu, Grogol, Kencana Bali, Klemas, Lampung Lawer, and Napa. Hybrid sterility is caused by partial sterility of male and female gametes. The WCVs from the present study can be used in hybrid rice breeding program to solve hybrid sterility in indica/japonica hybrids.
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Hairmansis, A., Hajrial Aswidinnoor, Trikoesoemaningtyas Trikoesoemaningtyas, and Suwarno Suwarno. "IDENTIFICATION OF WIDE COMPATIBILITY VARIETIES IN SOME TROPICAL JAPONICA RICE." Indonesian Journal of Agricultural Science 6, no. 1 (July 23, 2013): 28. http://dx.doi.org/10.21082/ijas.v6n1.2005.p28-31.
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The F1 hybrid sterility in indica/japonica crosses is the major barrier in developing hybrid rice varieties between these two diverse germplasm. The sterility problem in japonica/indica hybrids can be overcome by using wide compatibility genes. The objective of this study was to identify wide compatibility varieties (WCVs) in some tropical japonica rice. Twenty five tropical japonica varieties as male parents were crossed with indica (IR64) and japonica (Akitakomachi) testers as female parents. The crosses were planted following a randomized complete block design with three replications. Varieties having average spikelet fertility of more than 70% with both the indica and japonica testers were rated as WCVs. Result from this study showed that six tropical japonica varieties were classified as WCVs, i.e., Cabacu, Grogol, Kencana Bali, Klemas, Lampung Lawer, and Napa. Hybrid sterility is caused by partial sterility of male and female gametes. The WCVs from the present study can be used in hybrid rice breeding program to solve hybrid sterility in indica/japonica hybrids.
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Pacleb, Myrish, O.-Young Jeong, Jeom-Sig Lee, Thelma Padolina, Rustum Braceros, Lenie Pautin, Gideon Torollo, et al. "Breeding Temperate Japonica Rice Varieties Adaptable to Tropical Regions: Progress and Prospects." Agronomy 11, no. 11 (November 8, 2021): 2253. http://dx.doi.org/10.3390/agronomy11112253.
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Temperate japonica rice is mainly cultivated in temperate regions. Many temperate japonica varieties have a superior grain quality that is preferred in Northeast Asian countries such as Japan, Korea, and China. The changes in consumers’ preferences in Southeast Asia and Western countries has contributed to increasing the demand for temperate japonica. Most temperate japonica varieties developed in temperate regions typically exhibit extra-early flowering under the short-day conditions in the tropics, which usually results in severely reduced yields. Since 1992, we have been developing temperate japonica varieties that can adapt to tropical environments to meet the increasing demand for temperate japonica rice, having released six varieties in the Philippines. Especially, the yield of one of the temperate japonica varieties, Japonica 7, was comparable to the yields of leading indica varieties in the Philippines. Here, we discuss the current breeding initiatives and future plans for the development of tropical-region-bred temperate japonica rice.
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Nessreen, N. B., A. K. Ammar, and A. Ezzat. "Study of some cooking and eating quality characters on some Egyptian rice genotypes." Acta Agraria Debreceniensis, no. 59 (April 23, 2014): 77–82. http://dx.doi.org/10.34101/actaagrar/59/2008.
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Some Egyptian rice genotypes [i.e. Japonica (Sakha 104), Japonica/Indica (Egyptian hybrid1) and Indica (Giza 182)] were investigated to evaluate the cooking and eating quality characters. High significant differences in grain shape were observed among rice genotypes. Hulling, milling and head rice percentage were higher in Sakha 104 than other rice genotypes, while Indica type (Giza 182) recorded the lowest values in milling and physical characters. No significant differences were found in chemical composition of the three genotypes of rice was recorded, but Giza 182 had the highest protein content. All Egyptian rice genotypes were low in gelatinization temperature and soft in gel consistency. Japonica and Indica rice varieties were low in amylase content, while Japonica/Indica rice variety was intermediate. The use of RVA is considered a good index for palatability evaluation for milled rice flour and starch. The Indica and Japonica/Indica types are low in breakdown viscosity, but higher in cooked pasta than Japonica type. Japonica type recorded the best score in panel test, followed by Indica type, while Indica/Japonica rice variety was the least accepted by Egyptian consumer.
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Harushima, Yoshiaki, Masahiro Nakagahra, Masahiro Yano, Takuji Sasaki, and Nori Kurata. "Diverse Variation of Reproductive Barriers in Three Intraspecific Rice Crosses." Genetics 160, no. 1 (January 1, 2002): 313–22. http://dx.doi.org/10.1093/genetics/160.1.313.
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Abstract Reproductive barriers are thought to play an important role in the processes of speciation and differentiation. Asian rice cultivars, Oryza sativa, can be classified into two main types, Japonica and Indica, on the basis of several characteristics. The fertility of Japonica-Indica hybrids differs from one cross to another. Many genes involved in reproductive barriers (hybrid sterility, hybrid weakness, and gametophytic competition genes) have been reported in different Japonica-Indica crosses. To clarify the state of Japonica-Indica differentiation, all reproductive barriers causing deviation from Mendelian segregation ratios in F2 populations were mapped and compared among three different Japonica-Indica crosses: Nipponbare/Kasalath (NK), Fl1084/Dao Ren Qiao (FD), and Fl1007/Kinandang puti (FK). Mapping of reproductive barriers was performed by regression analysis of allele frequencies of DNA markers covering the entire genome. Allele frequencies were explained by 33 reproductive barriers (15 gametophytic and 18 zygotic) in NK, 32 barriers (15 gametophytic and 17 zygotic) in FD, and 37 barriers (19 gametophytic and 18 zygotic) in FK. The number of reproductive barriers in the three crosses was similar; however, most of the barriers were mapped at different loci. Therefore, these reproductive barriers formed after Japonica-Indica differentiation. Considering the high genetic similarity within Japonica and Indica cultivars, the differences in the reproductive barriers of each cross were unexpectedly numerous. The reproductive barriers of Japonica-Indica hybrids likely evolved more rapidly than other genetic elements. One possible force responsible for such rapid evolution of the barriers may have been the domestication of rice.
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Watanabe, Mamoru, Yutaka Sumita, Issaku Azechi, Kengo Ito, and Keigo Noda. "Production Costs and Benefits of Japonica Rice in Mwea, Kenya." Agriculture 11, no. 7 (July 5, 2021): 629. http://dx.doi.org/10.3390/agriculture11070629.
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From the perspective of national food security, strengthening domestic rice production is an urgent issue for Kenya. For this purpose, it is helpful to consider varieties that generate novel and competitive values different from those of conventional varieties. Recently, domestic japonica rice, which is now being distributed, has become an attractive variety with a high market price and its production is expected to increase. Although it is competitive and promising as a crop for small-scale farmers, the production stage costs and benefits are not clear. Thus, a study was conducted to perform a cost–benefit analysis of japonica rice in comparison to conventional rice at the production stage and evaluate strategies for strengthening the domestic production of rice. We conducted an experimental cultivation of japonica rice in the Mwea region, Kenya, where japonica rice is produced. As a result, although production costs for japonica rice are higher than costs for conventional varieties (24.46 KSh/kg versus 22.63 KSh/kg), when a high-yielding variety is grown (6.44 tons/ha for japonica rice compared to 6.07 tons/ha for conventional rice), a larger net profit can be obtained (65.54 KSh/kg versus 32.37 KSh/kg). We believe that initiatives to improve difficulties at the production stage would make the production of both japonica rice and conventional rice more economically viable and facilitate strengthening of the overall domestic rice production.
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Zhang, Peng, Zhuoran Ding, Zhengzheng Zhong, and Hanhua Tong. "Transcriptomic Analysis for Indica and Japonica Rice Varieties under Aluminum Toxicity." International Journal of Molecular Sciences 20, no. 4 (February 25, 2019): 997. http://dx.doi.org/10.3390/ijms20040997.
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Aluminum (Al) at high concentrations inhibits root growth, damage root systems, and causes significant reductions in rice yields. Indica and Japonica rice have been cultivated in distinctly different ecological environments with different soil acidity levels; thus, they might have different mechanisms of Al-tolerance. In the present study, transcriptomic analysis in the root apex for Al-tolerance in the seedling stage was carried out within Al-tolerant and -sensitive varieties belonging to different subpopulations (i.e., Indica, Japonica, and mixed). We found that there were significant differences between the gene expression patterns of Indica Al-tolerant and Japonica Al-tolerant varieties, while the gene expression patterns of the Al-tolerant varieties in the mixed subgroup, which was inclined to Japonica, were similar to the Al-tolerant varieties in Japonica. Moreover, after further GO (gene ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) analyses of the transcriptomic data, we found that eight pathways, i.e., “Terpenoid backbone biosynthesis”, “Ribosome”, “Amino sugar and nucleotide sugar metabolism”, “Plant hormone signal transduction”, “TCA cycle”, “Synthesis and degradation of ketone bodies”, and “Butanoate metabolism” were found uniquely for Indica Al-tolerant varieties, while only one pathway (i.e., “Sulfur metabolism”) was found uniquely for Japonica Al-tolerant varieties. For Al-sensitive varieties, one identical pathway was found, both in Indica and Japonica. Three pathways were found uniquely in “Starch and sucrose metabolism”, “Metabolic pathway”, and “Amino sugar and nucleotide sugar metabolism”.
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Ishii, Takashige, and Koichiro Tsunewaki. "Chloroplast genome differentiation in Asian cultivated rice." Genome 34, no. 5 (October 1, 1991): 818–26. http://dx.doi.org/10.1139/g91-126.
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Restriction endonuclease analysis of chloroplast DNA was carried out to clarify the chloroplast genome differentiation between Asian varieties of Oryza sativa. Based on the restriction fragment patterns obtained with six endonucleases, i.e., EcoRI, HindIII, PstI, PvuII, SmaI, and XhoI, chloroplast genomes of 68 local varieties from 15 Asian countries could be classified into five types (types 1, 3, 10, 11, and 12). Among these types, four length mutations and two base substitutions were found; these changes were located on the PstI physical map of rice chloroplast DNA. In a dendrogram showing genetic relationships among five chloroplast genomes, they are mainly divided into two groups, which we have named as the Japonica (types 1, 11, and 12) and Indica (types 3 and 10) chloroplast genome groups. Both groups are distributed widely in Asian countries. The Japonica isozyme group classified by J.C. Glaszmann (1985. Rice Genetics. International Rice Research Institute, Manila, Philippines, pp. 83–90) carries only the Japonica chloroplast genome, whereas the Indica isozyme group contains both Japonica and Indica chloroplast genomes.Key words: Oryza sativa, Asian varieties, chloroplast DNA, restriction endonuclease analysis, chloroplast genome differentiation.
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Uyeh, Daniel Dooyum, Senorpe Asem-Hiablie, Tusan Park, Kyungmin Kim, Alexey Mikhaylov, Seungmin Woo, and Yushin Ha. "Could Japonica Rice Be an Alternative Variety for Increased Global Food Security and Climate Change Mitigation?" Foods 10, no. 8 (August 12, 2021): 1869. http://dx.doi.org/10.3390/foods10081869.
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The growing importance of rice globally over the past three decades is evident in its strategic place in many countries’ food security planning policies. Still, its cultivation emits substantial greenhouse gases (GHGs). The Indica and Japonica sub-species of Oryza sativa L. are mainly grown, with Indica holding the largest market share. The awareness, economics, and acceptability of Japonica rice in a food-insecure Indica rice-consuming population were surveyed. The impact of parboiling on Japonica rice was studied and the factors which most impacted stickiness were investigated through sensory and statistical analyses. A comparison of the growing climate and greenhouse gas emissions of Japonica and Indica rice was carried out by reviewing previous studies. Survey results indicated that non-adhesiveness and pleasant aroma were the most preferred properties. Parboiling treatment altered Japonica rice’s physical and chemical properties, introducing gelatinization of starch and reducing adhesiveness while retaining micronutrient concentrations. Regions with high food insecurity and high consumption of Indica rice were found to have suitable climatic conditions for growing Japonica rice. Adopting the higher-yielding, nutritious Japonica rice whose cultivation emits less GHG in these regions could help strengthen food security while reducing GHGs in global rice cultivation.
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Watanabe, Mamoru, Yutaka Sumita, Issaku Azechi, Kengo Ito, and Keigo Noda. "The Value Chain of Locally Grown Japonica Rice in Mwea, Kenya." Agriculture 11, no. 10 (October 8, 2021): 974. http://dx.doi.org/10.3390/agriculture11100974.
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In Kenya, there is an urgent need to strengthen domestic rice production to improve food security. To achieve this, it is necessary to develop a value chain of competitive rice varieties that creates new value over and above that of conventional varieties. In this study, we focused on locally grown japonica rice produced in the Mwea area, which has recently begun to be distributed in Nairobi. Through interviews with Japanese restaurants, Japanese food stores, and consumers as well as interviews with stakeholders in the value chain the market price, consumer acceptability, and profitability of locally grown japonica rice were determined. We evaluated the value chain of locally grown japonica rice based on the interaction between the potential demand and a value chain analysis and examined improvement measures to establish the value chain. The results showed that 76% of consumers who eat staple foods other than rice rated locally grown japonica rice as “very good” or “good”, indicating that it may be acceptable to those who do not usually eat rice. The net profits for locally grown japonica rice were higher than those of conventional rice at the production, processing, and distribution stages, which is an advantage for producers and demonstrates that the elimination of middlemen is effective and highly profitable for each stakeholder. In contrast, the consumer price of locally grown japonica rice was higher than that of conventional rice, indicating that some challenges remain to be overcome. Our estimation approach will allow further study of target values such as selling price in other desired value chains. Together, our findings suggest the potential of the locally grown japonica rice value chain to contribute to the strengthening of domestic rice production.
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Zhang, Jianfeng, Zongmu Yao, Yalin Chen, Jiafan Zhang, Shouyang Luo, Chunjie Tian, and Lei Tian. "Study of Rhizosphere Microbial Community Structures of Asian Wild and Cultivated Rice Showed That Cultivated Rice Had Decreased and Enriched Some Functional Microorganisms in the Process of Domestication." Diversity 14, no. 2 (January 20, 2022): 67. http://dx.doi.org/10.3390/d14020067.
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Asian cultivated rice (Oryza sativa L.), domesticated from Asian wild rice, is a staple food crop for populations around the world. Asian cultivated rice has undergone physiological changes in the process of its evolution from Asian wild rice, and the closely related rhizosphere microorganisms may have changed in the process of plant domestication. However, the rhizosphere microorganisms of different Asian wild rice species and their related indica and japonica cultivated rice have not yet been illustrated clearly. This study aimed to illustrate the microbial community structures in the rhizosphere of Asian wild rice (common wild rice, nivara wild rice, medicinal wild rice, and spotted wild rice) and Asian cultivated rice (indica and japonica accessions) through the high-throughput sequencing of 16S rDNA, ITS amplifiers and metagenomic data. The results showed that there were significant differences between wild and cultivated rice in their rhizosphere microbial community structures. In view of the indica and japonica rice, the bacterial and fungal community structures of indica rice with the nivara wild rice and medicinal wild rice were more similar than the japonica rice species. The indica and japonica rice had the lowest proportion of Actinobacteria than the wild rice species, and indica rice has the highest relative abundance of Nitrospira. As for the microbial functions, methane metabolism and pyruvate metabolism were found to be the common pathway enriched in the rhizosphere of common and nivara wild rice in comparison with the indica and japonica rice; in addition, though it was found that the relative abundances of the pathogenic fungi in the rhizosphere soil of indica and japonica rice were significantly lower than that of the wild rice, the relative abundances of Magnaporthales and Ustilaginales were significantly higher in indica and japonica rice than that of the wild rice. This study is expected to provide a theoretical basis for the development and utilization of rhizosphere microbial resources for wild and cultivated rice.
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Jeong, O.-Young, Gideon Torollo, Maurene Bombay, Man-Kee Baek, Eok-keun Ahn, Woong-Jo Hyun, Hyun-Su Park, et al. "Adaptable Tropical Japonica High quality New Rice Cultivar ‘Japonica 6’." Journal of the Korean Society of International Agricultue 31, no. 3 (September 30, 2019): 249–54. http://dx.doi.org/10.12719/ksia.2019.31.3.249.
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Lu, Ruisen, Jia Liu, Xuegang Wang, Zhao Song, Xiangdong Ji, Naiwei Li, Gang Ma, and Xiaoqin Sun. "Chromosome-Level Genome Assembly of a Fragrant Japonica Rice Cultivar ‘Changxianggeng 1813’ Provides Insights into Genomic Variations between Fragrant and Non-Fragrant Japonica Rice." International Journal of Molecular Sciences 23, no. 17 (August 26, 2022): 9705. http://dx.doi.org/10.3390/ijms23179705.
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East Asia has an abundant resource of fragrant japonica rice that is gaining increasing interest among both consumers and producers. However, genomic resources and in particular complete genome sequences currently available for the breeding of fragrant japonica rice are still scarce. Here, integrating Nanopore long-read sequencing, Illumina short-read sequencing, and Hi-C methods, we presented a high-quality chromosome-level genome assembly (~378.78 Mb) for a new fragrant japonica cultivar ‘Changxianggeng 1813’, with 31,671 predicated protein-coding genes. Based on the annotated genome sequence, we demonstrated that it was the badh2-E2 type of deletion (a 7-bp deletion in the second exon) that caused fragrance in ‘Changxianggeng 1813’. Comparative genomic analyses revealed that multiple gene families involved in the abiotic stress response were expanded in the ‘Changxianggeng 1813’ genome, which further supported the previous finding that no generalized loss of abiotic stress tolerance associated with the fragrance phenotype. Although the ‘Changxianggeng 1813’ genome showed high genomic synteny with the genome of the non-fragrant japonica rice cultivar Nipponbare, a total of 289,970 single nucleotide polymorphisms (SNPs), 96,093 small insertion-deletion polymorphisms (InDels), and 8690 large structure variants (SVs, >1000 bp) were identified between them. Together, these genomic resources will be valuable for elucidating the mechanisms underlying economically important traits and have wide-ranging implications for genomics-assisted breeding in fragrant japonica rice.
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Prasetiyono, Joko, Nurul Hidayatun, and Tasliah Tasliah. "Genetic Diversity Analysis of 53 Indonesian Rice Genotypes using 6K Single Nucleotide Polymorphism Markers." Jurnal AgroBiogen 14, no. 1 (October 18, 2018): 1. http://dx.doi.org/10.21082/jbio.v14n1.2018.p1-10.
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<p>Indonesia is rich in rice genetic resources, however, only a small number has been used in variety improvement programs. This study aimed to determine the genetic diversity of Indonesian rice varieties using 6K SNP markers. The study was conducted at ICABIOGRAD for DNA isolation and IRRI for SNP marker analysis. Genetic materials were 53 rice genotypes consisting of 49 varieties and 4 check genotypes. SNP markers used were 6K loci. Results showed that among the markers analyzed, only 4,606 SNPs (76.77%) were successfully read. The SNP markers covered all twelve rice chromosomes of 945,178.27 bp. The most common allele observed was GG, whereas the least allele was TG. Dendrograms of the 53 rice varieties analyzed with 4,606 SNPs demonstrated several small groups containing genotypic mixtures between indica and japonica rice, and no groups were found to contain firmly indica or japonica type. Structure analysis (K = 2) with value of 0.8 showed that the 53 rice varieties were divided into several groups and each group consisted of 4 japonica, 2 tropical japonica, 46 indica, and 1 aus rice type, respectively. IR64 and Ciherang proved to have an indica genome, while Rojolele has japonica one. Dupa and Hawara Bunar, usually grouped into tropical japonica rice, were classified as indica type, and Hawara Bunar has perfectly 100% indica type. The results of this study indicated that rice classification (indica-japonica) which is usually classified based only on morphological characters, e.g. grain and leaf shapes, is not enough and classification based on SNP markers should be considered for that purpose.</p>
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Oh, So-Hyeong, Beom-Gyun Jeong, and Jiyeon Chun. "Nutritional and Functional Properties of Water Extracts from Achyranthes japonica Nakai-Rice Pilsner Byproducts." Journal of the Korean Society of Food Science and Nutrition 46, no. 2 (February 28, 2017): 185–95. http://dx.doi.org/10.3746/jkfn.2017.46.2.185.
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Yang, Yaolong, Xin Xu, Mengchen Zhang, Qun Xu, Yue Feng, Xiaoping Yuan, Hanyong Yu, Yiping Wang, and Xinghua Wei. "Genetic Basis Dissection for Eating and Cooking Qualities of Japonica Rice in Northeast China." Agronomy 10, no. 3 (March 20, 2020): 423. http://dx.doi.org/10.3390/agronomy10030423.
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The japonica rice in Northeast China is famous because of its high quality. Eating and cooking qualities (ECQs) are the most important factors that determine cooked rice quality. However, the genetic basis of ECQ of japonica varieties in Northeast China needs further study. In this study, 200 japonica varieties that are widely distributed in Northeast China were collected to evaluate the physicochemical indices of grain ECQs. The distribution of each trait was concentrated without large variations. Correlation analysis indicated that gel consistency (GC) had a significantly negative correlation with gelatinization temperature (GT). By integrating various analyses including kinship calculation, principal component analysis (PCA), linkage disequilibrium (LD) analysis, and original parent investigation, we found that the japonica varieties in Northeast China exhibited a narrow genetic basis. An association study for grain ECQs was performed and eight quantitative trait loci (QTLs) were detected. ALK was the major locus that regulated GT and also significantly affecting GC. Through the linkage disequilibrium (LD) and expression pattern analysis, one possible candidate gene (LOC_Os02g29980) was predicted and required further research for validation. Additionally, a different allele of Wx was identified in the variety CH4126, and ALK was not fixed in these japonica varieties. These results further elucidate the genetic basis of ECQs of japonica varieties in Northeast China and provide local breeders some assistance for improving ECQs of rice grain in rice breeding.
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Ma, Yichao, Shuang Zhang, Liyan Rong, Zhaoxia Wu, and Wentao Sun. "Polyphenol Composition and Antioxidant Activity of Japonica Rice Cultivars and Intake Status." Foods 11, no. 23 (November 24, 2022): 3788. http://dx.doi.org/10.3390/foods11233788.
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Japonica rice is produced mainly in northeast China, Japan, and the Korean Peninsula. Polyphenols and flavonoids are the main antioxidants in japonica rice. This study reported the polyphenol content and antioxidant activity of nine brown and white japonica rice cultivars. The total phenolic and flavonoid contents of brown rice were in the ranges of 241.98–296.76 GAE mg/100 g, and 225.30–276.80 RE mg/100 g, respectively. These values were significantly higher than that of white rice by 118.98–206.06% and 135.0–217%, respectively. The bound fraction from phenolics and flavonoids contributed 41.1–63.6% and 62.22–78.19% of the total phenolic and flavonoid content in brown rice, respectively, while these ranges were 55.5–73.5% and 46.07–66.83% in white rice, respectively. p-Hydroxybenzonic acid was the predominant phenolic acid in japonica rice. All four antioxidant capacities of brown rice (DPPH, ABTS, OH, FRAP) were higher by up to 1.68–2.85 times than those of white rice. The PZ21 (Yanfeng 47) japonica rice variety has outstanding antioxidant capacity based on the weights of each antioxidant index. According to the differences of functional substances among varieties, it can provide guidance for consumers and theoretical basis for the production of healthy food.
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Sun, Tao, Xin Yang, Xiaoli Tan, Kefeng Han, Sheng Tang, Weiming Tong, Siyi Zhu, Zhaoping Hu, and Lianghuan Wu. "Comparison of Agronomic Performance between Japonica/Indica Hybrid and Japonica Cultivars of Rice Based on Different Nitrogen Rates." Agronomy 10, no. 2 (January 25, 2020): 171. http://dx.doi.org/10.3390/agronomy10020171.
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Previous studies have revealed that the japonica/indica hybrid rice has a higher yield potential, biomass production, and nitrogen (N) accumulation than japonica rice in China, however, at a single N application rate. It remains unclear whether it also occurs at a higher or lower N application rate under the same field condition. To investigate the effects of nitrogen application rates on grain yield, N uptake, dry matter accumulation, and agronomic N use efficiency, field experiments were conducted in Jinhua City, Zhejiang Province during three consecutive growth seasons in 2016, 2017, and 2018. Two japonica/indica hybrid varieties (Yongyou 12 and Yongyou 538) and two japonica varieties (Xiushui 134 and Jia 58) were exposed to five N application rates (0, 150, 225, 300, and 375 kg ha−1). The results showed that grain yields of all the varieties increased with increasing nitrogen application rates, except for Jia 58 whose optimum nitrogen level was 225 kg ha−1, because no significant difference was observed between N225 and N300. Across the four rice varieties, N uptake increased significantly with increased N-fertilizer rates at all the growth stages (p < 0.05). Across the three planting years, the average grain yield of japonica/indica hybrid rice was higher than that of japonica rice by 75.6% at N0, 57.2% at N150, 41.1% at N225, 38.3% at N300, and 45.8% at N375. We also found that as compared with japonica rice, the japonica/indica hybrid rice had more grain yield, higher dry matter, and higher N uptake at all growth stages, regardless of the N application rate.
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KURNIASIH, NUR SITI, RATNA SUSANDARINI, FEBRI ADI SUSANTO, TRI RINI NURINGTYAS, GLYN JENKINS, and YEKTI ASIH PURWESTRI. "Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms." Biodiversitas Journal of Biological Diversity 20, no. 4 (April 1, 2019): 1208–14. http://dx.doi.org/10.13057/biodiv/d200437.
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Abstract. Kurniasih NS, Susandarini R, Susanto FA, Nuringtyas TR, Jenkins G, Purwestri YA. 2019. Characterization of Indonesian pigmented rice (Oryza sativa) based on morphology and Single Nucleotide Polymorphisms. Biodiversitas 20: 1208-1214. Indonesia has many cultivars of pigmented rice, but many variants have not been characterized using morphological characters and molecular markers. SNPs (Single Nucleotide polymorphisms) have been used in previous studies to identify the Indica and Japonica subspecies. Characterization of whether a line belongs to the Indica or Japonica subspecies is useful information for rice breeders, especially to generate line exhibiting the strong hybrid vigor. Morphological characters are used to determine the relationship between cultivars using cluster analysis. The SNP markers were amplified by PCR, sequenced and compared with sequences in the GenBank. Based on morphological characters, ten cultivars divide into two clusters. SNPs distinguish Indica and Japonica subspecies, and show that Hitam Lampung, Aek Sibundong, Melik, Hitam Toraja, Merah Kalimantan, and Merah Sumbawa belong to the Indica subspecies while Cempo Ireng and Pare Eja belong to Japonica. Abang Segreng and Hitam Toraja could not be clearly assigned to either the Indica or Japonica subspecies.
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Ma, Zhongtao, Huizhen Ma, Zhifeng Chen, Xinyi Chen, Guodong Liu, Qun Hu, Fangfu Xu, Haiyan Wei, and Hongcheng Zhang. "Quality Characteristics of Japonica Rice in Southern and Northern China and the Effect of Environments on Its Quality." Agronomy 12, no. 11 (November 5, 2022): 2757. http://dx.doi.org/10.3390/agronomy12112757.
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Four types of japonica rice including non-soft japonica rice from northern China planted in the northern region (NSJRNN), non-soft japonica rice from northern China planted in the southern region (NSJRNS), non-soft japonica rice from southern China planted in the southern region (NSJRSS), and soft japonica rice from southern China planted in the southern region (SJRSS) were adopted as materials to reveal the quality characteristics of japonica rice in southern and northern China and the effect of environments on its quality. Compared with NSJRNN, higher temperatures during the grain-filling stage in southern China resulted in poor processing and appearance qualities of NSJRNS and NSJRSS. Due to the increased protein content (PC), the eating qualities of NSJRNS and NSJRSS were bad. While for SJRSS, with low apparent amylose content (AAC) and few large-sized starch granules, the eating quality was better than that of NSJRNS and NSJRSS and even comparable to NSJRNN. Therefore, with a relative high PC of rice under high temperature condition in southern China, it could be one of the effective ways to reduce AAC appropriately to obtain a good eating quality of rice.
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Zhu, Ying, Dong Xu, Zhongtao Ma, Xinyi Chen, Mingyue Zhang, Chao Zhang, Guodong Liu, Haiyan Wei, and Hongcheng Zhang. "Differences in Eating Quality Attributes between Japonica Rice from the Northeast Region and Semiglutinous Japonica Rice from the Yangtze River Delta of China." Foods 10, no. 11 (November 11, 2021): 2770. http://dx.doi.org/10.3390/foods10112770.
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Differences in cooked rice and starch and protein physicochemical properties of three japonica rice were compared systematically. Cultivars of japonica rice, Daohuaxiang2, from Northeast China (NR) and two semiglutinous japonica rice (SGJR), Nangeng46 and Nangeng2728, from the Yangtze River Delta (YRD) were investigated. Both Daohuaxiang2 and Nangeng46 achieved high taste values, but there were great differences in starch and protein physicochemical properties. Daohuaxiang2 showed higher apparent amylose content (AAC), lower protein content (PC), and longer amylopectin (especially fb2 and fb3) and amylose chain lengths, resulting in thicker starch lamellae and larger starch granule size. Its cooked rice absorbed more water and expanded to larger sizes. All of these differences created a more compact gel network and harder but more elastic cooked rice for Daohuaxiang2. Nangeng46 produced a lower AAC, a higher PC, shorter amylopectin and amylose chain lengths, thinner starch lamellae, and smaller starch granule sizes, creating a looser gel network and softer cooked rice. The two SGJR, Nangeng46 and Nangeng2728, had similar low AACs but great differences in taste values. The better-tasting Nangeng46 had a lower PC (especially glutelin content) and higher proportion of amylopectin fa chains, which likely reduced the hardness, improved the appearance, and increased the adhesiveness of its cooked rice. Overall, both types of japonica rice from the NR and YRD could potentially have good eating qualities where Nangeng46’s cooked rice was comparable to that of Daohuaxiang2 because of its lower AC. Moreover, its lower PC and higher proportion of amylopectin fa chains likely improved its eating quality over the inferior-tasting SGJR, Nangeng2728. This research lays a foundation for the improvement of the taste of japonica rice in rice breeding.
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Ding, Chao, Congshan Xu, Bo Lu, Xuhui Zhu, Xikun Luo, Bin He, Cambula Elidio, et al. "Comprehensive Evaluation of Rice Qualities under Different Nitrogen Levels in South China." Foods 12, no. 4 (February 6, 2023): 697. http://dx.doi.org/10.3390/foods12040697.
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There is a need to comprehensively evaluate the rice quality of different rice varieties under different nitrogen treatments. Therefore, in this study, we used twenty-one hybrid indica rice varieties and twenty-three inbred japonica rice varieties with three nitrogen fertilizer levels to investigate differences in rice qualities. As compared with hybrid indica rice, inbred japonica rice had lower coefficient of variation values for grain shape, mild rice percentage, and head rice percentage, but relatively higher coefficient of variation values for chalkiness traits, appearance, and taste value of cooked rice. A principal component analysis and membership function method were used to comprehensively evaluate the qualities of rice. The overall eating quality value by sensory evaluation and head rice percentage explained 61.3% and 67.9% of the variations in comprehensive quality of hybrid indica rice and inbred japonica rice across different nitrogen levels, respectively. We also found that rice comprehensive quality was better under low nitrogen levels for hybrid indica rice, while for inbred japonica rice, properly increasing nitrogen application could improve the comprehensive quality.
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Ansari, TH, T. Yoshida, Y. Yamamoto, and A. Miyazaki. "Distribution and Interrelationship of Differentiated, Degenerated and Surviving Spikelets on Panicle Branches in Rice (Oryza sativa)." Bangladesh Rice Journal 17, no. 1-2 (November 18, 2014): 49–63. http://dx.doi.org/10.3329/brj.v17i1-2.20901.
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The present investigation evaluated distribution pattern of differentiated, degenerated and surviving spikelets and interrelationship of spikelets on the basis of their position on rachis branches in a panicle of both japonica and indica cultivars. Distribution of differentiated spikelets on primary brances (PBs) and secondary brances (SBs) followed 1:1 ratio in the japonica cultivars and 1:2 or more than 2 in the indica ones irrespective of plant types revealed the genetic factor had the more influence on the observed distribution pattern in both japonica and indica cultivars. The percentage of degenerated spikelets to the differentiated ones on PBs was slightly higher in the japonica (4.2%?8.3%) than in the indica (0.5%?6.6%) cultivars. The degenerated percentage of differentiated spikelets on SBs varied more widely in the indica (11.9%?56.2%) than in the japonica (26.1%?48.2%) cultivars, although average was almost the same (37.7% in the japonica and 38.9% in the indica cultivars). Correlation coefficients showed that the increase of differentiated spikelets on PBs strongly increase the number of surviving spikelet per panicle or on PBs per panicle in both cultivar groups. But this was not significantly increase the number of degenerated spikelets on PBs but showed possibility of increase the number of degenerated spikelets on SBs per panicle in both cultivar groups. Increased number of differentiated spikelets on SBs substantially increased the numbers of both surviving and degenerated spikelets on SBs per panicle and showed weak negative (in japonica) and positive (in indica) significant correlation with the percentage of degenerated spikelets on SBs. The number of surviving PBs was highly correlated with the surviving spikelets on PBs per panicle. Therefore, above results imply that the increase of differentiated spikelets on PBs of both cultivar groups and on SBs in the japonica group could sustain the survivility of spikelets with higher number of differentiated PBs per panicle.DOI: http://dx.doi.org/10.3329/brj.v17i1-2.20901Bangladesh Rice j. 2013, 17(1&2): 49-63
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Zhang, Xiaoxiang, Niansheng Huang, Lanjing Mo, Minjia Lv, Yingbo Gao, Junpeng Wang, Chang Liu, et al. "Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation." International Journal of Molecular Sciences 20, no. 18 (September 5, 2019): 4358. http://dx.doi.org/10.3390/ijms20184358.
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Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice.
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Zhang, Xincheng, Liangbo Fu, Yishan Tu, Huifang Zhao, Liuhui Kuang, and Guoping Zhang. "The Influence of Nitrogen Application Level on Eating Quality of the Two Indica-Japonica Hybrid Rice Cultivars." Plants 9, no. 12 (November 27, 2020): 1663. http://dx.doi.org/10.3390/plants9121663.
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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.
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Fu, Jin-Dong, Yong-Feng Yan, Moon Young Kim, Suk-Ha Lee, and Byun-Woo Lee. "Population-specific quantitative trait loci mapping for functional stay-green trait in rice (Oryza sativa L.)." Genome 54, no. 3 (March 2011): 235–43. http://dx.doi.org/10.1139/g10-113.
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The functional stay-green trait gives leaves a longer duration of greenness and photosynthetic capacity during the grain-filling period. We developed two independent recombinant inbred line populations from the intra- and intersubspecific crosses of Oryza sativa L. subsp. japonica ‘Suweon490’ (japonica) × O. sativa subsp. japonica ‘SNU-SG1’ (japonica) and O. sativa subsp. indica ‘Andabyeo’ (indica) × O. sativa subsp. japonica ‘SNU-SG1’ (japonica), respectively. The common parental line ‘SNU-SG1’ was the functional source for the stay-green trait. Quantitative trait locus (QTL) mapping based on simple sequence repeat markers identified a total of six QTLs associated with two stay-green traits across two populations. The two traits were cumulative chlorophyll content (SPAD value) of flag leaf (CSFL) and total cumulative SPAD value of the four upper leaves (TCS). Four QTLs, tcs4, csfl6, csfl9 (or tcs9), and csfl12, located on chromosomes 4, 6, 9, and 12, respectively, were detected simultaneously in both populations. The remaining two QTLs, csfl2 (or tcs2) and tcs5, on chromosomes 2 and 5, respectively, were found to be population specific. Moreover, the functional stay-green trait of ‘SNU-SG1’ positively correlated with grain yield performance. Two yield QTLs, yld6 and yld9, on chromosomes 6 and 9 found in both populations were positioned at the same locations with the csfl6 and tcs9 QTLs for stay-green traits. Thus, the identified chromosomal regions can be promising targets of marker-assisted introgression of the functional stay-green trait into breeding materials for improvement of rice yield.
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Mao, Donghai, Yeyun Xin, Yongjun Tan, Xiaojie Hu, Jiaojiao Bai, Zhao-ying Liu, Yilan Yu, et al. "Natural variation in the HAN1 gene confers chilling tolerance in rice and allowed adaptation to a temperate climate." Proceedings of the National Academy of Sciences 116, no. 9 (February 11, 2019): 3494–501. http://dx.doi.org/10.1073/pnas.1819769116.
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Rice (Oryza sativa L.) is a chilling-sensitive staple crop that originated in subtropical regions of Asia. Introduction of the chilling tolerance trait enables the expansion of rice cultivation to temperate regions. Here we report the cloning and characterization of HAN1, a quantitative trait locus (QTL) that confers chilling tolerance on temperate japonica rice. HAN1 encodes an oxidase that catalyzes the conversion of biologically active jasmonoyl-L-isoleucine (JA-Ile) to the inactive form 12-hydroxy-JA-Ile (12OH-JA-Ile) and fine-tunes the JA-mediated chilling response. Natural variants in HAN1 diverged between indica and japonica rice during domestication. A specific allele from temperate japonica rice, which gained a putative MYB cis-element in the promoter of HAN1 during the divergence of the two japonica ecotypes, enhances the chilling tolerance of temperate japonica rice and allows it to adapt to a temperate climate. The results of this study extend our understanding of the northward expansion of rice cultivation and provide a target gene for the improvement of chilling tolerance in rice.
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Efrina, Efrina, Yoshiyuki Komoda, Hiroshi Suzuki, and Ruri Hidema. "Deformation profile of a piece of japonica cooked rice with squeezing test." MATEC Web of Conferences 197 (2018): 04005. http://dx.doi.org/10.1051/matecconf/201819704005.
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The texture of cooked rice plays an important role in the characteristics of cooked rice. It can be firmness or stickiness depends on the amount of amylopectin inside the cooked rice, the higher the content will be more stickiness. Japonica rice is the type of rice with highest amylopectin content. Therefore the texture is the most stickiness. This research is to define the stickiness of japonica cooked rice using stress-strain behavior through uniaxial compression test. Stress defined as a normal force divided by a cross-sectional area in the horizontal plane while strain as a shrinking ratio of cooked rice. A single Japonica cooked rice squeezed using parallel plate type rheometer with constant velocity (0,2; 0,5; 1; 2; 4 mm/s). The deformation process of cooked rice was recorded from both side and bottom views to measure area transformation. The result showed that stress-strain of the deformation of cooked japonica rice was strongly depended on velocity. The low velocity (0,2;0,5;1 and 1 mm/s) are same with high velocity (2 and 4 mm/s) the during first deformation but significantly different statistically in the later deformation.
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Peng, Bo, Kun Xu, Kun He, Juan Peng, Xia-Yu Tian, Ling Sun, Xiao-Hua Song, et al. "Detection and Analysis of Mineral Elements in Giant Embryo Rice." Journal of Biotechnology Research, no. 66 (June 1, 2020): 50–56. http://dx.doi.org/10.32861/jbr.66.50.56.
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Mineral elements are essential micronutrients necessary to constitute human tissue and maintain normal physiological functions. Micronutrient deficiencies are an important issue currently faced in the world. The best strategy to solve this problem is to breed special functional types of rice varieties rich in trace elements (special rice for short). A special type of rice that can produce rich nutrients. In order to explore the nutritional value of giant embryo rice, the contents of 17 mineral elements ((K, Ca, Fe, Se, Zn, Cu, Na, Mn, Mg, Ni, Cr, Co, Pb, As, Cd, Ag, Al)) in 5 kinds of giant embryo rice (white giant embryo, giant japonica-GB-12, giant japonica-GB-11 and giant japonica-GB-5, giant japonica-GB-1) were detected by inductively coupled plasma mass spectrometry. After comparison with ordinary rice, it was found that the content of the same mineral element in different samples has a large variation, suggesting that different rice varieties have different absorption, transformation and storage efficiency of the same element; different giant embryo brown rice in some mineral elements (such as Cr, Ni, Cu and Zn) are extremely low in content and almost undetectable. Meanwhile, the brown rice of giant embryo rice has a more powerful enrichment effect on some mineral elements, which means that embryo rice has a unique advantage in cultivating new rice varieties with special functions rich in minerals.
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Seo, Jeonghwan, So-Myeong Lee, Jae-Hyuk Han, Na-Hyun Shin, Yoon Kyung Lee, Backki Kim, Joong Hyoun Chin, and Hee-Jong Koh. "Characterization of the Common Japonica-Originated Genomic Regions in the High-Yielding Varieties Developed from Inter-Subspecific Crosses in Temperate Rice (Oryza sativa L.)." Genes 11, no. 5 (May 18, 2020): 562. http://dx.doi.org/10.3390/genes11050562.
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The inter-subspecific crossing between indica and japonica subspecies in rice have been utilized to improve the yield potential of temperate rice. In this study, a comparative study of the genomic regions in the eight high-yielding varieties (HYVs) was conducted with those of the four non-HYVs. The Next-Generation Sequencing (NGS) mapping on the Nipponbare reference genome identified a total of 14 common genomic regions of japonica-originated alleles. Interestingly, the HYVs shared japonica-originated genomic regions on nine chromosomes, although they were developed through different breeding programs. A panel of 94 varieties was classified into four varietal groups with 38 single nucleotide polymorphism (SNP) markers from 38 genes residing in the japonica-originated genomic regions and 16 additional trait-specific SNPs. As expected, the japonica-originated genomic regions were only present in the japonica (JAP) and HYV groups, except for Chr4-1 and Chr4-2. The Wx gene, located within Chr6-1, was present in the HYV and JAP variety groups, while the yield-related genes were conserved as indica alleles in HYVs. The japonica-originated genomic regions and alleles shared by HYVs can be employed in molecular breeding programs to further develop the HYVs in temperate rice.
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Redoña, Edilberto D., and David J. Mackill. "Molecular mapping of quantitative trait loci in japonica rice." Genome 39, no. 2 (April 1, 1996): 395–403. http://dx.doi.org/10.1139/g96-050.
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Rice (Oryza sativa L.) molecular maps have previously been constructed using interspecific crosses or crosses between the two major subspecies: indica and japonica. For japonica breeding programs, however, it would be more suitable to use intrasubspecific crosses. A linkage map of 129 random amplified polymorphic DNA (RAPD) and 18 restriction fragment length polymorphism (RFLP) markers was developed using 118 F2 plants derived from a cross between two japonica cultivars with high and low seedling vigor, Italica Livorno (IL) and Labelle (LBL), respectively. The map spanned 980.5 cM (Kosambi function) with markers on all 12 rice chromosomes and an average distance of 7.6 cM between markers. Codominant (RFLP) and coupling phase linkages (among RAPDs) accounted for 79% of total map length and 71% of all intervals. This map contained a greater percentage of markers on chromosome 10, the least marked of the 12 rice chromosomes, than other rice molecular maps, but had relatively fewer markers on chromosomes 1 and 2. We used this map to detect quantitative trait loci (QTL) for four seedling vigor related traits scored on 113 F3 families in a growth chamber slantboard test at 18 °C. Two coleoptile, five root, and five mesocotyl length QTLs, each accounting for 9–50% of the phenotypic variation, were identified by interval analysis. Single-point analysis confirmed interval mapping results and detected additional markers significantly influencing each trait. About two-thirds of alleles positive for the putative QTLs were from the high-vigor parent, IL. One RAPD marker (OPAD13720) was associated with a IL allele that accounted for 18.5% of the phenotypic variation for shoot length, the most important determinant of seedling vigor in water-seeded rice. Results indicate that RAPDs are useful for map development and QTL mapping in rice populations with narrow genetic base, such as those derived from crosses among japonica cultivars. Other potential uses of the map are discussed. Key words : QTL mapping, RAPD, RFLP, seedling vigor, japonica, Oryza sativa.
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Badro, Hayba, Agnelo Furtado, and Robert Henry. "Relationships between Iraqi Rice Varieties at the Nuclear and Plastid Genome Levels." Plants 8, no. 11 (November 7, 2019): 481. http://dx.doi.org/10.3390/plants8110481.
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Due to the importance of the rice crop in Iraq, this study was conducted to determine the origin of the major varieties and understand the evolutionary relationships between Iraqi rice varieties and other Asian rice accessions that could be significant in the improvement of this crop. Five varieties of Oryza sativa were obtained from Baghdad/Iraq, and the whole genomic DNA was sequenced, among these varieties, Amber33, Furat, Yasmin, Buhooth1 and Amber al-Baraka. Raw sequence reads of 33 domesticated Asian rice accessions were obtained from the Sequence Read Archive (SRA-NCBI). The sequence of the whole chloroplast-genome was assembled while only the sequence of 916 concatenated nuclear-genes was assembled. The phylogenetic analysis of both chloroplast and nuclear genomes showed that two main clusters, Indica and Japonica, and further five sub-clusters based upon their ecotype, indica, aus, tropical-japonica, temperate-japonica and basmati were created; moreover, Amber33, Furat, Yasmin and Buhooth1 belonged to the basmati, indica and japonica ecotypes, respectively, where Amber33 was placed in the basmati group as a sister of cultivars from Pakistan and India. This confirms the traditional story that Amber was transferred by a group of people who had migrated from India and settled in southern Iraq a long time ago.
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Liu, Qiuyuan, Shuang Chen, Lei Zhou, Yu Tao, Jinyu Tian, Zhipeng Xing, Haiyan Wei, and Hongcheng Zhang. "Characteristics of Population Quality and Rice Quality of Semi-Waxy japonica Rice Varieties with Different Grain Yields." Agriculture 12, no. 2 (February 8, 2022): 241. http://dx.doi.org/10.3390/agriculture12020241.
Full textAbstract:
A primary focus of rice breeding and production is the optimization of yield and quality. Currently, semi-waxy japonica rice is widely planted in the middle and lower reaches of the Yangtze River due to its good eating quality and strong reputation among consumers. However, little information is yet available on grain yield formation and rice quality characteristics of these semi-waxy japonica rice varieties with different grain yields. In this study, three high-yielding (HGY) semi-waxy japonica rice varieties and three low-yielding (LGY) semi waxy japonica rice varieties were compared for population quality and rice quality in 2018 and 2019. The average values of spikelet per panicle, 1000-grain weight, and total spikelet number of the HGY varieties were significantly higher than those of the LGY varieties, while the panicle number and filled grain rate showed the opposite. Compared with the LGY varieties, the HGY varieties had a larger leaf area index at each growth stage, with a larger high efficient leaf area composed of a larger leaf length and width and smaller leaf angles of the top three leaves, as well as a greater single stem-sheath weight, more total dry matter accumulation, and longer growth duration from elongating to maturity. There were significant differences in rice quality between the HGY and LGY varieties. Compared with the LGY varieties, the head milled rice rate of the HGY varieties decreased significantly, and the chalky kernel rate and chalkiness degree increased significantly. Due to the low protein content, high peak viscosity, trough viscosity, and final viscosity and breakdown, as well as low setback, consistence, and pasting temperature of the HGY varieties, their taste values were significantly better than those of the LGY varieties. These results suggest that the HGY varieties could achieve a synergistic improvement of grain yield and eating quality, but the milling quality and appearance quality require further improvement.
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Silva, Fabio, Alison Weisskopf, Cristina Castillo, Charlene Murphy, Eleanor Kingwell-Banham, Ling Qin, and Dorian Q. Fuller. "A tale of two rice varieties: Modelling the prehistoric dispersals of japonica and proto-indica rices." Holocene 28, no. 11 (August 7, 2018): 1745–58. http://dx.doi.org/10.1177/0959683618788634.
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We model the prehistoric dispersals of two rice varieties, japonica and proto- indica, across Asia using empirical evidence drawn from an archaeobotanical dataset of 400 sites from mainland East, Southeast and South Asia. The approach is based on regression modelling wherein goodness of fit is obtained from log–log quantile regressions of the archaeologically inferred age versus a least-cost distance from the origin(s) of dispersal. The Fast Marching method is used to estimate the least-cost distances based on simple geographical features. We explicitly test three hypotheses for the arrival of japonica rice to India where, it has been proposed, it hybridized with the indigenous proto- indica, subsequently spreading again throughout India. Model selection, based on information criteria, highlights the role of the Inner Asia Mountain Corridor in introducing japonica rice into northeast India, followed closely by a ‘mixed-route’ model, where japonica was also almost simultaneously introduced via Assam, Bangladesh and Myanmar. Finally, we estimate the impact of future archaeological work on model selection, further strengthening the importance of the Inner Asia Mountain Corridor.
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Sun, Tao, Xin Yang, Sheng Tang, Kefeng Han, Ping He, and Lianghuan Wu. "Genotypic Variation in Nutrient Uptake Requirements of Rice Using the QUEFTS Model." Agronomy 11, no. 1 (December 24, 2020): 26. http://dx.doi.org/10.3390/agronomy11010026.
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Nutrient requirements for single-season rice using the quantitative evaluation of the fertility of tropical soils (QUEFTS) model in China have been estimated in a previous study, which involved all the rice varieties; however, it is unclear whether a similar result can be obtained for different rice varieties. In this study, data were collected from field experiments conducted from 2016 to 2019 in Zhejiang Province, China. The dataset was separated into two parts: japonica/indica hybrid rice and japonica rice. To produce 1000 kg of grain, 13.5 kg N, 3.6 kg P, and 20.4 kg K were required in the above-ground plant dry matter for japonica/indica hybrid rice, and the corresponding internal efficiencies (IEs) were 74.0 kg grain per kg N, 279.1 kg grain per kg P, and 49.1 kg grain per kg K. For japonica rice, 17.6 kg N, 4.1 kg P, and 23.0 kg K were required to produce 1000 kg of grain, and the corresponding IEs were 56.8 kg grain per kg N, 244.6 kg grain per kg P, and 43.5 kg grain per kg K. Field validation experiments indicated that the QUEFTS model could be used to estimate nutrient uptake of different rice varieties. We suggest that variety should be taken into consideration when estimating nutrient uptake for rice using the QUEFTS model, which would improve this model.
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Mackill, D. J., Z. Zhang, E. D. Redoña, and P. M. Colowit. "Level of polymorphism and genetic mapping of AFLP markers in rice." Genome 39, no. 5 (October 1, 1996): 969–77. http://dx.doi.org/10.1139/g96-121.
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Amplified fragment length polymorphism (AFLP) has been proposed as a valuable tool for gene mapping in plant species. We compared the levels of polymorphism for AFLP, RAPD, and microsatellite markers on 12 japonica and 2 indica rice cultivars. For AFLPs, seven EcoRI and seven MseI primers used in 18 primer combinations generated a total of 529 bands, of which 147 were clearly polymorphic among the accessions. The 21 RAPD primers produced 103 bands of which 43 were polymorphic. For the microsatellite markers the number of alleles per locus ranged from one (1 locus) to six. All marker types gave the same classification of the rice accessions into subspecies. Within japonica cultivars, the average percent polymorphism between any two accessions was 22% for AFLP, 24% for RAPD, and 36% for microsatellite markers (monomorphic bands excluded). The average percent polymorphism between indica and japonica accessions was 65, 35, and 76%, for AFLP, RAPD, and microsatellite markers, respectively. The total number of polymorphic bands was much higher for AFLPs, averaging over eight per gel. Seven AFLP primer combinations were assayed on 80 F2 plants of an indica × japonica cross previously mapped with RFLP markers. Of 54 AFLP bands scored, 50 could be mapped to specific chromosomes, and these appeared to be distributed throughout the rice genome. This indicates that AFLPs are a promising marker for mapping important genes in rice. Key words : Oryza sativa, AFLP, genetic mapping, polymorphism.
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Ali, Jauhar, Katrina Leslie C. Nicolas, Shahana Akther, Azerkhsh Torabi, Ali Akbar Ebadi, Corinne M. Marfori-Nazarea, and Anumalla Mahender. "Improved Anther Culture Media for Enhanced Callus Formation and Plant Regeneration in Rice (Oryza sativa L.)." Plants 10, no. 5 (April 22, 2021): 839. http://dx.doi.org/10.3390/plants10050839.
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Anther culture technique is the most viable and efficient method of producing homozygous doubled haploid plants within a short period. However, the practical application of this technology in rice improvement is still limited by various factors that influence culture efficiency. The present study was conducted to determine the effects of two improved anther culture media, Ali-1 (A1) and Ali-2 (A2), a modified N6 medium, to enhance the callus formation and plant regeneration of japonica, indica, and hybrids of indica and japonica cross. The current study demonstrated that genotype and media had a significant impact (p < 0.001) on both callus induction frequency and green plantlet regeneration efficiency. The use of the A1 and A2 medium significantly enhanced callus induction frequency of japonica rice type, Nipponbare, and the hybrids of indica × japonica cross (CXY6, CXY24, and Y2) but not the indica rice type, NSIC Rc480. However, the A1 medium is found superior to the N6 medium as it significantly improved the green plantlet regeneration efficiency of CXY6, CXY24, and Y2 by almost 36%, 118%, and 277%, respectively. Furthermore, it substantially reduced the albino plantlet regeneration of the induced callus in two hybrids (CXY6 and Y2). Therefore, the improved anther culture medium A1 can produce doubled haploid rice plants for indica × japonica, which can be useful in different breeding programs that will enable the speedy development of rice varieties for resource-poor farmers.
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Wang, Qian, Dong Zhang, Jianlei Liu, Bo Shang, Xiaoliang Duan, and Hui Sun. "Storage Drives Alterations of Proteomic and Protein Structural Properties in Rice (Oryza sativa L.)." Foods 11, no. 21 (November 7, 2022): 3541. http://dx.doi.org/10.3390/foods11213541.
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Rice quality changes during storage. However, few studies have reported the difference in protein structure between the indica and japonica varieties of rice during storage. The current research characterized the structural properties of the rice protein, and further investigated the proteomic profiles of Jianzhen 2 (indica rice) and Nanjing 9108 (japonica rice) during storage using the TMT labeling method. A significant reduction in free sulfhydryl content and an increase in disulfide bonds content and surface hydrophobicity were observed in both varieties after storage. The results of FTIR indicated that the changes in the protein’s secondary structure of Nanjing 9108 (japonica rice) were more significant than in Jianzhen 2 (indica rice). A total of 4039 proteins in Nanjing 9108 and 4301 proteins in Jianzhen 2 were identified by TMT-labeled proteomics analysis in this study. Significantly, changes were detected in 831 proteins in Nanjing 9108, while only in 60 proteins in Jianzhen 2. Protein processing in endoplasmic reticulum, starch, and sucrose metabolism were both accelerated in both varieties, while oxidative phosphorylation in mitochondria, glycolysis, fatty acid metabolism, and glutathione metabolism were enhanced in Nanjing 9108 (japonica rice). This study provides insight into the proteomic changes and protein structure in rice induced by storage.
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Yoo, Yo-Han, N. C. Anil Kumar, Jong-Chan Park, Sang-Won Lee, and Ki-Hong Jung. "Global analysis of differentially expressed genes between japonica and indica rice roots reveals the molecular basis for enhanced cold tolerance in japonic a rice." Plant Biotechnology Reports 11, no. 6 (December 2017): 461–73. http://dx.doi.org/10.1007/s11816-017-0466-3.
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Zadorozhna, OA, TP Shyianova, MYu Skorokhodov, and TM Shpak. "Rice (Orysa sativa L.) seed storage under controlled conditions." Genetičnì resursi roslin (Plant Genetic Resources), no. 28 (2021): 109–18. http://dx.doi.org/10.36814/pgr.2021.28.11.
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Viability of rice (Orysa sativa L.) seeds accessions: subsp. japonica: var. italica, var. nigro-apiculata, var. subvulgaris; subsp. indica, var. mutica and var. fortuna was analised. The seed accessions were grown in the southern steppe of Ukraine and then stored at 4°C and −20°C. According to the research results, it is established that rice seeds in favorable cultivation years are able to maintain the original germination without significant changes for 10 years and longer with 6-8% moisture content even at 4°C storage temperature. There were no differences of rice seeds longevity of the same accessions stored at 4°C and −20°C. Differences of rice seed longevity of subsp. japonica and subsp. indica are discussed.
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Jiao, Demao, and Benhua Ji. "Photoinhibition in indica and japonica subspecies of rice (Oryza sativa) and their reciprocal F1 hybrids." Functional Plant Biology 28, no. 4 (2001): 299. http://dx.doi.org/10.1071/pp00089.
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Photoinhibitory performance and its physiological basis have been studied in Oryza sativa L. subspecies indica and japonica, and their reciprocal F1 hybrids. The results demonstrate that the japonica ssp. was usually more tolerant to photoinhibition, indicated by higher maintaining capacity of D1 protein (less degradation), higher induced superoxide dismutase (SOD) activity and longer duration of the activity. Compared with japonica, the indica ssp. was more sensitive to photoinhibition, and exhibited more degradation of D1 protein and a much larger xanthophyll pool. A statistically significant positive correlation exists between D1 protein content and Fv/Fm, PSII activity and Pn during photoinhibition (r2 = 0.98, 0.93, 0.95, respectively, P < 0.01). This result further supported the hypothesis that D1 protein encoded by plastid genes might play an important physiological role in the mechanism of photoinhibition. This hypothesis is also enhanced by the fact that the capacity of D1 protein synthesis mediated the components and cycle of xanthophyll and non-photochemical quenching in treatment with streptomycin, a D1 protein synthesis inhibitor, while the xanthophyll cycle had a photoprotective role for D1 protein and Fv/Fm in treatment with DDT, a xanthophyll cycle inhibitor. The photoinhibition of reciprocal F1 hybrids between japonica and indica is mainly intermediate, but somewhat inclined to the maternal line. This demonstrates that the basic feature of photoinhibition was controlled by the interaction of an intrinsic factor, D1 protein encoded by plastid genes, with the xanthophyll cycle, as well as SOD, controlled by nuclear genes. Since the response to photoinhibitory treatment of indica–japonica F1 hybrids seems to depend on female parents, we propose to select and use photoinhibition-tolerant varieties as female parents for generation of photoinhibition-tolerant hybrids.
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Rakowski, Andrzej Z., Marek Krąpiec, Mathias Huels, Jacek Pawlyta, and Mathieu Boudin. "Increase in Radiocarbon Concentration in Tree Rings from Kujawy Village (Se Poland) Around Ad 993–994." Radiocarbon 60, no. 4 (August 2018): 1249–58. http://dx.doi.org/10.1017/rdc.2018.74.
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ABSTRACTAn increase in atmospheric radiocarbon (14C) content of about 11.3‰ in the period AD 993–994 was observed in annual tree rings from Japanese cedar (Cryptomeria japonica) and Hinoki cypress (Chamaecyparis obtusa) (Miyake et al. 2013, 2014). Single-year samples of dendrochronologically dated tree rings (English oak, Quercus robur) from Kujawy, a village near Krakow (SE Poland), spanning the years AD 981–1000, were collected, and their 14C content was measured using the AMS system in the Leibniz Laboratory. The results clearly show an increase of 6.2±1.6‰ in the 14C concentration in tree rings between AD 993 and 994, with a maximum increase of 10.9±1.7‰ between AD 991 and 994.
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Wu, Zhiguo, Wei Xi, Zixuan Han, Yanhua Wu, Yongzhuo Guan, and Yuxian Zhu. "Genome-Wide Comparative Analysis of Transposable Elements by Matrix-TE Method Revealed Indica and Japonica Rice Evolution." Agronomy 12, no. 7 (June 22, 2022): 1490. http://dx.doi.org/10.3390/agronomy12071490.
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Transposons (TEs) are known to change the gene expression and function, and subsequently cause plant speciation and evolution. Nevertheless, efficient and new approaches are required to investigate the role of TEs in the plant genome structural variations. Here, we reported the method named matrix-TE to investigate the differentiation of intact and truncated LTR/TEs comprehensively in Indica and Japonica rice throughout whole genomes with a special eye on centromeric regions. Six LTR/TE super-families were identified in both Indica and Japonica rice genomes, and the TE ORF references were extracted by phylogenetic analysis. Indica rice specific TE peak P-Gypsy and Japonica rice specific TE peak P-Copia were observed, and were further analyzed by Gaussian probability density function (GPDF) fit. The individual TE peak P-Gypsy was observed in centromeric regions of the Indica genome. By the matrix-TE method, the divergence of Indica and Japonica genomes, especially their centromeric regions, mainly resulted from the Ty3/Gypsy insertion events at 0.77 Mya. Our data indicate that the optimized matrix-TE approach may be used to specifically analyze the TE content, family evolution, and time of the TE insertions.
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Jeong, O.-Young, Jeom-Sig Lee, Maurene Bombay, Gideon Torollo, Thelma Padolina, Rustum Braceros, Lenie Pautin, et al. "A New High quality Japonica Rice Cultivar ‘Japonica 7’ Adaptable to Tropical Region." Journal of the Korean Society of International Agricultue 32, no. 2 (June 30, 2020): 151–57. http://dx.doi.org/10.12719/ksia.2020.32.2.151.
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Jeon, Yun-A., Hyun-Sook Lee, Sun-Ha Kim, Kyu-Chan Shim, Ju-Won Kang, Hyun-Jung Kim, Thomas H. Tai, and Sang-Nag Ahn. "Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster." Journal of Experimental Botany 72, no. 12 (April 8, 2021): 4254–68. http://dx.doi.org/10.1093/jxb/erab155.
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Abstract We previously identified a cluster of yield-related quantitative trait loci (QTLs) including plant height in CR4379, a near-isogenic line from a cross between Oryza sativa spp. japonica cultivar ‘Hwaseong’ and the wild relative Oryza rufipogon. Map-based cloning and transgenic approaches revealed that APX9, which encodes an l-ascorbate peroxidase 4, is associated with this cluster. A 3 bp InDel was observed leading to the addition of a valine in Hwaseong compared with O. rufipogon. APX9-overexpressing transgenic plants in the Hwaseong background were taller than Hwaseong. Consistent with these results, APX9 T-DNA insertion mutants in the japonica cultivar Dongjin were shorter. These results confirm that APX9 is the causal gene for the QTL cluster. Sequence analysis of APX9 from 303 rice accessions revealed that the 3 bp InDel clearly differentiates japonica (APX9HS) and O. rufipogon (APX9OR) alleles. indica accessions shared both alleles, suggesting that APX9HS was introgressed into indica followed by crossing. The finding that O. rufipogon accessions with different origins carry APX9OR suggests that the 3 bp insertion was specifically selected in japonica during its domestication. Our findings demonstrate that APX9 acts as a major regulator of plant development by controlling a valuable suite of agronomically important traits in rice.
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Molina-Risco, Marco, Oneida Ibarra, Mayra Faion-Molina, Backki Kim, Endang M. Septiningsih, and Michael J. Thomson. "Optimizing Agrobacterium-Mediated Transformation and CRISPR-Cas9 Gene Editing in the tropical japonica Rice Variety Presidio." International Journal of Molecular Sciences 22, no. 20 (October 9, 2021): 10909. http://dx.doi.org/10.3390/ijms222010909.
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Bottlenecks in plant transformation and regeneration have slowed progress in applying CRISPR/Cas-based genome editing for crop improvement. Rice (Oryza sativa L.) has highly efficient temperate japonica transformation protocols, along with reasonably efficient indica protocols using immature embryos. However, rapid and efficient protocols are not available for transformation and regeneration in tropical japonica varieties, even though they represent the majority of rice production in the U.S. and South America. The current study has optimized a protocol using callus induction from mature seeds with both Agrobacterium-mediated and biolistic transformation of the high-yielding U.S. tropical japonica cultivar Presidio. Gene editing efficiency was tested by evaluating knockout mutations in the phytoene desaturase (PDS) and young seedling albino (YSA) genes, which provide a visible phenotype at the seedling stage for successful knockouts. Using the optimized protocol, transformation of 648 explants with particle bombardment and 532 explants with Agrobacterium led to a 33% regeneration efficiency. The YSA targets had ambiguous phenotypes, but 60% of regenerated plants for PDS showed an albino phenotype. Sanger sequencing of edited progeny showed a number of insertions, deletions, and substitutions at the gRNA target sites. These results pave the way for more efficient gene editing of tropical japonica rice varieties.
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Shahbaz Farooq, Muhammad, Amatus Gyilbag, Ahmad Latif Virk, and Yinlong Xu. "Adaptability Mechanisms of Japonica Rice Based on the Comparative Temperature Conditions of Harbin and Qiqihar, Heilongjiang Province of Northeast China." Agronomy 11, no. 11 (November 22, 2021): 2367. http://dx.doi.org/10.3390/agronomy11112367.
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Japonica rice has been considerably impacted from climate change, mainly regarding temperature variations. Adjusting the crop management practices based on the assessment of adaptability mechanisms to take full advantage of climate resources during the growing season is an important technique for japonica rice adaptation to climate changed conditions. Research based on the adaptability mechanisms of japonica rice to temperature and other environmental variables has theoretical and practical significance to constitute a theoretical foundation for sustainable japonica rice production system. A contrived study was arranged with method of replacing time with space having four different japonica cultivars namely Longdao-18, Longdao-21, Longjing-21, and Suijing-18, and carried out in Harbin and Qiqihar during the years 2017–2019 to confer with the adaptability mechanisms in terms of growth, yield and quality. The formation of the grain-filling material for superior and inferior grains was mainly in the middle phase which shared nearly 60% of whole grain-filling process. Maximum yield was noticed in Longdao-18 at Harbin and Qiqihar which was 9500 and 13,250 kg/ha, respectively. The yield contributing components fertile tillers, number of grains per panicle, and 1000-grain weight were higher at Qiqihar; therefore, there was more potential to get higher yield. The data for grain-filling components demonstrated that the filling intensity and duration at Qiqihar was contributive to increase the grain yield, whereas the limiting agents to limit yield at Harbin were the dry weights of inferior grains. The varietal differences in duration and time of day of anthesis were small. Across all cultivars and both study sites, nearly 85% of the variation of the maximum time of anthesis could be justified with mean atmospheric temperature especially mean minimum temperature. Mean onset of anthesis was earliest in Longdao-21 at Harbin, whereas it was latest in Longdao-18 at Qiqihar. The maximum time to end anthesis and the longest duration of anthesis were taken by Longdao-18, i.e., 9.0 hasr and 4.2 h, respectively. Chalkiness and brown rice percentages were elevated at Qiqihar showing Harbin produced good quality rice. This study investigated the adaptability mechanisms of japonica rice under varying temperature conditions to distinguish the stress tolerance features for future sustainability and profitability in NEC. It was concluded that there is an adaptive value for anthesis especially regarding Tmin and, moreover, earlier transplantation may produce tall plants. The results demonstrated that high temperature at the onset of anthesis at the start of the day enhanced the escape from high temperature later during the day. Early transplantation is recommended in NEC because earlier anthesis during humid days rendered for potential escape from high ambient temperature later during that day. Temperature influenced japonica rice significantly and coherently, whereas the influence of growing season precipitation was not significant. Daily mean sunshine influenced the japonica rice significantly, but the impact was less spatially coherent. The results foregrounded the response of the japonica rice to external driving factors focusing climate, but ignored socioeconomic suggesting emphasis on both driving factors to target future research and render important insights into how japonica rice can adapt in mid-high-latitude regions.
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Jia, Yulin, Gregory T. Bryan, Leonard Farrall, and Barbara Valent. "Natural Variation at the Pi-ta Rice Blast Resistance Locus." Phytopathology® 93, no. 11 (November 2003): 1452–59. http://dx.doi.org/10.1094/phyto.2003.93.11.1452.
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The resistance gene Pi-ta protects rice crops against the fungal pathogen Magnaporthe grisea expressing the avirulence gene AVR-Pita in a gene-for-gene manner. Pi-ta, originally introgressed into japonica rice from indica origin, was previously isolated by positional cloning. In this study, we report the nucleotide sequence of a 5,113-base pair region containing a japonica susceptibility pi-ta allele, which has overall 99.6% nucleotide identity to the indica Pi-ta allele conferring resistance. The intron region shows the levels of sequence diversity that typically differentiate genes from indica and japonica rices, but the other gene regions show less diversity. Sequences of the Pi-ta allele from resistant cultivars Katy and Drew from the southern United States are identical to the resistance Pi-ta sequence. Sequences from susceptible cultivars El Paso 144 and Cica 9 from Latin America define a third susceptibility haplotype. This brings the total number of Pi-ta haplotypes identified to four, including the resistance allele and three susceptibility alleles. The Pi-ta locus shows low levels of DNA polymorphism compared with other analyzed R genes. Understanding the natural diversity at the Pi-ta locus is important for designing specific markers for incorporation of this R gene into rice-breeding programs.