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Journal articles on the topic 'Oryza sativa japonica'

Author: Grafiati

Published: 18 April 2022

Last updated: 30 July 2025

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1

Kim, Bongsong. "Classifying Oryza sativa accessions into Indica and Japonica using logistic regression model with phenotypic data." PeerJ 7 (November 7, 2019): e7259. http://dx.doi.org/10.7717/peerj.7259.

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In Oryza sativa, indica and japonica are pivotal subpopulations, and other subpopulations such as aus and aromatic are considered to be derived from indica or japonica. In this regard, Oryza sativa accessions are frequently viewed from the indica/japonica perspective. This study introduces a computational method for indica/japonica classification by applying phenotypic variables to the logistic regression model (LRM). The population used in this study included 413 Oryza sativa accessions, of which 280 accessions were indica or japonica. Out of 24 phenotypic variables, a set of seven phenotypic

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2

Long, Weixiong, Yonghui Li, Zhengqing Yuan, et al. "Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing." PLOS ONE 17, no. 10 (2022): e0274418. http://dx.doi.org/10.1371/journal.pone.0274418.

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Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining. However, only a few whole-genome variation analyses have been performed in Oryza sativa ssp. Javanica (tropical japonica rice), and this has hampered the utilization of such an important resource. In this study

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3

Uhrinová, A., and N. Poľančíková. "Antioxidant Activity of the Fungus Cordyceps sinensis Grown on Two Different Media." Folia Veterinaria 62, no. 3 (2018): 68–73. http://dx.doi.org/10.2478/fv-2018-0030.

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Abstract Cordyceps sinensis, a species of the genus Ascomycetes, is recognised as the most famous tonic herb and natural remedy in traditional Chinese medicine for centuries. Various pharmacological actions of the chemical constituents of C. sinensis have been reported, including: antitumour effects, hepatoprotective and anti-inflammatory effects, and antioxidant, nephroprotective and anti-apoptotic properties. In this study we tested the antioxidant activity of extracts of the fungus C. sinensis grown on two subspecies of rice, Oryza sativa var. Indica and Oryza sativa var. Japonica. The extr

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4

Zhou, Mingao, Yifei Jiang, Xuhui Liu, et al. "Genome-Wide Identification and Evolution Analysis of the CYP76 Subfamily in Rice (Oryza sativa)." International Journal of Molecular Sciences 24, no. 10 (2023): 8522. http://dx.doi.org/10.3390/ijms24108522.

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The CYP76 subfamily, a member of the CYP superfamily, plays crucial roles in the biosynthesis of phytohormones in plants, involving biosynthesis of secondary metabolites, hormone signaling, and response to environmental stresses. Here, we conducted a genome-wide analysis of the CYP76 subfamily in seven AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, and Oryza glumaepatula. These were identified and classified into three groups, and it was found that Group 1 contained the largest number of members. An

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5

Nascimento, Silva dos Passos Kévila Kelma, and de Morais Jéssica Santana. "POR QUE A CASCA DA BANANA ESCURECE? UMA ANÁLISE GENÉTICA E FILOGENÉTICA DO GENE EIL1 NA REGULAÇÃO DO AMADURECIMENTO DA BANANA MUSA ACUMINATA SUBSP. MALACCENSIS." I ENCONTRO REGIONAL DE CIÊNCIAS AGRÁRIAS 01 (September 20, 2024): 11. https://doi.org/10.5281/zenodo.13800561.

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Este estudo foca na análise filogenética e genética do gene EIL1 (ETHYLENE INSENSITIVE3-like 1 protein) em Musa acuminata e em outras espécies de plantas, utilizando dados do bancode dados NCBI e ferramentas de bioinformática. O objetivo principal é compreender o grau deparentesco e os processos evolutivos relacionados ao gene EIL1 e ao gene 18S. O alinhamentodas sequências revelou que Musa acuminata compartilha sinapomorfias com Arabidopsisthaliana e Solanum lycopersicum, enquanto Oryza sativa subsp. japonica está mais distante,indicando

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6

Lee, Yoo-Jin, Michael J. Thomson, and Joong Hyoun Chin. "Application of indica–japonica single-nucleotide polymorphism markers for diversity analysis of Oryza AA genome species." Plant Genetic Resources 12, S1 (2014): S36—S40. http://dx.doi.org/10.1017/s1479262114000215.

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High-throughput genotyping using single-nucleotide polymorphisms (SNP) is one tool that can be used to study the genetic relationships between wild rice relatives and cultivated rice. In this study, a set of 96 indica–japonica SNP markers, which can differentiate indica and japonica subspecies of rice, were used to characterize 227 Oryza accessions including 93 AA genome accessions from seven wild Oryza species. A total of 72 markers of the 96 markers were selected for the phylogenetic study and allele polymorphism survey. A subset of SNP markers were present only in Oryza sativa and evolution

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7

GAO, LI-ZHI, CHI-HONG ZHANG, LI-PING CHANG, JI-ZENG JIA, ZONG-EN QIU, and YU-SHEN DONG. "Microsatellite diversity within Oryza sativa with emphasis on indica–japonica divergence." Genetical Research 85, no. 1 (2005): 1–14. http://dx.doi.org/10.1017/s0016672304007293.

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The molecular evolution of cultivated rice Oryza sativa L. has long been a subject of rice evolutionists. To investigate genetic diversity within and differentiation between the indica and japonica subspecies, 22 accessions of indica and 35 of japonica rice were examined by five microsatellite loci from each chromosome totalling 60 loci. Mean gene diversity value in the indica rice (H=0·678) was 1·18 times larger than in the japonica rice (H=0·574). Taking the sampling effect into consideration, average allele number in the indica rice was 1·40 times higher than that in the japonica rice (14·6

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8

Grover, Anil, and Deepak Pental. "Interrelationships of Oryza species based on electrophoretic patterns of alcohol dehydrogenase." Canadian Journal of Botany 70, no. 2 (1992): 352–58. http://dx.doi.org/10.1139/b92-047.

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Nineteen different species belonging to the genus Oryza were studied for variation in electrophoretic patterns of alcohol dehydrogenase (ADH) extracted from germinating seeds. The ADH patterns were similar for aerobically and anaerobically germinating seeds of all the species. Oryza saliva accessions, both indica and japonica, revealed a five-band pattern on polyacrylamide gels. African cultivated rice, Oryza glaberrima, had an alcohol dehydrogenase pattern similar to that of O. sativa. Oryza perennis complex comprising of Oryza nivara, Oryza rufipogon in Asia, Oryza barthii, Oryza longistamin

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9

Lu, Yingqing. "Gene Genealogy-Based Mutation Analysis Reveals Emergence of Aus, Tropical japonica, and Aromatic of Oryza sativa during the Later Stage of Rice Domestication." Genes 14, no. 7 (2023): 1412. http://dx.doi.org/10.3390/genes14071412.

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Asian rice (Oryza sativa L.) has become a model for understanding gene functions and domestication in recent decades; however, its own diversification is still controversial. Although the division of indica and japonica and five subgroups (aus, indica (sensu stricto), japonica (sensu stricto), tropical japonica, and aromatic) are broadly accepted, how they are phylogenetically related is not transparent. To clarify their relationships, a sample of 121 diverse genes was chosen here from 12 Oryza genomes (two parental and ten O. sativa (Os)) in parallel to allow gene genealogy-based mutation (GG

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10

Li, Li, Che Wang, Qian Liang, Dian Rong Ma, and Wen Fu Chen. "Microtubules Dynamics Regulates Mesocotyl Elongation in Rice." Applied Mechanics and Materials 513-517 (February 2014): 4277–80. http://dx.doi.org/10.4028/www.scientific.net/amm.513-517.4277.

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Mesocotyl elongation in rice is essential for seedling emergence. Our previous screening identified weedy rice accessions (Oryza sativa f. spontanea L.) (WR04-6) with unusual long mesocotyl. In this study, using rice cultivar Akihikari (Oryza sativa, subspecies japonica) as control, we observed that weedy rice accessions display more extensive microtubules (MTs) depolymerization in the early stage of mesocotyl elongation. At the end of mesocotyl elongation, the predominant MTs in weedy rice are transversely oriented, while, Akihikari has oblique MTs arrays.

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11

Liu, K. D., Qifa Zhang, G. P. Yang, M. A. Saghai Maroof, S. H. Zhu, and X. M. Wang. "Extraordinarily polymorphic ribosomal DNA in wild and cultivated rice." Genome 39, no. 6 (1996): 1109–16. http://dx.doi.org/10.1139/g96-139.

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A collection of 481 rice accessions was surveyed for ribosomal DNA (rDNA) intergenic spacer length polymorphism to assess the extent of genetic diversity in Chinese and Asian rice germplasm. The materials included 83 accessions of common wild rice, Oryza rufipogon, 75 of which were from China; 348 entries of cultivated rice (Oryza sativa), representing almost all the rice growing areas in China; and 50 cultivars from South and East Asia. A total of 42 spacer length variants (SLVs) were detected. The size differences between adjacent SLVs in the series were very heterogeneous, ranging from ca.

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12

Ingle, P. B., S. S. Rokade, and R. V. Raut. "Review on double haploid in rice plant (Oryza sativa L.)." NewBioWorld 5, no. 1 (2023): 1–4. http://dx.doi.org/10.52228/nbw-jaab.2023-5-1-1.

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Rice (Oryza sativa L.) is an important and indigenous crop in India. Rice is a plant belonging to the family of grasses, Gramineae (Poaceae). It is a major food crop of the world and forms the staple diet of about half of the world's population. Rice is repeatedly mentioned in ancient Indian texts, including the Yajur Veda. The area under cultivation of rice in India is 45416 thousand hectare, Total production of Rice during 2020-21 is estimated at record 122.27 million tonnes. Two major Asian cultivated varieties of rice have been historically recognized as japonica and indica subspecies. Jap

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13

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 (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

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14

Maľučká, Lucia Ungvarská, Anna Uhrinová, and Patricia Lysinová. "Medicinal mushrooms Ophiocordyceps sinensis and Cordyceps militaris." Česká a slovenská farmacie 71, no. 6 (2022): 259–65. http://dx.doi.org/10.5817/csf2022-5-259.

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The main component of Ophiocordyceps sinensis and Cordyceps militaris extracts are polysaccharides. These are natural biopolymers that represent a large class of biologically active components. These contribute to their pharmacological activity and effect on health. They contain monosaccharides that include rhamnose, ribose, arabinose, xylose, mannose, glucose, galactose, mannitol, fructose, and sorbose. The exopolysaccharide fraction has a large number of pharmacological effects, the two most important of which are immunomodulatory and antitumour. Among the contained polysaccharides is also m

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15

Maľučká, Lucia Ungvarská, Anna Uhrinová, and Patricia Lysinová. "Medicinal mushrooms Ophiocordyceps sinensis and Cordyceps militaris." Česká a slovenská farmacie 71, no. 6 (2022): 259–65. http://dx.doi.org/10.5817/csf2022-6-259.

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The main component of Ophiocordyceps sinensis and Cordyceps militaris extracts are polysaccharides. These are natural biopolymers that represent a large class of biologically active components. These contribute to their pharmacological activity and effect on health. They contain monosaccharides that include rhamnose, ribose, arabinose, xylose, mannose, glucose, galactose, mannitol, fructose, and sorbose. The exopolysaccharide fraction has a large number of pharmacological effects, the two most important of which are immunomodulatory and antitumour. Among the contained polysaccharides is also m

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16

Ishii, Takashige, and Koichiro Tsunewaki. "Chloroplast genome differentiation in Asian cultivated rice." Genome 34, no. 5 (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

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17

Yuan, Zhengqing, Weixiong Long, Haifei Hu, et al. "Genome-Wide Identification and Expansion Patterns of SULTR Gene Family in Gramineae Crops and Their Expression Profiles under Abiotic Stress in Oryza sativa." Genes 12, no. 5 (2021): 634. http://dx.doi.org/10.3390/genes12050634.

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Sulfate transporters (SULTRs), also known as H+/SO42− symporters, play a key role in sulfate transport, plant growth and stress responses. However, the evolutionary relationships and functional differentiation of SULTRs in Gramineae crops are rarely reported. Here, 111 SULTRs were retrieved from the genomes of 10 Gramineae species, including Brachypodium disachyon, Hordeum vulgare, Setaria italica, Sorghum bicolor, Zea mays, Oryza barthii, Oryza rufipogon, Oryza glabbermia and Oryza sativa (Oryza sativa ssp. indica and Oryza sativa ssp. japonica). The SULTRs were clustered into five clades bas

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18

Roma-Burgos, Nilda, Maggie Pui San Sudo, Kenneth M. Olsen, Isabel Werle, and Beng-Kah Song. "Weedy rice (Oryza spp.): what’s in a name?" Weed Science 69, no. 5 (2021): 505–13. http://dx.doi.org/10.1017/wsc.2021.22.

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AbstractThere are two species of cultivated rice in the world—Oryza sativa L. from Asia and Oryza glaberrima Steud. from Africa. The former was domesticated from the wild progenitor Oryza rufipogon Griff. and the latter from the African wild rice species Oryza barthii A. Shiv. The first known center of rice cultivation in China generated the O. sativa subspecies japonica. The indica subspecies arose from the second center of domestication in the Ganges River plains of India. Variants of domesticated lines and the continuous hybridization between cultivated varieties and the wild progenitor(s)

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19

Ilias, Iqmal Asyraf, Alina Wagiran, Kamalrul Azlan Azizan, and Abdul Fatah A. Samad. "Expression Analysis of OsWRKY11 and OsNAC2 Genes in New Malaysian Drought-tolerance Rice Cultivar MR303." Malaysian Journal of Fundamental and Applied Sciences 18, no. 6 (2022): 693–702. http://dx.doi.org/10.11113/mjfas.v18n6.2717.

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Local drought-tolerant rice variety MR303 (Oryza sativa spp. Indica) has higher tolerance towards abiotic stress while maintaining its high yield and grain quality. Expression of OsWRKY11 has shown to be a positive modulator while OsNAC2 is a negative modulator for drought-tolerance in Oryza sativa spp. Japonica. However, these transcription factor (TF) genes regulation are species-specific and its regulation may differ in our local rice variety. Thus, our study aimed to identify the relative expression of these genes and its effects on plant morphology and drought-tolerance capabilities. Our

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20

Kong, Weilong, Hua Zhong, Xiaoxiao Deng, et al. "Evolutionary Analysis of GH3 Genes in Six Oryza Species/Subspecies and Their Expression under Salinity Stress in Oryza sativa ssp. japonica." Plants 8, no. 2 (2019): 30. http://dx.doi.org/10.3390/plants8020030.

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Glycoside Hydrolase 3 (GH3), a member of the Auxin-responsive gene family, is involved in plant growth, the plant developmental process, and various stress responses. The GH3 gene family has been well-studied in Arabidopsis thaliana and Zea mays. However, the evolution of the GH3 gene family in Oryza species remains unknown and the function of the GH3 gene family in Oryza sativa is not well-documented. Here, a systematic analysis was performed in six Oryza species/subspecies, including four wild rice species and two cultivated rice subspecies. A total of 13, 13, 13, 13, 12, and 12 members were

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21

Xu, Fenghua, Chengming Fan, and Yueqiu He. "Chitinases in Oryza sativa ssp. japonica and Arabidopsis thaliana." Journal of Genetics and Genomics 34, no. 2 (2007): 138–50. http://dx.doi.org/10.1016/s1673-8527(07)60015-0.

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22

Liang, Dong, Junjie Yu, Tianqiao Song, et al. "Genome-Wide Prediction and Analysis of Oryza Species NRP Genes in Rice Blast Resistance." International Journal of Molecular Sciences 23, no. 19 (2022): 11967. http://dx.doi.org/10.3390/ijms231911967.

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Members of the N-rich proteins (NRPs) gene family play important roles in the plant endoplasmic reticulum stress in response, which can be triggered by plant pathogens’ infection. Previous studies of the NRP gene family have been limited to only a few plants, such as soybean and Arabidopsis thaliana. Thus, their evolutionary characteristics in the Oryza species and biological functions in rice defense against the pathogenic fungus Magnaporthe oryzae have remained unexplored. In the present study, we demonstrated that the NRP genes family may have originated in the early stages of plant evoluti

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23

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 (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 use

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Jiang, Yifei, Xuhui Liu, Mingao Zhou, Jian Yang, Simin Ke, and Yangsheng Li. "Genome-Wide Identification of the AGC Protein Kinase Gene Family Related to Photosynthesis in Rice (Oryza sativa)." International Journal of Molecular Sciences 23, no. 20 (2022): 12557. http://dx.doi.org/10.3390/ijms232012557.

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The cAMP-dependent protein kinase A, cGMP-dependent protein kinase G and phospholipid-dependent protein kinase C (AGC) perform various functions in plants, involving growth, immunity, apoptosis and stress response. AGC gene family is well described in Arabidopsis, however, limited information is provided about AGC genes in rice, an important cereal crop. This research studied the AGC gene family in the AA genome species: Oryza sativa ssp. japonica, Oryza sativa ssp. indica, Oryza nivara, Oryza rufipogon, Oryza glaberrima, Oryza meridionalis, Oryza barthii, Oryza glumaepatula and Oryza longista

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Lathif, Yudrik, Riri Wiyanti Retnaningtyas, Dwi Listyorini, and Suharti Suharti. "Berlian, SOJ A3 and Jawa Local Rice Varieties Phylogenetically Distinct From Oryza sativa Indica and Oryza sativa Japonica." El-Hayah 6, no. 4 (2019): 112–25. http://dx.doi.org/10.18860/elha.v6i4.5883.

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The genetic resources identification of Indonesian local rice varieties is a crucial work should be done to conserve our native germplasm. This research aimed to know the taxonomical position of East Java local rice varieties including Jawa (JW), Berlian (BR), and SOJ A3 (SJ) using DNA barcode based on rbcL gene. Total DNA of each sample was isolated from leaves. A pair of forward 5'-ATG TCA CCA CAA ACA SJA AC-3' and reverse 5'-TCG GTA CCT GCA GTA GC-3' primers were used to amplify fragments of rbcL gene resulting in 751bp, 755bp, and 754bp fragments from BR, SJ, and JW varieties, respectively

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Wu, Yunyu, Yu Chen, Cunhong Pan, et al. "Development and Evaluation of Near-Isogenic Lines with Different Blast Resistance Alleles at the Piz Locus in japonica Rice from the Lower Region of the Yangtze River, China." Plant Disease 101, no. 7 (2017): 1283–91. http://dx.doi.org/10.1094/pdis-12-16-1855-re.

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Rice blast, caused by Magnaporthe oryzae, threatens rice production in most of the rice-growing areas in China, especially in regions that have grown Oryza sativa subsp. japonica in recent years. The use of resistance genes is the most effective and economical approach for blast control. In our study, a set of six near-isogenic lines (NIL) were developed by introgression of six resistance alleles of the Piz locus (Pi2, Pigm, Pi40, Pi9, Piz, and Pizt) into a blast-susceptible, high-yielding, high-quality japonica ‘07GY31’ via marker-assisted backcross breeding. Artificial inoculation using 144

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Feng, Qi, Wei-Cai Song, Yun-Jiao Zhang, and Chao Shi. "The complete chloroplast genome sequence of Oryza sativa Temperate japonica." Mitochondrial DNA Part B 6, no. 3 (2021): 927–28. http://dx.doi.org/10.1080/23802359.2021.1888331.

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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 (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 i

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Tohno, Masanori, Maki Kitahara, Tomohiro Irisawa, et al. "Lactobacillus oryzae sp. nov., isolated from fermented rice grain (Oryza sativa L. subsp. japonica)." International Journal of Systematic and Evolutionary Microbiology 63, Pt_8 (2013): 2957–62. http://dx.doi.org/10.1099/ijs.0.048918-0.

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The taxonomic position of three Lactobacillus -like micro-organisms (strains SG293T, SG296 and SG310) isolated from fermented rice grain (Oryza sativa L. subsp. japonica) in Japan was investigated. These heterofermentative lactic acid bacteria were Gram-stain-positive, rod-shaped, facultatively anaerobic, non-motile, non-spore-forming and did not show catalase activity. 16S rRNA gene sequence analysis of strain SG293T revealed that the type strains of Lactobacillus malefermentans (98.3 %), Lactobacillus odoratitofui (96.2 %), Lactobacillus similis (96.1 %), Lactobacillus kimchicus (96.1 %), La

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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 (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 percentag

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Klees, Selina, Felix Heinrich, Armin Otto Schmitt, and Mehmet Gültas. "agReg-SNPdb-Plants: A Database of Regulatory SNPs for Agricultural Plant Species." Biology 11, no. 5 (2022): 684. http://dx.doi.org/10.3390/biology11050684.

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Single nucleotide polymorphisms (SNPs) that are located in the promoter regions of genes and affect the binding of transcription factors (TFs) are called regulatory SNPs (rSNPs). Their identification can be highly valuable for the interpretation of genome-wide association studies (GWAS), since rSNPs can reveal the biologically causative variant and decipher the regulatory mechanisms behind a phenotype. In our previous work, we presented agReg-SNPdb, a database of regulatory SNPs for agriculturally important animal species. To complement this previous work, in this study we present the extensio

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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 significan

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Kameswara Rao, N., and M. T. Jackson. "Seed production environment and storage longevity of japonica rices (Oryza sativa L.)." Seed Science Research 6, no. 1 (1996): 17–21. http://dx.doi.org/10.1017/s0960258500002956.

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AbstractChanges in seed dry weight, moisture content and germinability of three japonica cultivars of rice during development and maturation in the dry season (November–May) field multiplication at Los Baños, Philippines were compared with those in a cooler controlled environment (24°/18°C). Under field conditions, maximum dry weight accumulation, which indicates mass maturity, was attained 18–21 days after flowering in all cultivars. In the cooler environment however, mass maturity was achieved 21 days after flowering in Fujisaka 5 and Minehikare, and 28 days in Shuang cheng nuo. The moisture

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Biselli, Chiara, Andrea Volante, Francesca Desiderio, et al. "GWAS for Starch-Related Parameters in Japonica Rice (Oryza sativa L.)." Plants 8, no. 8 (2019): 292. http://dx.doi.org/10.3390/plants8080292.

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Rice quality is mainly related to the following two starch components, apparent amylose content (AAC) and resistant starch (RS). The former affects grain cooking properties, while RS acts as a prebiotic. In the present study, a Genome Wide Association Scan (GWAS) was performed using 115 rice japonica accessions, including tropical and temperate genotypes, with the purpose of expanding the knowledge of the genetic bases affecting RS and AAC. High phenotypic variation was recorded for the two traits, which positively correlated. Moreover, both the parameters correlated with seed length (positive

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Lee, David, Elisabetta Lupotto, and Wayne Powell. "G-string slippage turns white rice red." Genome 52, no. 5 (2009): 490–93. http://dx.doi.org/10.1139/g09-025.

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The mutations that convey the white pericarp phenotype to rice ( Oryza sativa subsp. japonica) are in a regulatory gene, Rc. We have identified a genetic difference between the cultivar ‘Perla’ and its natural red rice mutant ‘Perla Rosso’ in the Rc gene. The deletion of a G base restores the reading frame for the Rc gene, lost by the original 14 bp deletion that gave rise to white rice.

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Nadarajah, Kalaivani, and Grace Kai Lee Law. "Meneroka Keluarga Gen WRKY dalam Tanaman Bijirin." Semarak Proceedings of Natural and Environmental Sciences 1, no. 1 (2025): 1–5. https://doi.org/10.37934/spnes.1.1.15a.

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Kajian ini meneliti gen WRKY dalam tanaman bijirin yang berperanan penting dalam tindak balas terhadap tekanan abiotik dan biotik. Dengan menggunakan 26 jujukan gen WRKY dari spesies seperti Oryza sativa (Japonica Group), Glycine max, Sorghum bicolor, dan Zea mays, kajian ini mengkaji motif dan domain yang berkaitan dengan tindak balas terhadap tekanan menggunakan alat bioinformatik seperti MEME dan Mega11. Analisis mengenal pasti 10 motif utama, termasuk motif terpulihara dalam semua gen WRKY. Analisis filogeni menunjukkan pengelompokkan gen WRKY adalah berdasarkan spesies tanaman. Kajian ini

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Jeon, Yun-A., Hyun-Sook Lee, Sun-Ha Kim, et al. "Natural variation in rice ascorbate peroxidase gene APX9 is associated with a yield-enhancing QTL cluster." Journal of Experimental Botany 72, no. 12 (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 w

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Ali, Jauhar, Katrina Leslie C. Nicolas, Shahana Akther, et al. "Improved Anther Culture Media for Enhanced Callus Formation and Plant Regeneration in Rice (Oryza sativa L.)." Plants 10, no. 5 (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

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vonHoldt, Bridgett M., Shohei Takuno, and Brandon S. Gaut. "Recent Retrotransposon Insertions Are Methylated and Phylogenetically Clustered in Japonica Rice (Oryza sativa spp. japonica)." Molecular Biology and Evolution 29, no. 10 (2012): 3193–203. http://dx.doi.org/10.1093/molbev/mss129.

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Li, Zi-Yin, Shou-Yi Chen, Xian-Wu Zheng, and Li-Huang Zhu. "Identification and chromosomal localization of a transcriptionally active retrotransposon of Ty3-gypsy type in rice." Genome 43, no. 2 (2000): 404–8. http://dx.doi.org/10.1139/g99-137.

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A DNA fragment representing a transcriptionally active retrotransposon of Ty3-gypsy type was isolated and characterized from rice (Oryza sativa L.). The fragment (named RIRE9) includes the coding sequences for the C-terminal part of the RNase H domain and the N-terminal part of the integrase domain in the polyprotein region. Northern blot hybridization indicated that this element was expressed in rice leaves and stems, suggesting that it is potentially active to transpose under normal growth conditions. Using dot-blot hybridization, the copy number of RIRE9 was estimated to be about 1600 copie

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Hong, Fang, Kotb Attia, Chun Wei, et al. "Overexpression of the rFCA RNA Recognition Motif Affects Morphologies Modifications in Rice (Oryza sativa L.)." Bioscience Reports 27, no. 4-5 (2007): 225–34. http://dx.doi.org/10.1007/s10540-007-9047-y.

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RNA recognition motifs as important regulators of gene expression are highly conserved in animals and plants. The FCA floral promotion gene in Arabidopsis encodes a protein, containing two RNA recognition motifs (RRM) and a WW protein interaction domain. Here we isolated FCA cDNA from rice. FCA in rice (rFCA) was homologous to FCA-gamma of Arabidopsis and contained conserved domains. To investigate the function of RRM domain, fragment RRM1 and RRM2 of rFCA were introduced into rice subspecies Oryza sativa L. subsp. Indica var. 9311 and another rice subspecies Oryza sativa L. subsp. Japonica va

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Serrat, X., M. Cardona, J. Gil, et al. "A Mediterranean japonica rice (Oryza sativa) cultivar improvement through anther culture." Euphytica 195, no. 1 (2013): 31–44. http://dx.doi.org/10.1007/s10681-013-0955-6.

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Shih, Ming-Kuei, Qiao-Yu Hsu, Bo-Kang Liou, Yu-Han Peng, and Chih-Yao Hou. "Deep Ocean Water Concentrate Changes Physicochemical Characteristics, the Profile of Volatile Components and Consumer Acceptance for Taiwanese Rice Shochu." Foods 9, no. 12 (2020): 1806. http://dx.doi.org/10.3390/foods9121806.

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To study the effects of deep-ocean water concentrate (DOWC) on sake quality, Taichung No. 10 indica rice (Oryza sativa subsp. indica) and Tainan No. 11 japonica rice (O. sativa subsp. japonica) were used as raw materials, and basic physicochemical property parameters in shochu were analyzed differentially. Sake fermentation mash analysis results revealed that DOWC addition did not significantly affect the basic physicochemical properties during sake brewing, but it significantly reduced citric acid and malic acid contents in Taichung No. 10 indica rice sake sample by 52–66% and 73–93%, respect

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Courtois, Brigitte, Raffaella Greco, Gianluca Bruschi, et al. "Molecular characterization of the European rice collection in view of association mapping." Plant Genetic Resources 9, no. 2 (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 low

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Redoña, Edilberto D., and David J. Mackill. "Molecular mapping of quantitative trait loci in japonica rice." Genome 39, no. 2 (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 fun

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Fongfon, Suksan, Tonapha Pusadee, Chanakan Prom-u-thai, Benjavan Rerkasem, and Sansanee Jamjod. "Diversity of Purple Rice (Oryza sativa L.) Landraces in Northern Thailand." Agronomy 11, no. 10 (2021): 2029. http://dx.doi.org/10.3390/agronomy11102029.

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Purple rice is a functional food with health benefits and industrial potentials. In northern Thailand, purple rice landraces are grown either as wetland or upland rice, in the lowlands and highlands, in small amounts along with the staple rice. This study examined diversity of 37 accessions of purple rice collected from farmers with InDel cytoplasm markers for subspecies differentiation, 16 SSRs markers for within and between accessions variation, and selected grain quality features, namely, anthocyanin, iron, zinc, and gamma oryzanol content, when grown together as wetland rice. Most of the p

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Xu, Z., S. Rafi, and W. Ramakrishna. "Polymorphisms and evolutionary history of retrotransposon insertions in rice promoters." Genome 54, no. 8 (2011): 629–38. http://dx.doi.org/10.1139/g11-030.

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Retrotransposons are ubiquitous in higher plant genomes. The presence or absence of retrotransposons in whole genome and high throughput genomic sequence (HTGS) from cultivated and wild rice was investigated to understand the organization and evolution of retrotransposon insertions in promoter regions. Approximately half of the Oryza sativa subsp. japonica ‘Nipponbare’ promoters with retrotransposons conserved in Oryza sativa subsp. indica ‘93-11’ and four wild rice species showed higher sequence conservation in retrotransposon than nonretrotransposon regions. We further investigated, in detai

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Uyeh, Daniel Dooyum, Senorpe Asem-Hiablie, Tusan Park, et al. "Could Japonica Rice Be an Alternative Variety for Increased Global Food Security and Climate Change Mitigation?" Foods 10, no. 8 (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 sensor

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Mao, Donghai, Yeyun Xin, Yongjun Tan, 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 (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 HA

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Xu, J. L. "Heavy genetic load associated with the subspecific differentiation of japonica rice (Oryza sativa ssp. japonica L.)." Journal of Experimental Botany 57, no. 11 (2006): 2815–24. http://dx.doi.org/10.1093/jxb/erl046.

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