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Journal articles on the topic 'Oryza sativa subsp'

Author: Grafiati

Published: 4 June 2021

Last updated: 11 February 2022

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1

Tamura, Satoru, Ke Yan, Hiroshi Shimoda, and Nobutoshi Murakami. "Anthocyanins from Oryza sativa L. subsp. indica." Biochemical Systematics and Ecology 38, no. 3 (2010): 438–40. http://dx.doi.org/10.1016/j.bse.2010.01.017.

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2

Luo, Hongfa, Yunfeng Li, Zhenglin Yang, et al. "Fine mapping of a pistilloid-stamen (PS) gene on the short arm of chromosome 1 in rice." Genome 49, no. 8 (2006): 1016–22. http://dx.doi.org/10.1139/g06-056.

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A novel floral organ mutant of rice (Oryza sativa L. subsp. indica), termed pistilloid-stamen (ps) here, has flowers with degenerated lemma and palea, with some stamens transformed into pistils and pistil–stamen chimeras. Genetic analysis confirmed that the ps trait is controlled by a single recessive gene. F2 and F3 segregation populations derived from PS ps heterozygote crossed with Oryza sativa subsp. indica 'Luhui-17' (PS PS) were used for molecular mapping of the gene using simple sequence repeat (SSR) markers. With 97 recessive individuals from an F2 segregation population, the ps locus

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3

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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4

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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5

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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6

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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7

Falqueto, Antelmo Ralph, Daniela Cassol, Ariano Martins de Magalhães Júnior, Antônio Costa de Oliveira, and Marcos Antonio Bacarin. "Physiological analysis of leaf senescence of two rice cultivars with different yield potential." Pesquisa Agropecuária Brasileira 44, no. 7 (2009): 695–700. http://dx.doi.org/10.1590/s0100-204x2009000700007.

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The objective of this work was to evaluate the physiological changes that occur in different leaves during the early and late grain-filling stages of two rice genotypes (Oryza sativa subsp. indica , BRS Pelota cultivar, and O. sativa subsp. japonica , BRS Firmeza cultivar), which present differences in grain yield potential. The plants were cultivated in greenhouse. Pigment content, chlorophyll fluorescence, electron transport and oxygen evolution rate were determined in the grain-filling stage, from the first to the forth leaf (top to bottom). Pigment content, photochemical efficiency of phot

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8

Waters, Daniel L. E., Gopala Krishnan Subbaiyan, Elangovan Mani, et al. "Genome wide polymorphisms and yield heterosis in rice (Oryza sativa subsp. indica)." Tropical Plant Biology 8, no. 3-4 (2015): 117–25. http://dx.doi.org/10.1007/s12042-015-9156-x.

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9

Boonpa, Krissana, Suparuk Tantong, Kamonwan Weerawanich, et al. "In Silico Analyses of Rice Thionin Genes and the Antimicrobial Activity of OsTHION15 Against Phytopathogens." Phytopathology® 109, no. 1 (2019): 27–35. http://dx.doi.org/10.1094/phyto-06-17-0217-r.

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Thionins are a family of antimicrobial peptides. We performed in silico expression analyses of the 44 rice (Oryza sativa) thionins (OsTHIONs). Modulated expression levels of OsTHIONs under different treatments suggest their involvement in many processes, including biotic, abiotic, and nutritional stress responses, and in hormone signaling. OsTHION15 (LOC_Os06g32600) was selected for further characterization based on several in silico analyses. OsTHION15 in O. sativa subsp. indica ‘KDML 105’ was expressed in all of the tissues and organs examined, including germinating seed, leaves, and roots o

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10

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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11

Wang, Baoxiang, Ling Jiang, Yingxin Zhang, et al. "Genetic dissection of the resistance to Rice stripe virus present in the indica rice cultivar ‘IR24’." Genome 54, no. 8 (2011): 611–19. http://dx.doi.org/10.1139/g11-022.

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Rice stripe disease, caused by Rice stripe virus (RSV) and transmitted by the small brown planthopper (Laodelphax striatellus Fallen), is one of the most serious viral diseases of rice in temperate East Asian production regions. Prior quantitative trait loci (QTL) mapping has established that Oryza sativa L. subsp. indica ‘IR24’ carries positive alleles at the three loci qSTV3, qSTV7, and qSTV11-i. Here, we report an advanced backcross analysis based on three selected chromosome segment substitution lines (CSSLs), each predicted to carry one of these three QTL. Three sets of BC4F2:3 population

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12

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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13

Prashanth, S. R., M. Parani, B. P. Mohanty, V. Talame, R. Tuberosa, and A. Parida. "Genetic diversity in cultivars and landraces of Oryza sativa subsp. indica as revealed by AFLP markers." Genome 45, no. 3 (2002): 451–59. http://dx.doi.org/10.1139/g02-003.

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Genetic diversity among 49 Indian accessions of rice (Oryza sativa subsp. indica), including 29 landraces from Jeypore, 12 modern cultivars, and 8 traditional cultivars from Tamil Nadu, was investigated using AFLP markers. In total, nine primer combinations revealed 664 AFLPs, 408 of which were found to be polymorphic. The percentage of polymorphic AFLPs was approximately the same within the cultivars and landraces. Similar results were obtained when genetic diversity values were estimated using the ShannonWeiner index of diversity. Genetic diversity was slightly higher in the modern cultivar

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14

Reddy, Arjula R., W. Ramakrishna, A. Chandra Sekhar, et al. "Novel genes are enriched in normalized cDNA libraries from drought-stressed seedlings of rice (Oryza sativa L. subsp. indica cv. Nagina 22)." Genome 45, no. 1 (2002): 204–11. http://dx.doi.org/10.1139/g01-114.

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We have utilized an efficient method to enrich cDNA libraries for novel genes and genes responsive to drought stress in rice (Oryza sativa L. subsp. indica). We separately constructed standard and normalized cDNA libraries from leaf tissue of rice seedlings grown under controlled drought stress. Sequencing from the 3' end was performed on 1000 clones from the normalized leaf cDNA library and 200 clones from the standard leaf cDNA library. For the first 200 clones, the clone redundancy in the non-normalized library was about 10%, compared with 3.5% in the normalized cDNA library. Comparison of

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15

WANG, QIANJIE, WEIWEI QI, YING WANG, et al. "Isolation and identification of an AP2/ERF factor that binds an allelic cis-element of rice gene LRK6." Genetics Research 93, no. 5 (2011): 319–32. http://dx.doi.org/10.1017/s0016672311000218.

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SummaryAllelic expression of the rice yield-related gene, leucine-rich receptor-like kinase 6 (LRK6), in the hybrid of 93-11 (Oryza sativa L. subsp. Indica var. 93-11) and Nipponbare (O. sativa L. subsp. Japonica var. Nipponbare) is determined by allelic promoter cis-elements. Using deletion analysis of the LRK6 promoter, we identified two distinct regions that might contribute to LRK6 expression. Sequence alignment revealed differences in these LRK6 promoter regions in 93-11 and Nipponbare. One of the segments, named differential sequence of LRK6 promoter 2 (DSLP2), contains potential transcr

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16

Girija, Anil Madhusoodana, Bipin Kumar Kinathi, Mylavarapu B. Madhavi, et al. "Rice Leaf Transcriptional Profiling Suggests a Functional Interplay Between Xanthomonas oryzae pv. oryzae Lipopolysaccharide and Extracellular Polysaccharide in Modulation of Defense Responses During Infection." Molecular Plant-Microbe Interactions® 30, no. 1 (2017): 16–27. http://dx.doi.org/10.1094/mpmi-08-16-0157-r.

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Treatment of rice leaves with isolated Xanthomonas oryzae pv. oryzae lipopolysaccharide (LPS) induces the production of callose deposits, reactive oxygen species, and enhanced resistance against subsequent bacterial infection. Expression profiling of X. oryzae pv. oryzae LPS-treated rice (Oryza sativa subsp. indica) leaves showed that genes involved in the biosynthetic pathways for lignins, phenylpropanoids, chorismate, phenylalanine, salicylic acid, and ethylene, as well as a number of pathogenesis-related proteins are up-regulated. Gene ontology categories like cell-wall organization, defens

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17

Rashid, Muhammad Abdul Rehman, Yan Zhao, Hongliang Zhang, Jinjie Li, and Zichao Li. "Nucleotide diversity, natural variation, and evolution of Flexible culm-1 and Strong culm-2 lodging resistance genes in rice." Genome 59, no. 7 (2016): 473–83. http://dx.doi.org/10.1139/gen-2016-0019.

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Lodging resistance is one of the vital traits in yield improvement and sustainability. Culm wall thickness, diameter, and strength are different traits that can govern the lodging resistance in rice. The genes SCM2 and FC1 have been isolated for culm thickness, strength, and flexibility, but their functional nucleotide variations were still unknown. We used a 13× deep sequence of 795 diverse genotypes to present the functional variation and SNP diversity in SCM2 and FC1. The major functional variant for the SCM2 gene was at position 27480181 and for the FC1 gene at position 31072992. Haplotype

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18

Chen, J., C. Zhu, D. Lin, and Z. X. Sun. "The effects of Cd on lipid peroxidation, hydrogen peroxide content and antioxidant enzyme activities in Cd-sensitive mutant rice seedlings." Canadian Journal of Plant Science 87, no. 1 (2007): 49–57. http://dx.doi.org/10.4141/p06-048.

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Cadmium-sensitive rice (Oryza sativa L. subsp. Japonica ‘Zhonghua11’) mutants were obtained using an Agrobacterium tumefaciens-based gene delivery system. Significant phenotypic differences were observed between a Cd-sensitive mutant (ST) and wild type (WT) rice seedlings. Results indicated that Cd accumulation in the leaves of the mutant was twice that of the wild type after 10 d of 0.5 mM Cd2+ treatment. Furthermore, a rapid Cd-induced H2O2 increase was observed in the mutant leaves, which induced abnormally early activity in antioxidant enzymes such as superoxide dismutase (SOD). However, t

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19

Tohno, Masanori, Maki Kitahara, Hidehiko Inoue, et al. "Weissella oryzae sp. nov., isolated from fermented rice grains." International Journal of Systematic and Evolutionary Microbiology 63, Pt_4 (2013): 1417–20. http://dx.doi.org/10.1099/ijs.0.043612-0.

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A taxonomic study was conducted on two Gram-reaction-positive, catalase-negative, irregular short-rod-shaped or coccoid lactic acid bacteria, designated strains SG25T and SG23, that were isolated from grains of fermented Japanese rice (Oryza sativa L. subsp. japonica). A phylogenetic analysis based on 16S rRNA gene sequence data clearly showed that the strains belonged to the genus Weissella and were most closely related to Weissella soli LMG 20113T (with a sequence similarity of 96.9 % for each novel strain). The peptidoglycan of each strain contained the amino acids glutamic acid, lysine, se

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20

Chen, Wan Guang, Yan Zhao Zhang, Yan Wei Cheng, and Hui Yuan Ya. "Analysis of Coexpression Genes in Oryza sativa L. Treated with Low-Energy Ion-Beam." Applied Mechanics and Materials 675-677 (October 2014): 1129–32. http://dx.doi.org/10.4028/www.scientific.net/amm.675-677.1129.

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Xindao-18(Oryza sativa L. subsp. japonica Kato) were irratiated with a low-energy ion-beam, the growth form were observed and transcriptome of samples were sequenced by Illumina HiSeq2000 platform. The different expression genes were identified from transcriptomes control and treated samples. Finally, the coexpression of different gene expression were construce and seventy DEGs were annotated as transcription factor (TF). Among them, ten transcripts have the higher network density, and two genes, LOC_Os06g15330 and LOC_Os03g51970, had a still higher network density while elevate PCC paramater,

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21

Yoshino, Kyoji, Toshio Miyase, Masahiko Takeuchi, Kenichi Nisizawa, Kazuya Taguchi, and Mitsuaki Sano. "Preventive Effects of Saccharified Solution of Rice, Oryza sativa subsp. japonica, in Mouse Allergic Models." JOURNAL OF HEALTH SCIENCE 56, no. 2 (2010): 208–14. http://dx.doi.org/10.1248/jhs.56.208.

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22

KIM, HYUNG-MIN, CHANG-SOON KANG, EUN-HEE LEE, and TAE-YONG SHIN. "THE EVALUATION OF THE ANTIANAPHYLACTIC EFFECT OF ORYZA SATIVA L. SUBSP. HSIEN TING IN RATS." Pharmacological Research 40, no. 1 (1999): 31–36. http://dx.doi.org/10.1006/phrs.1998.0386.

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23

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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24

Onishi, Kazumitsu, Kyoko Takagi, Manabu Kontani, Takumi Tanaka, and Yoshio Sano. "Different patterns of genealogical relationships found in the two major QTLs causing reduction of seed shattering during rice domestication." Genome 50, no. 8 (2007): 757–66. http://dx.doi.org/10.1139/g07-051.

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The three quantitative trait loci (qSH1, qSH3, and qSH4) causing reduction of seed shattering were investigated to examine their relative importance during rice domestication. The qSH1 and qSH4 loci showed a distinct effect on the reduction of shattering, compared with the qSH3 locus. Fine mapping and sequence analysis strongly suggested that the qSH1 and qSH4 loci are the same as the recently reported genes. A non-shattering allele at qSH1 drastically changed the shattering phenotype to a non-shattering phenotype even in the presence of shattering alleles at the qSH3 and qSH4 loci, showing th

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25

Yang, Yaolong, Mengchen Zhang, Qun Xu, et al. "Exploration of genetic selection in rice leaf length and width." Botany 96, no. 4 (2018): 249–56. http://dx.doi.org/10.1139/cjb-2017-0161.

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Leaf length and width are two of the most important components of rice (Oryza sativa L.) plant architecture and directly contribute to yield. The genetic effects of leaf length and width are controlled by quantitative trait loci (QTLs). In this study, a double haploid (DH) population derived from a cross of O. sativa subsp. japonica cultivar ‘Maybelle’ and subsp. indica cultivar ‘Baiyeqiu’ (‘BYQ’) was used to determine genetic effects on leaf length and width. Analysis of phenotypic effects indicated that all of the detected traits exhibited continuous, transgressive distributions in the DH po

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26

Civáň, P., and M. Švec. "Genome-wide analysis of rice (Oryza sativa L. subsp. japonica) TATA box and Y Patch promoter elements." Genome 52, no. 3 (2009): 294–97. http://dx.doi.org/10.1139/g09-001.

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The TATA box is one of the best characterized transcription factor binding sites. However, it is not a ubiquitous element of core promoters, and other sequence motifs such as Y Patches seem to play a major role in plants. Here, we present a first genome-wide computational analysis of the TATA box and Y Patch distribution in rice ( Oryza sativa L. subsp. japonica) promoter sequences. Utilizing a probabilistic sequence model, we ascertain that only ~19% of rice genes possess the TATA box, but ~50% contain one or more Y Patches in their core promoters. By computational processing of identified el

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27

Wang, Wen-Ying, Han-Feng Ding, Guang-Xian Li, et al. "Delimitation of thePSH1(t) gene for rice purple leaf sheath to a 23.5 kb DNA fragment." Genome 52, no. 3 (2009): 268–74. http://dx.doi.org/10.1139/g08-121.

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Leaf sheath color plays an important role as a marker for rice genetic improvement. A recombinant inbred line (RIL) population consisting of 220 individuals was developed from a cross between an Oryza sativa subsp. indica variety, IRBB60, and an Oryza sativa subsp. japonica variery, 9407. Within the RIL population, a line, RI51, was found to have purple leaf sheath (PSH). To map the gene governing PSH, RI51 was crossed with 9407 green leaf sheath (GSH) to develop an F2segregating population. The distribution of F2plants with PSH and GSH fitted a segregation ratio of 3:1, indicating that the PS

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28

Zhang, Jianwei, Ling-Ling Chen, Feng Xing, et al. "Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63." Proceedings of the National Academy of Sciences 113, no. 35 (2016): E5163—E5171. http://dx.doi.org/10.1073/pnas.1611012113.

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Asian cultivated rice consists of two subspecies: Oryza sativa subsp. indica and O. sativa subsp. japonica. Despite the fact that indica rice accounts for over 70% of total rice production worldwide and is genetically much more diverse, a high-quality reference genome for indica rice has yet to be published. We conducted map-based sequencing of two indica rice lines, Zhenshan 97 (ZS97) and Minghui 63 (MH63), which represent the two major varietal groups of the indica subspecies and are the parents of an elite Chinese hybrid. The genome sequences were assembled into 237 (ZS97) and 181 (MH63) co

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Tisarum, Rujira, Cattarin Theerawitaya, Thapanee Samphumphuang, and Suriyan Cha-um. "Regulation of anthocyanin accumulation in rice (Oryza sativa L. subsp. indica) using MgSO4 spraying and low temperature." Archives of Agronomy and Soil Science 64, no. 12 (2018): 1663–77. http://dx.doi.org/10.1080/03650340.2018.1450501.

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Safdar, Waseem, Haroon Ahmed, Nazish Bostan, et al. "Comparative analysis of nine different small heat shock protein gene promoters in Oryza sativa L. subsp. indica." Plant Systematics and Evolution 302, no. 9 (2016): 1195–206. http://dx.doi.org/10.1007/s00606-016-1325-3.

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31

Chakraborty, Debarati, Debal Deb, and Avik Ray. "An analysis of variation of the aroma gene in rice (Oryza sativa L. subsp. indica Kato) landraces." Genetic Resources and Crop Evolution 63, no. 6 (2016): 953–59. http://dx.doi.org/10.1007/s10722-016-0414-z.

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Chin, Joong Hyoun, Yoo-Jin Lee, Wenzhu Jiang, Hee-Jong Koh, and Michael J. Thomson. "Characterization of indica–japonica subspecies-specific InDel loci in wild relatives of rice (Oryza sativa L. subsp. indica Kato and subsp. japonica Kato)." Genetic Resources and Crop Evolution 64, no. 2 (2016): 405–18. http://dx.doi.org/10.1007/s10722-016-0368-1.

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33

Cui, Di, Chang-ying Xu, Chun-gang Yang, et al. "Association mapping of salinity and alkalinity tolerance in improved japonica rice (Oryza sativa L. subsp. japonica Kato) germplasm." Genetic Resources and Crop Evolution 62, no. 4 (2014): 539–50. http://dx.doi.org/10.1007/s10722-014-0179-1.

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Kanneganti, Vydehi, and Aditya Kumar Gupta. "Isolation and Expression analysis of OsPME1, encoding for a putative Pectin Methyl Esterase from Oryza sativa (subsp. indica)." Physiology and Molecular Biology of Plants 15, no. 2 (2009): 123–31. http://dx.doi.org/10.1007/s12298-009-0014-x.

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35

Rahman, L., S. Khanam, J. H. Roh, and H. J. Koh. "Mapping of QTLs involved in resistence to rice blast (Magnaporthe grisea) using Oryza minuta introgression lines." Czech Journal of Genetics and Plant Breeding 47, No. 3 (2011): 85–94. http://dx.doi.org/10.17221/19/2011-cjgpb.

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&nbsp; Introgression lines derived from Oryza minuta and O. sativa subsp. japonica var. Junambyeo were crossed for a mapping of the population composed of 112 recombinant lines to identify putative QTLs against rice blast disease using the percentage of diseased leaf area. By using 148&nbsp;Sequence Tagged Site (STS) and Single Sequence Repeat (SSR) markers, five QTLs on chromosomes 6, 7, 9 and 11 and seven epistatic QTLs were identified against two blast isolates (KI307 and KI209). Of them two QTLs (qKI307-2 and qKI209-3) shared a similar position on chromosome 11. O. minuta introgres

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Yeo, Sang-Min, Yeo-Tae Yun, Dong-Min Kim, Chong-Tae Chung, and Sang-Nag Ahn. "Validation of QTLs associated with spikelets per panicle and grain weight in rice." Plant Genetic Resources 12, S1 (2014): S151—S154. http://dx.doi.org/10.1017/s1479262114000562.

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In this study, a near-isogenic line (BC4F10) CR572 developed by introgressing a chromosomal segment from Oryza rufipogon (accession no. 105491) into the Oryza sativa subsp. japonica cv. Hwaseong was found to exhibit a significant increase in the number of spikelets per panicle (SPP) and grain weight compared with the recurrent parent Hwaseong. Quantitative trait locus (QTL) analysis in F2 generation derived from the cross between CR572 and Hwaseong revealed that two QTLs, qSPP1 and qTGW1, were linked to a simple sequence repeat marker, RM283, on chromosome 1. The additive effect of the O. rufi

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Pongprayoon, Wasinee, Rujira Tisarum, Cattarin Theerawittaya, and Suriyan Cha-um. "Evaluation and clustering on salt-tolerant ability in rice genotypes (Oryza sativa L. subsp. indica) using multivariate physiological indices." Physiology and Molecular Biology of Plants 25, no. 2 (2019): 473–83. http://dx.doi.org/10.1007/s12298-018-00636-2.

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Wu, Y. J., Y. Chen, J. Wang, C. X. Zhu, and B. L. Xu. "RAPD analysis of jasmine rice-specific genomic structure." Genome 49, no. 6 (2006): 716–19. http://dx.doi.org/10.1139/g06-018.

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Total genomic DNA was extracted from 29 samples of rice seed, including jasmine rice Oryza sativa L. subsp indica 'KDML105', 'KDML105'-derived varieties, nonaromatic Thailand rice, and japonica rice. Polymorphism in RAPD profiles was analyzed to explore the genomic structure specific to jasmine rice. The degree of band sharing was used to evaluate genetic distance between varieties and to construct a phylogenetic tree. RD15, CNTLR85033, and CNT87040 were found to be closest to 'KDML105', which was consistent with the true relation among them. Four RAPD fragments that cooperatively distinguishe

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Park, K. C., S. J. Kwon, P. H. Kim, T. Bureau, and N. S. Kim. "Gene structure dynamics and divergence of the polygalacturonase gene family of plants and fungus." Genome 51, no. 1 (2008): 30–40. http://dx.doi.org/10.1139/g07-093.

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Whole copies of the polygalacturonase (PG) genes from rice ( Oryza sativa subsp. japonica) and a filamentous fungus ( Aspergillus oryzae ) were isolated. The orthologs of the rice PGs were also retrieved from other plant species. The 106 plant PGs analyzed were divided into 5 clades, A, B, C, D, and E. The fungus PGs were classified into 3 clades, of which one formed a loose cluster with clade E of the plant PGs. Four domain motifs (I, II, III, IV) were identified in all PGs. Motifs II and III were split by introns such as G/DDC and CGPGHGIS/IGSLG, respectively. In plant PGs there were 446 int

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ZHANG, Dong-ling, Mei-xing WANG, Yong-wen QI, et al. "Genetic Structure and Eco-Geographical Differentiation of Cultivated Keng Rice (Oryza sativa L. subsp. japonica) in China Revealed by Microsatellites." Journal of Integrative Agriculture 11, no. 11 (2012): 1755–66. http://dx.doi.org/10.1016/s2095-3119(12)60180-4.

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Jia, Chunping, Fengbin Wang, Jie Yuan, et al. "Screening and comprehensive evaluation of rice (Oryza sativa L. subsp. japonica Kato) germplasm resources for nitrogen efficiency in Xinjiang, China." Plant Genetic Resources: Characterization and Utilization 18, no. 3 (2020): 179–89. http://dx.doi.org/10.1017/s1479262120000118.

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AbstractComprehensive screening of rice (Oryza sativa L. subsp. japonica Kato) germplasm resources with different nitrogen (N) efficiency levels is effective for improving N use efficiency (NUE) while reducing pollution and providing high quality, yield, and efficiency agriculture. We investigated 14 indices of 38 varieties under three N application levels to assess differences among genotypes. Rice varieties were classified for screening and identifying N efficient. Descriptive statistical analysis results indicated significant differences in relative yield, and also in NUE indices (agronomic

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Zhang, DongLing, HongLiang Zhang, YongWen Qi, et al. "Genetic structure and eco-geographical differentiation of cultivated Hsien rice (Oryza sativa L. subsp. indica) in China revealed by microsatellites." Chinese Science Bulletin 58, no. 3 (2012): 344–52. http://dx.doi.org/10.1007/s11434-012-5396-4.

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Xie, Wengang, Joseph G. Robins, and B. Shaun Bushman. "A genetic linkage map of tetraploid orchardgrass (Dactylis glomerata L.) and quantitative trait loci for heading date." Genome 55, no. 5 (2012): 360–69. http://dx.doi.org/10.1139/g2012-026.

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Orchardgrass ( Dactylis glomerata L.), or cocksfoot, is indigenous to Eurasia and northern Africa, but has been naturalized on nearly every continent and is one of the top perennial forage grasses grown worldwide. To improve the understanding of genetic architecture of orchardgrass and provide a template for heading date candidate gene search in this species, the goals of the present study were to construct a tetraploid orchardgrass genetic linkage map and identify quantitative trait loci associated with heading date. A combination of SSR markers derived from an orchardgrass EST library and AF

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Rahman, L., M. S. Khanam, and H. J. Koh. "QTL analysis for yield related traits using populations derived from an indica-japonica hybrid in rice (Oryza sativaL.)." Czech Journal of Genetics and Plant Breeding 44, No. 3 (2008): 93–104. http://dx.doi.org/10.17221/16/2008-cjgpb.

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Introgression has been achieved from a wild species Oryza minuta (2n = 48, BBCC, Acc No.101141) into O. sativa subsp. indica IR71033-121-15. This introgression line was developed at International Rice Research Institute (IRRI) through embryo rescue as well as three backcrosses using IR31917-45-3-2 as a recurrent parent. These two IR lines resemble each other but differ in several important agronomic traits, which can be attributable to O. minuta introgressions. Out of 530 STS markers tested for introgression analysis, at least 14 introgressed chromosomal segments from O. minuta were detected t

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Luo, Zengke, Zhenglin Yang, Bingqiang Zhong, et al. "Genetic analysis and fine mapping of a dynamic rolled leaf gene, RL10(t), in rice (Oryza sativa L.)." Genome 50, no. 9 (2007): 811–17. http://dx.doi.org/10.1139/g07-064.

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A dynamically rolled leaf mutant (rl10) was identified from a spontaneous mutation in an Oryza sativa L. subsp. indica line, II-32B. The leaf chlorophyll content of rl10 is higher than that of the wild type. Genetic analysis using 3 F2 segregating populations derived from crosses between rl10 and the rice lines Mian5B, II-32B, and D62B, respectively, confirmed that the rolled leaf trait of rl10 is controlled by a single recessive gene. Of 719 SSR primer pairs that showed polymorphism between D62B and rl10, 151 were adopted to map the RL10(t) gene using an F2 segregating population of the cross

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Raghuvanshi, S. "Isolation and Molecular Characterization of the COP 1 Gene Homolog from Rice, Oryza sativa L. subsp. Indica var. Pusa Basmati 1." DNA Research 8, no. 2 (2001): 73–79. http://dx.doi.org/10.1093/dnares/8.2.73.

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Tisarum, Rujira, Cattarin Theerawitaya, Thapanee Samphumphuang, Muenduen Phisalaphong, Harminder Pal Singh, and Suriyan Cha-um. "Promoting water deficit tolerance and anthocyanin fortification in pigmented rice cultivar (Oryza sativa L. subsp. indica) using arbuscular mycorrhizal fungi inoculation." Physiology and Molecular Biology of Plants 25, no. 4 (2019): 821–35. http://dx.doi.org/10.1007/s12298-019-00658-4.

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Liu, Shaolin, Nicholas A. Tinker, and Diane E. Mather. "Exact word matches in rice pseudomolecules." Genome 49, no. 8 (2006): 1047–51. http://dx.doi.org/10.1139/g06-055.

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Using pseudomolecules of assembled genomic sequence, we computed the frequencies of 6 to 24 bp oligonucleotide (oligo) "words" across the genome of rice (Oryza sativa L. subsp. japonica). All oligos of 10 or fewer basepairs were repeated at least 12 times in the genome. The percentage of unique (non-repeated) oligos ranged from 0.1% for 12 bp oligos to 76.0% for 24 bp oligos. For three 200 kb regions, we annotated each nucleotide position with the genome-wide frequency of the 18 bp oligo starting at that position. These frequencies formed landscapes consisting of high- and low-frequency zones.

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Matsukura, Keiichiro, Sachiyo Sanada-Morimura, Tomohisa Fujii, and Masaya Matsumura. "Potential Risks of Poaceous Plants as Infectious Sources of Rice Black-Streaked Dwarf Virus Transmitted by the Small Brown Planthopper, Laodelphax striatellus." Plant Disease 103, no. 6 (2019): 1244–48. http://dx.doi.org/10.1094/pdis-08-18-1340-re.

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The recent reemergence of rice black-streaked dwarf virus (RBSDV) has caused severe rice yield losses in several areas of East Asia. To identify the most important infectious sources of RBSDV, we compared the susceptibility of major poaceous plants to RBSDV infection and survival and the RBSDV acquisition efficiency of a vector insect, the small brown planthopper Laodelphax striatellus. RBSDV infection and survival rates of L. striatellus were significantly high in wheat (Triticum aestivum ‘Norin61’) and rice (Oryza sativa ‘Reiho’), indicating that these crops can be important sources of RBSDV

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Jin-Guang, Yang, Wang Wen-Ting, Ding Xin-Lun, et al. "Auxin regulation in the interaction between Rice stripe virus and rice." Chinese Journal of Agricultural Biotechnology 6, no. 1 (2009): 27–33. http://dx.doi.org/10.1017/s1479236209002502.

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AbstractThe expression of the YUCAA1 gene and the amount of endogenous indole acetic acid (IAA) in rice (Oryza sativa subsp. japonica) plants and rice suspension cells infected by Rice stripe virus (RSV) were investigated by real-time reverse transcriptase–polymerase chain reaction (RT-PCR) and high-performance liquid chromatography, respectively. The results showed that the expression of the YUCAA1 gene and the amount of endogenous IAA increased at various times (16, 32, 48 and 64 h) after infection of rice suspension cells by RSV. In rice plants infected with RSV, the expression of the YUCAA

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