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Oryza meridionalis

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https://www.readbyqxmd.com/read/27889940/sequencing-of-australian-wild-rice-genomes-reveals-ancestral-relationships-with-domesticated-rice
#1
Marta Brozynska, Dario Copetti, Agnelo Furtado, Rod A Wing, Darren Crayn, Glen Fox, Ryuji Ishikawa, Robert J Henry
The related A genome species of the Oryza genus are the effective gene pool for rice. Here we report draft genomes for two Australian wild A genome taxa: O. rufipogon-like population, referred to as Taxon A and O. meridionalis-like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short and long read next generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A, has a sequence that is much closer to that of domesticated rice (O...
November 27, 2016: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/27145723/heat-tolerance-in-a-wild-oryza-species-is-attributed-to-maintenance-of-rubisco-activation-by-a-thermally-stable-rubisco-activase-ortholog
#2
Andrew P Scafaro, Alexander Gallé, Jeroen Van Rie, Elizabete Carmo-Silva, Michael E Salvucci, Brian J Atwell
The mechanistic basis of tolerance to heat stress was investigated in Oryza sativa and two wild rice species, Oryza meridionalis and Oryza australiensis. The wild relatives are endemic to the hot, arid Australian savannah. Leaf elongation rates and gas exchange were measured during short periods of supra-optimal heat, revealing species differences. The Rubisco activase (RCA) gene from each species was sequenced. Using expressed recombinant RCA and leaf-extracted RCA, the kinetic properties of the two isoforms were studied under high temperatures...
August 2016: New Phytologist
https://www.readbyqxmd.com/read/27133567/evolutionary-trajectory-of-phytoalexin-biosynthetic-gene-clusters-in-rice
#3
Koji Miyamoto, Masahiro Fujita, Matthew R Shenton, Shota Akashi, Chizu Sugawara, Arisa Sakai, Kiyotaka Horie, Morifumi Hasegawa, Hiroshi Kawaide, Wataru Mitsuhashi, Hideaki Nojiri, Hisakazu Yamane, Nori Kurata, Kazunori Okada, Tomonobu Toyomasu
Plants frequently possess operon-like gene clusters for specialized metabolism. Cultivated rice, Oryza sativa, produces antimicrobial diterpene phytoalexins represented by phytocassanes and momilactones, and the majority of their biosynthetic genes are clustered on chromosomes 2 and 4, respectively. These labdane-related diterpene phytoalexins are biosynthesized from geranylgeranyl diphosphate via ent-copalyl diphosphate or syn-copalyl diphosphate. The two gene clusters consist of genes encoding diterpene synthases and chemical-modification enzymes including P450s...
August 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/26687860/inconsistent-diversities-between-nuclear-and-plastid-genomes-of-aa-genome-species-in-the-genus-oryza
#4
Hao Yin, Masahiro Akimoto, Reunreudee Kaewcheenchai, Masahiro Sotowa, Takashige Ishii, Ryuji Ishikawa
AA genome species in the genus Oryza are valuable resources for improvement of cultivated rice. Oryza rufipogon and O. barthii were progenitors of two domesticated rice species, O. sativa and O. glaberrima, respectively. We used chloroplast single-nucleotide repeats (RCt1-10) to evaluate genetic diversity among AA genome species. Higher diversity was detected in the American species O. glumaepatula and the Asian species O. rufipogon. Other chloroplast sequences indicated that O. glumaepatula shares high similarity with O...
2015: Genes & Genetic Systems
https://www.readbyqxmd.com/read/26506948/complete-chloroplast-and-ribosomal-sequences-for-30-accessions-elucidate-evolution-of-oryza-aa-genome-species
#5
Kyunghee Kim, Sang-Choon Lee, Junki Lee, Yeisoo Yu, Kiwoung Yang, Beom-Soon Choi, Hee-Jong Koh, Nomar Espinosa Waminal, Hong-Il Choi, Nam-Hoon Kim, Woojong Jang, Hyun-Seung Park, Jonghoon Lee, Hyun Oh Lee, Ho Jun Joh, Hyeon Ju Lee, Jee Young Park, Sampath Perumal, Murukarthick Jayakodi, Yun Sun Lee, Backki Kim, Dario Copetti, Soonok Kim, Sunggil Kim, Ki-Byung Lim, Young-Dong Kim, Jungho Lee, Kwang-Su Cho, Beom-Seok Park, Rod A Wing, Tae-Jin Yang
Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species...
2015: Scientific Reports
https://www.readbyqxmd.com/read/26366120/pcr-based-indel-markers-co-dominant-between-oryza-sativa-japonica-cultivars-and-closely-related-wild-oryza-species
#6
Mitsuru Niihama, Misato Mochizuki, Nori Kurata, Ken-Ichi Nonomura
Wild relatives genetically close to cultivars are precious genetic resources for plant breeding. Oryza rufipogon, O. barthii, O. glumaepatula, O. meridionalis and O. longistaminata are such wild species, and are also categorized as AA genome species based on their structural similarities. Chromosome segment substitution lines (CSSLs) are a powerful resource in breeding and genetics, and numerous rice CSSLs have been produced. This study aimed to develop DNA markers for evaluation of CSSLs directly by PCR and subsequent gel electrophoresis...
September 2015: Breeding Science
https://www.readbyqxmd.com/read/25926037/molecular-characterization-and-application-of-a-novel-cytoplasmic-male-sterility-associated-mitochondrial-sequence-in-rice
#7
Yanping Tan, Xin Xu, Chuntai Wang, Gang Cheng, Shaoqing Li, Xuequn Liu
BACKGROUND: Cytoplasmic male sterility (CMS) is a maternally inherited inability to produce functional pollen found in numerous flowering plant species. CMS is associated with mitochondrial DNA mutation, novel chimeric open reading frames (ORFs), and rearrangement of coding and noncoding regions of the mitochondrial genome. RESULTS: BLAST (Basic Local Alignment Search Tool) analysis indicated that L-sp1, a new sequence-characterized amplified region, is non-homologous to atp6-orfH79 (or atp6-orf79) and WA352 cloned CMS-associated genes...
2015: BMC Genetics
https://www.readbyqxmd.com/read/25911477/effects-of-colonization-of-the-roots-of-domestic-rice-oryza-sativa-l-cv-amaroo-by-burkholderia-pseudomallei
#8
Noppadol Prasertsincharoen, Constantin Constantinoiu, Christopher Gardiner, Jeffrey Warner, Jennifer Elliman
Burkholderia pseudomallei is a saprophytic bacterium that causes melioidosis and is often isolated from rice fields in Southeast Asia, where the infection incidence is high among rice field workers. The aim of this study was to investigate the relationship between this bacterium and rice through growth experiments where the effect of colonization of domestic rice (Oryza sativa L. cv Amaroo) roots by B. pseudomallei could be observed. When B. pseudomallei was exposed to surface-sterilized seeds, the growth of both the root and the aerosphere was retarded compared to that in controls...
July 2015: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/25705117/development-and-gbs-genotyping-of-introgression-lines-ils-using-two-wild-species-of-rice-o-meridionalis-and-o-rufipogon-in-a-common-recurrent-parent-o-%C3%A2-sativa-cv-curinga
#9
Juan D Arbelaez, Laura T Moreno, Namrata Singh, Chih-Wei Tung, Lyza G Maron, Yolima Ospina, César P Martinez, Cécile Grenier, Mathias Lorieux, Susan McCouch
Two populations of interspecific introgression lines (ILs) in a common recurrent parent were developed for use in pre-breeding and QTL mapping. The ILs were derived from crosses between cv Curinga, a tropical japonica upland cultivar, and two different wild donors, Oryza meridionalis Ng. accession (W2112) and Oryza rufipogon Griff. accession (IRGC 105491). The lines were genotyped using genotyping-by-sequencing (GBS) and SSRs. The 32 Curinga/O. meridionalis ILs contain 76.73 % of the donor genome in individual introgressed segments, and each line has an average of 94...
2015: Molecular Breeding: New Strategies in Plant Improvement
https://www.readbyqxmd.com/read/25485030/chloroplast-genome-of-novel-rice-germplasm-identified-in-northern-australia
#10
Marta Brozynska, Ernnie Syafika Omar, Agnelo Furtado, Darren Crayn, Bryan Simon, Ryuji Ishikawa, Robert James Henry
Rice (Oryza sativa L.) was probably domesticated from O. rufipogon in Asia in the last 10,000 years. Relatives of cultivated rice (A genome species of Oryza) are found in South America, Africa, Australia and Asia. These A genome species are the close relatives of cultivated rice and represent the effective gene pool for rice improvement. Members of this group in Northern Australia include, an annual species, O. meridionalis, and two recently distinguished perennial taxa, to one of which the name O. rufipogon has been applied and the other a perennial form of O...
2014: Tropical Plant Biology
https://www.readbyqxmd.com/read/25368197/rapid-diversification-of-five-oryza-aa-genomes-associated-with-rice-adaptation
#11
COMPARATIVE STUDY
Qun-Jie Zhang, Ting Zhu, En-Hua Xia, Chao Shi, Yun-Long Liu, Yun Zhang, Yuan Liu, Wen-Kai Jiang, You-Jie Zhao, Shu-Yan Mao, Li-Ping Zhang, Hui Huang, Jun-Ying Jiao, Ping-Zhen Xu, Qiu-Yang Yao, Fan-Chun Zeng, Li-Li Yang, Ju Gao, Da-Yun Tao, Yue-Ju Wang, Jeffrey L Bennetzen, Li-Zhi Gao
Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation...
November 18, 2014: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/24905808/australian-wild-rice-reveals-pre-domestication-origin-of-polymorphism-deserts-in-rice-genome
#12
Gopala Krishnan S, Daniel L E Waters, Robert J Henry
BACKGROUND: Rice is a major source of human food with a predominantly Asian production base. Domestication involved selection of traits that are desirable for agriculture and to human consumers. Wild relatives of crop plants are a source of useful variation which is of immense value for crop improvement. Australian wild rices have been isolated from the impacts of domestication in Asia and represents a source of novel diversity for global rice improvement. Oryza rufipogon is a perennial wild progenitor of cultivated rice...
2014: PloS One
https://www.readbyqxmd.com/read/24684265/transcriptome-population-genomics-reveals-severe-bottleneck-and-domestication-cost-in-the-african-rice-oryza-glaberrima
#13
Benoit Nabholz, Gautier Sarah, François Sabot, Manuel Ruiz, Hélène Adam, Sabine Nidelet, Alain Ghesquière, Sylvain Santoni, Jacques David, Sylvain Glémin
The African cultivated rice (Oryza glaberrima) was domesticated in West Africa 3000 years ago. Although less cultivated than the Asian rice (O. sativa), O. glaberrima landraces often display interesting adaptation to rustic environment (e.g. drought). Here, using RNA-seq technology, we were able to compare more than 12,000 transcripts between 9 O. glaberrima, 10 wild O. barthii and one O. meridionalis individuals. With a synonymous nucleotide diversity πs = 0.0006 per site, O. glaberrima appears as the least genetically diverse crop grass ever documented...
May 2014: Molecular Ecology
https://www.readbyqxmd.com/read/24388514/could-abiotic-stress-tolerance-in-wild-relatives-of-rice-be-used-to-improve-oryza-sativa
#14
REVIEW
Brian J Atwell, Han Wang, Andrew P Scafaro
Oryza sativa and Oryza glaberrima have been selected to acquire and partition resources efficiently as part of the process of domestication. However, genetic diversity in cultivated rice is limited compared to wild Oryza species, in spite of 120,000 genotypes being held in gene banks. By contrast, there is untapped diversity in the more than 20 wild species of Oryza, some having been collected from just a few coastal locations (e.g. Oryza schlechteri), while others are widely distributed (e.g. Oryza nivara and Oryza rufipogon)...
February 2014: Plant Science: An International Journal of Experimental Plant Biology
https://www.readbyqxmd.com/read/24320720/physiological-and-molecular-characterization-of-si-uptake-in-wild-rice-species
#15
Namiki Mitani-Ueno, Hisao Ogai, Naoki Yamaji, Jian Feng Ma
Cultivated rice (Oryza sativa) accumulates high concentration of silicon (Si), which is required for its high and sustainable production. High Si accumulation in cultivated rice is achieved by a high expression of both influx (Lsi1) and efflux (Lsi2) Si transporters in roots. Herein, we physiologically investigated Si uptake, isolated and functionally characterized Si transporters in six wild rice species with different genome types. Si uptake by the roots was lower in Oryza rufipogon, Oryza barthii (AA genome), Oryza australiensis (EE genome) and Oryza punctata (BB genome), but similar in Oryza glumaepatula and Oryza meridionalis (AA genome) compared with the cultivated rice (cv...
July 2014: Physiologia Plantarum
https://www.readbyqxmd.com/read/24280095/molecular-relationships-between-australian-annual-wild-rice-oryza-meridionalis-and-two-related-perennial-forms
#16
Masahiro Sotowa, Kenta Ootsuka, Yuu Kobayashi, Yin Hao, Katsunori Tanaka, Katsuyuki Ichitani, Jonathan M Flowers, Michael D Purugganan, Ikuo Nakamura, Yo-Ichiro Sato, Tadashi Sato, Darren Crayn, Bryan Simon, Daniel LE Waters, Robert J Henry, Ryuji Ishikawa
BACKGROUND: The perennial, Oryza rufipogon distributed from Asia to Australia and the annual O. meridionalis indigenous to Australia are AA genome species in the Oryza. However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of O. meridionalis than to those found in Asian populations of O. rufipogon suggesting that the Australian perennials may represent a new distinct gene pool for rice. RESULTS: Analysis of an Oryza core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of O meridionalis (meridionalis-type)...
2013: Rice
https://www.readbyqxmd.com/read/24202673/polymorphism-and-phylogenetic-relationships-among-species-in-the-genus-oryza-as-determined-by-analysis-of-nuclear-rflps
#17
Z Y Wang, G Second, S D Tanksley
Ninety-three accessions representing 21 species from the genus Oryza were examined for restriction fragment length polymorphism. The majority (78%) of the accessions, for which five individuals were tested, were found to be monomorphic. Most of the polymorphic accessions segregated for only one or two probes and appeared to be mixed pure lines. For most of the Oryza species tested, the majority of the genetic variation (83%) was found between accessions from different species with only 17% between accessions within species...
March 1992: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/24197239/assessment-of-genome-relationships-in-the-genus-oryza-l-based-on-seed-protein-profile-analysis
#18
R Sarkar, S N Raina
Cultivated and wild Oryza species belonging to different genomic groups were studied with regard to their soluble seed-protein profiles. There is an essential uniformity in the banding patterns within various genomes and the basic patterns are not species-specific but genome-specific. O. meridionalis contains a subgenome similar to the A genome of O. rufipogon. Certain specific bands present among A genome species have been found to be useful in tracing the phylogenetic affinity between the cultivated species and their presumed wild progenitors...
October 1992: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/24148990/phylogenetic-relationships-and-genome-divergence-among-the-aa-genome-species-of-the-genus-oryza-as-revealed-by-53-nuclear-genes-and-16-intergenic-regions
#19
Ting Zhu, Ping-Zhen Xu, Jiang-Peng Liu, Sheng Peng, Xin-Chun Mo, Li-Zhi Gao
Rapid radiations have long been regarded as the most challenging issue for elucidating poorly resolved phylogenies in evolutionary biology. The eight diploid AA- genome species in the genus Oryza represent a typical example of a closely spaced series of recent speciation events in plants. However, questions regarding when and how they diversified have long been an issue of extensive interest but remain a mystery. Here, a data set comprising >60 kb of 53 singleton fragments and 16 intergenic regions is used to perform phylogenomic analyses of all eight AA- genome species plus four diploid Oryza species with BB-, CC-, EE- and GG- genomes...
January 2014: Molecular Phylogenetics and Evolution
https://www.readbyqxmd.com/read/24101993/local-differentiation-amidst-extensive-allele-sharing-in-oryza-nivara-and-o-rufipogon
#20
Maria Celeste N Banaticla-Hilario, Ronald G van den Berg, Nigel Ruaraidh Sackville Hamilton, Kenneth L McNally
Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa...
September 2013: Ecology and Evolution
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