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Oryza glumaepatula

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
Eric J Fuchs, Allan Meneses Martínez, Amanda Calvo, Melania Muñoz, Griselda Arrieta-Espinoza
Wild crop relatives are an important source of genetic diversity for crop improvement. Diversity estimates are generally lacking for many wild crop relatives. The objective of the present study was to analyze how genetic diversity is distributed within and among populations of the wild rice species Oryza glumaepatula in Costa Rica. We also evaluated the likelihood of gene flow between wild and commercial rice species because the latter is commonly sympatric with wild rice populations. Introgression may change wild species by incorporating alleles from domesticated species, increasing the risk of losing original variation...
2016: PeerJ
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
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
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
Peterson W Wambugu, Marta Brozynska, Agnelo Furtado, Daniel L Waters, Robert J Henry
Rice is the most important crop in the world, acting as the staple food for over half of the world's population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species...
2015: Scientific Reports
Aluana Gonçalves Abreu, Thalita Marra Rosa, Tereza Cristina de Oliveira Borba, Rosana Pereira Vianello, Paulo Hideo Nakano Rangel, Claudio Brondani
The level and distribution of the genetic variability in 18 natural populations of Oryza glumaepatula that were collected from two Brazilian states were estimated using a set of 23 highly informative SSR markers. Samples comprising 78 and 117 individuals from populations of the states of Tocantins and Roraima, respectively, were evaluated in order to integrate and support previous studies that were carried out with populations of O. glumaepatula from Brazil. A total of 189 alleles were identified with an average of 8...
August 2015: Genetica
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
Mitsukazu Sakata, Yoshiyuki Yamagata, Kazuyuki Doi, Atsushi Yoshimura
Hybrid incompatibility plays an important role in establishment of post-zygotic reproductive isolation. To unveil genetic basis of hybrid incompatibilities between diverged species of genus Oryza AA genome species, we conducted genetic dissection of hybrid sterility loci, S22(t), which had been identified in backcross progeny derived from Oryza sativa ssp. japonica (recurrent parent) and South American wild rice O. glumaepatula near the end of the short arm of chromosome 2. The S22(t) region was found to be composed of two loci, designated S22A and S22B, that independently induce F1 pollen sterility...
December 2014: Breeding Science
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
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
Paulo Ivan Fernandes Júnior, Gilmara Maria Duarte Pereira, Liamara Perin, Luana Mesquita da Silva, Alexandre Cardoso Baraúna, Francilene Muniz Alvess, Samuel Ribeiro Passos, Jerri Edson Zilli
The association of wild grasses with diazotrophic bacteria in Brazilian biomes is poorly understood. The isolation and characterization of bacteria associated with wild grasses can contribute to understand the diazotrophic ecology as well as to identify bacteria with biotechnological applications. In this study, we isolated and characterized diazotrophic bacterial isolates from Oryza glumaepatula collected in Cerrado and Forest areas of the Amazon in Roraima State, Brazil. Healthy O. glumepatula plants were collected at five sampling sites at Forest and seven at Cerrado, respectively...
June 2013: Revista de Biología Tropical
Marines M G Karasawa, Roland Vencovsky, Cynthia M Silva, Daruska C Cardim, Eduardo de A Bressan, Giancarlo C X Oliveira, Elizabeth A Veasey
The study of the genetic structure of wild plant populations is essential for their management and conservation. Several DNA markers have been used in such studies, as well as isozyme markers. In order to provide a better comprehension of the results obtained and a comparison between markers which will help choose tools for future studies in natural populations of Oryza glumaepatula, a predominantly autogamous species, this study used both isozymes and microsatellites to assess the genetic diversity and genetic structure of 13 populations, pointing to similarities and divergences of each marker, and evaluating the relative importance of the results for studies of population genetics and conservation...
December 2012: Revista de Biología Tropical
Khin Thanda Win, Yoshiyuki Yamagata, Yuta Miyazaki, Kazuyuki Doi, Hideshi Yasui, Atsushi Yoshimura
Loss of function of duplicated genes plays an important role in the evolution of postzygotic reproductive isolation. The widespread occurrence of gene duplication followed by rapid loss of function of some of the duplicate gene copies suggests the independent evolution of loss-of-function alleles of duplicate genes in divergent lineages of speciation. Here, we found a novel loss-of-function allele of S27 in the Asian annual wild species Oryza nivara, designated S27-niv (s), that leads to F(1) pollen sterility in a cross between O...
February 2011: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Yoshiyuki Yamagata, Eiji Yamamoto, Kohichiro Aya, Khin Thanda Win, Kazuyuki Doi, Sobrizal, Tomoko Ito, Hiroyuki Kanamori, Jianzhong Wu, Takashi Matsumoto, Makoto Matsuoka, Motoyuki Ashikari, Atsushi Yoshimura
Hybrid incompatibility in F(1) hybrids or later generations is often observed as sterility or inviability. This incompatibility acts as postzygotic reproductive isolation, which results in the irreversible divergence of species. Here, we show that the reciprocal loss of duplicated genes encoding mitochondrial ribosomal protein L27 causes hybrid pollen sterility in F(1) hybrids of the cultivated rice Oryza sativa and its wild relative O. glumaepatula. Functional analysis revealed that this gene is essential for the later stage of pollen development, and distribution analysis suggests that the gene duplication occurred before the divergence of the AA genome species...
January 26, 2010: Proceedings of the National Academy of Sciences of the United States of America
Julie Petit, Emmanuelle Bourgeois, Wilfried Stenger, Martine Bès, Gaétan Droc, Donaldo Meynard, Brigitte Courtois, Alain Ghesquière, François Sabot, Olivier Panaud, Emmanuel Guiderdoni
Retrotransposons are mobile genetic elements, ubiquitous in Eukaryotic genomes, which have proven to be major genetic tools in determining phylogeny and structuring genetic diversity, notably in plants. We investigate here the diversity of the Ty1-copia retrotransposon Tos17 in the cultivated rice of Asian origin (Oryza sativa L.) and related AA genome species of the Oryza genus, to contribute understanding of the complex evolutionary history in this group of species through that of the element in the lineages...
December 2009: Molecular Genetics and Genomics: MGG
Julie Orjuela, Andrea Garavito, Matthieu Bouniol, Juan David Arbelaez, Laura Moreno, Jennifer Kimball, Gregory Wilson, Jean-François Rami, Joe Tohme, Susan R McCouch, Mathias Lorieux
To facilitate the creation of easily comparable, low-resolution genetic maps with evenly distributed markers in rice (Oryza sativa L.), we conceived of and developed a Universal Core Genetic Map (UCGM). With this aim, we derived a set of 165 anchors, representing clusters of three microsatellite or simple sequence repeat (SSR) markers arranged into non-recombining groups. Each anchor consists of at least three, closely linked SSRs, located within a distance below the genetic resolution provided by common, segregating populations (<500 individuals)...
February 2010: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Seonghee Lee, Stefano Costanzo, Yulin Jia, Kenneth M Olsen, Ana L Caicedo
The race-specific resistance gene Pi-ta has been effectively used to control blast disease, one of the most destructive plant diseases worldwide. A single amino acid change at the 918 position of the Pi-ta protein was known to determine resistance specificity. To understand the evolutionary dynamics present, we examined sequences of the Pi-ta locus and its flanking regions in 159 accessions composed of seven AA genome Oryza species: O. sativa, O. rufipogon, O. nivara, O. meridionalis, O. glaberrima, O. barthii, and O...
December 2009: Genetics
Ana Rosa de Campos Vaz, Tereza Cristina de Oliveira Borba, Claudio Brondani, Paulo Hideo Nakano Rangel, Graziela Silvia de Oliveira Camargo, Mariana Pires de Campos Telles, José Alexandre Felizola Diniz Filho, Rosana Pereira Vianello Brondani
Knowledge of natural diversity and population structures of wild species, which might be related to cultivated species, is fundamental for conservation and breeding purposes. In this study, a genetic characterization of a large population of Oryza glumaepatula, occurring in a 10 km(2) area located at Tamengo Basin (Paraguay River, Brazil), was performed using SSR markers. This population is annually dragged from the river to permit navigation; one goal of this study was to examine the impact of this removal on genetic variability...
November 2009: Genetica
P N Rangel, R P V Brondani, P H N Rangel, C Brondani
The reduced genetic variability of modern rice varieties (Oryza sativa) is of concern because it reduces the possibilities of genetic gain in breeding programs. Introgression lines (ILs) containing genomic fragments from wild rice can be used to obtain new improved cultivars. The objective of the present study was to perform the agronomic and molecular characterizations of 35 BC2F8 ILs from the cross O. glumaepatula x O. sativa, aiming to select high-yielding ILs to be used in rice-breeding programs. All 35 ILs were field evaluated in the season 2002/2003 in three locations and the 15 best performing ones were evaluated in the season 2003/2004 in five locations...
2008: Genetics and Molecular Research: GMR
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