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Oryza barthii

Ying Yang, Jiawu Zhou, Jing Li, Peng Xu, Yu Zhang, Dayun Tao
In order to know the genetic nature of hybrid sterility further, three populations, a BC4F2 population derived from Oryza nivara crossed with Yundao 1, a BC4F2 population derived from O. rufipogon crossed with Yundao 1, and a BC10F1 population derived from a cross between O. barthii and Dianjingyou 1 were developed, respectively. Three hybrid sterility QTLs, qHS-6a, qHS-6b, and qHS-6c, detected from those three populations, were mapped into the region between RM190 and RM510, RM190 and RM3414, RM190 and RM587 on chromosome 6, respectively...
June 2016: Breeding Science
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
K N Ta, F Sabot, H Adam, Y Vigouroux, S De Mita, A Ghesquière, N V Do, P Gantet, S Jouannic
BACKGROUND: Rice exhibits a wide range of panicle structures. To explain these variations, much emphasis has been placed on changes in transcriptional regulation, but no large-scale study has yet reported on changes in small RNA regulation in the various rice species. To evaluate this aspect, we performed deep sequencing and expression profiling of small RNAs from two closely related species with contrasting panicle development: the cultivated African rice Oryza glaberrima and its wild relative Oryza barthii...
December 2016: Rice
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
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
Kai Wang, Peterson W Wambugu, Bin Zhang, Alex Chi Wu, Robert J Henry, Robert G Gilbert
The molecular structure and gelatinization properties of starches from domesticated African rice (Oryza glaberrima) and its wild progenitor (Oryza barthii) are determined and comparison made with Asian domesticated rice (Oryza sativa), the commonest commercial rice. This suggests possible enzymatic processes contributing to the unique traits of the African varieties. These have similar starch structures, including smaller amylose molecules, but larger amounts of amylose chains across the whole amylose chain-length distribution, and higher amylose contents, than O...
September 20, 2015: Carbohydrate Polymers
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
Julie Orjuela, François Sabot, Sophie Chéron, Yves Vigouroux, Hélène Adam, Harold Chrestin, Kayode Sanni, Mathias Lorieux, Alain Ghesquière
We present here the first curated collection of wild and cultivated African rice species. For that, we designed specific SNPs and were able to structure these very low diverse species. Oryza glaberrima, the cultivated African rice, is endemic from Africa. This species and its direct ancestor, O. barthii, are valuable tool for improvement of Asian rice O. sativa in terms of abiotic and biotic stress resistance. However, only a few limited studies about the genetic diversity of these species were performed. In the present paper, and for the first time at such extend, we genotyped 279 O...
October 2014: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Muhua Wang, Yeisoo Yu, Georg Haberer, Pradeep Reddy Marri, Chuanzhu Fan, Jose Luis Goicoechea, Andrea Zuccolo, Xiang Song, Dave Kudrna, Jetty S S Ammiraju, Rosa Maria Cossu, Carlos Maldonado, Jinfeng Chen, Seunghee Lee, Nick Sisneros, Kristi de Baynast, Wolfgang Golser, Marina Wissotski, Woojin Kim, Paul Sanchez, Marie-Noelle Ndjiondjop, Kayode Sanni, Manyuan Long, Judith Carney, Olivier Panaud, Thomas Wicker, Carlos A Machado, Mingsheng Chen, Klaus F X Mayer, Steve Rounsley, Rod A Wing
The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa...
September 2014: Nature Genetics
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
K Palanichamy, E A Siddiq
The interrelationships among ten different A-genome species of the genus Oryza were studied based on variations in the electrophoretic pattern of isoenzymes of two non-specific enzymes, esterase and peroxidase. There were 16 isoenzymes of esterase and 14 of peroxidase. The esterase pattern could be classified into 3 different Zymograms 1e, 2e & 3e based on the presence and/or absence of bands at particular Rf values. The pattern le was found exclusively among the species and varietal groups of sativa complex, whereas 2e and 3e were distributed exclusively among the species of the glaberrima complex and related wild forms...
September 1977: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
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
Chengjun Zhang, Jun Wang, Nicholas C Marowsky, Manyuan Long, Rod A Wing, Chuanzhu Fan
In an effort to identify newly evolved genes in rice, we searched the genomes of Asian-cultivated rice Oryza sativa ssp. japonica and its wild progenitors, looking for lineage-specific genes. Using genome pairwise comparison of approximately 20-Mb DNA sequences from the chromosome 3 short arm (Chr3s) in six rice species, O. sativa, O. nivara, O. rufipogon, O. glaberrima, O. barthii, and O. punctata, combined with synonymous substitution rate tests and other evidence, we were able to identify potential recently duplicated genes, which evolved within the last 1 Myr...
2013: Genome Biology and Evolution
Khidir W Hilu, Lioudmila V Sharova
Patterns of sequence variation of nuclear genes encoding 10-kDa and 16-kDa prolamin seed storage proteins were examined in Oryza glaberrima (African rice, Poaceae) and O. barthii and compared to available sequences for the genus to assess potential application of these gene families in evolutionary studies. Sequence variation among species in 10-kDa genes was very low. In contrast, the 16-kDa genes have undergone rapid evolution, displaying a larger number of length and point mutations that in some cases result in frame shift or produce truncated protein or pseudogenes...
February 2002: American Journal of Botany
Zhi-Ming Li, Xiao-Ming Zheng, Song Ge
Nucleotide variation in 14 unlinked nuclear genes was investigated in species-wide samples of African rice (Oryza glaberrima) and its wild progenitor (O. barthii). Average estimates of nucleotide diversity were extremely low in both species (θ (sil) = 0.0007 for O. glaberrima; θ (sil) = 0.0024 for O. barthii). About 70% less diversity was found in O. glaberrima than in its progenitor O. barthii. Coalescent simulation indicated that such dramatic reduction of nucleotide diversity in African rice could be explained mainly by a severe bottleneck during its domestication...
June 2011: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Bo-Feng Zhu, Lizhen Si, Zixuan Wang, Yan Zhou, Jinjie Zhu, Yingying Shangguan, Danfeng Lu, Danlin Fan, Canyang Li, Hongxuan Lin, Qian Qian, Tao Sang, Bo Zhou, Yuzo Minobe, Bin Han
The genetic mechanism involved in a transition from the black-colored seed hull of the ancestral wild rice (Oryza rufipogon and Oryza nivara) to the straw-white seed hull of cultivated rice (Oryza sativa) during grain ripening remains unknown. We report that the black hull of O. rufipogon was controlled by the Black hull4 (Bh4) gene, which was fine-mapped to an 8.8-kb region on rice chromosome 4 using a cross between O. rufipogon W1943 (black hull) and O. sativa indica cv Guangluai 4 (straw-white hull). Bh4 encodes an amino acid transporter...
March 2011: Plant Physiology
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
X Wang, Y Jia, Q Y Shu, D Wu
The Pi-ta gene in rice confers resistance to races of Magnaporthe oryzae that contain AVR-Pita. Pi-ta encodes a predicted cytoplasmic receptor protein with a nucleotide-binding site and a leucine-rich domain. A panel of 51 Oryza accessions of AA genome species Oryza sativa, O. glaberrima, O. rufipogon, O. nivara, and O. barthii, and CC genome species O. officinalis were sequenced to investigate the diversity present in the exon and intron regions of the Pi-ta gene. Two major clades were identified, consisting of 16 different sequences with numerous insertion and deletions...
December 2008: Phytopathology
Yutaka Iwamatsu, Chizuru Aoki, Masaaki Takahashi, Mika Teranishi, Yuanying Ding, Chuanqing Sun, Tadashi Kumagai, Jun Hidema
We investigated the UVB-sensitivity in 12 rice strains belonging to two cultivated species (O. sativa and O. glaberrima) and three wild species (O. barthii, O. meridionalis and O. rufipogon) of rice possessing the AA genome, while focusing on the CPD photolyase activity and the genotypes of CPD photolyase. Although the UVB sensitivity, CPD photolyase activity, and CPD photolyase genotype varied widely among these rice species, the sensitivity to UVB radiation depended on the activity of the CPD photolyase, regardless of grass shape, habitat, or species...
March 2008: Photochemical & Photobiological Sciences
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