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Oryza barthii

Min Hu, Shuwei Lv, Wenguang Wu, Yongcai Fu, Fengxia Liu, Bingbing Wang, Weiguo Li, Ping Gu, Hongwei Cai, Chuanqing Sun, Zuofeng Zhu
Plant architecture is a key agronomical factor determining crop yield and has been a major target of cereal crop domestication. The transition of plant architecture from the prostrate tiller of typical African wild rice (Oryza barthii) to the erect tiller of African cultivated rice (Oryza glaberrima) was a key step during domestication of African rice. Here we show that PROG7 (PROSTRATE GROWTH 7), a zinc-finger transcription factor gene on chromosome 7, is required for the prostrate growth of African wild rice...
May 2018: Plant Journal: for Cell and Molecular Biology
Theophile Odjo, Yohei Koide, Drissa Silue, Seiji Yanagihara, Takashi Kumashiro, Yoshimichi Fukuta
The genetic variation in resistance to blast ( Pyricularia oryzae Cavara) in 195 rice accessions comprising 3 species of the AA genome complex (Asian rice [ Oryza sativa L.], African rice [ Oryza glaberrima Steud.] and wild rice [ Oryza barthii ]) was investigated based on their patterns of reaction to standard differential blast isolates (SDBIs) and SSR marker polymorphism data. Cluster analysis of the polymorphism data of 61 SSR markers identified 3 major clusters: cluster A (mainly Japonica Group or upland accessions), cluster B (mainly Indica Group or lowland accessions) and cluster C ( O...
December 2017: Breeding Science
Wenguang Wu, Xiaoyun Liu, Muhua Wang, Rachel S Meyer, Xiaojin Luo, Marie-Noelle Ndjiondjop, Lubin Tan, Jianwei Zhang, Jianzhong Wu, Hongwei Cai, Chuanqing Sun, Xiangkun Wang, Rod A Wing, Zuofeng Zhu
Grain size is one of the most important components of grain yield and selecting large seeds has been a main target during plant domestication. Surprisingly, the grain of African cultivated rice (Oryza glaberrima Steud.) typically is smaller than that of its progenitor, Oryza barthii. Here we report the cloning and characterization of a quantitative trait locus, GL4, controlling the grain length on chromosome 4 in African rice, which regulates longitudinal cell elongation of the outer and inner glumes. Interestingly, GL4 also controls the seed shattering phenotype like its orthologue SH4 gene in Asian rice...
May 8, 2017: Nature Plants
K N Ta, H Adam, Y M Staedler, J Schönenberger, T Harrop, J Tregear, N V Do, P Gantet, A Ghesquière, S Jouannic
BACKGROUND: The African rice Oryza glaberrima was domesticated from its wild relative Oryza barthii about 3000 years ago. During the domestication process, panicle complexity changed from a panicle with low complexity in O. barthii, to a highly branched panicle carrying more seeds in O. glaberrima. To understand the basis of this differential panicle development between the two species, we conducted morphological and molecular analyses of early panicle development. RESULTS: Using X-ray tomography, we analyzed the morphological basis of early developmental stages of panicle development...
2017: EvoDevo
Khin Thanda Win, Yoshiyuki Yamagata, Kazuyuki Doi, Kazuhiro Uyama, Yasuko Nagai, Yosuke Toda, Takahiro Kani, Motoyuki Ashikari, Hideshi Yasui, Atsushi Yoshimura
Reduced seed shattering was a critical evolutionary step in crop domestication. Two cultivated rice species, Oryza sativa and Oryza glaberrima, were independently domesticated from the wild species Oryza rufipogon in Asia and Oryza barthii in Africa, respectively. A single nucleotide polymorphism (SNP) in the c gene, which encodes a trihelix transcription factor, causes nonshattering in O. sativa. However, the genetic mechanism of nonshattering in O. glaberrima is poorly understood. We conducted an association analysis for the coding sequences of SH3/SH4 in AA- genome rice species and the mutation suggested to cause nonshattering was demonstrated to do so using a positional-cloning approach in the O...
March 2017: New Phytologist
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
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