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Oryza glaberrima

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, which has been a major target of cereal crop domestication. The plant architecture transition from the prostrate tiller of typical African wild rice (O. barthii) to the erect tiller of African cultivated rice (Oryza glaberrima) was a key step during African rice domestication. Here we show that PROG7 (PROSTRATE GROWTH 7), a zinc-finger transcription factor gene on chromosome 7, was required for the prostrate growth of African wild rice. Mutations in the promoter region of prog7 reduced the level of gene expression in the tiller base, leading to erect growth in African cultivated rice...
March 14, 2018: Plant Journal: for Cell and Molecular Biology
Yohei Koide, Atsushi Ogino, Takanori Yoshikawa, Yuki Kitashima, Nozomi Saito, Yoshitaka Kanaoka, Kazumitsu Onishi, Yoshihiro Yoshitake, Takuji Tsukiyama, Hiroki Saito, Masayoshi Teraishi, Yoshiyuki Yamagata, Aiko Uemura, Hiroki Takagi, Yoriko Hayashi, Tomoko Abe, Yoshimichi Fukuta, Yutaka Okumoto, Akira Kanazawa
Understanding the genetic basis of reproductive barriers between species has been a central issue in evolutionary biology. The S 1 locus in rice causes hybrid sterility and is a major reproductive barrier between two rice species, Oryza sativa and Oryza glaberrima The O. glaberrima -derived allele (denoted S 1 g ) on the S 1 locus causes preferential abortion of gametes with its allelic alternative (denoted S 1 s ) in S 1 g / S 1 s heterozygotes. Here, we used mutagenesis and screening of fertile hybrid plants to isolate a mutant with an allele, S 1 mut , which does not confer sterility in the S 1 mut / S 1 g and S 1 mut / S 1 s hybrids...
February 14, 2018: Proceedings of the National Academy of Sciences of the United States of America
Abubakar Mohammad Gumi, Pritam Kanti Guha, Abhishek Mazumder, Pawan Jayaswal, Tapan Kumar Mondal
In this study, AP2 DNA-binding domain-containing transcription factor, OglDREB2A, was cloned from the African rice ( Oryza glaberrima ) and compared with 3000 rice genotypes. Further, the phylogenetic and various structural analysis was performed using in silico approaches. Further, to understand its allelic variation in rice, SNPs and indels were detected among the 3000 rice genotypes which indicated that while coding region is highly conserved, yet noncoding regions such as UTR and intron contained most of the variation...
February 2018: 3 Biotech
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
Tapan Kumar Mondal, Alok Kumar Panda, Hukam C Rawal, Tilak Raj Sharma
Oryza glaberrima is the second edible rice in the genus Oryza. It is grown in the African countries. miRNAs are regulatory molecules that are involved in every domains of gene expression including salinity stress response. Although several miRNAs have been reported from various species of Oryza, yet none of them are from this species. Salt treated (200 mM NaCl for 48 h) and control smallRNA libraries of RAM-100, a salt tolerant genotype, each with 2 replications generated 150 conserve and 348 novel miRNAs...
January 12, 2018: Scientific Reports
Ngan Thi Phan, Dirk De Waele, Mathias Lorieux, Lizhong Xiong, Stephane Bellafiore
Meloidogyne graminicola (M. graminicola) is a major plant-parasitic nematode affecting rice cultivation in Asia. Resistance to this nematode was found in the African rice genotypes Oryza glaberrima and O. longistaminata, however, due to interspecific hybrid sterility, the introgression of resistance genes in the widely consumed O. sativa varieties remains challenging. Recently, resistance was found in O. sativa and here we report for the first time the histological and genetic characterization of the resistance to M...
November 21, 2017: Phytopathology
Marie-Noelle Ndjiondjop, Kassa Semagn, Arnaud C Gouda, Sèdjro B Kpeki, Daniel Dro Tia, Mounirou Sow, Alphonse Goungoulou, Moussa Sie, Xavier Perrier, Alain Ghesquiere, Marilyn L Warburton
The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection...
2017: Frontiers in Plant Science
Lautaro Hilbert, Eduardo Góes Neves, Francisco Pugliese, Bronwen S Whitney, Myrtle Shock, Elizabeth Veasey, Carlos Augusto Zimpel, José Iriarte
The development of agriculture is one of humankind's most pivotal achievements. Questions about plant domestication and the origins of agriculture have engaged scholars for well over a century, with implications for understanding its legacy on global subsistence strategies, plant distribution, population health and the global methane budget. Rice is one of the most important crops to be domesticated globally, with both Asia (Oryza sativa L.) and Africa (Oryza glaberrima Steud.) discussed as primary centres of domestication...
October 9, 2017: Nature Ecology & Evolution
Wenjing Ouyang, Paul C Struik, Xinyou Yin, Jianchang Yang
Increasing leaf transpiration efficiency (TE) may provide leads for growing rice like dryland cereals such as wheat (Triticum aestivum). To explore avenues for improving TE in rice, variations in stomatal conductance (gs) and mesophyll conductance (gm) and their anatomical determinants were evaluated in two cultivars from each of lowland, aerobic, and upland groups of Oryza sativa, one cultivar of O. glaberrima, and two cultivars of T. aestivum, under three water regimes. The TE of upland rice, O. glaberrima, and wheat was more responsive to the gm/gs ratio than that of lowland and aerobic rice...
September 15, 2017: Journal of Experimental Botany
Showkat Ahmad Ganie, Ananda Bhusan Debnath, Abubakar Mohammad Gumi, Tapan Kumar Mondal
BACKGROUND: MicroRNAs (miRNAs) are non-coding RNAs that play versatile roles in post-transcriptional gene regulation. Although much is known about their biogenesis, and gene regulation very little is known about their evolutionary relation among the closely related species. RESULT: All the orthologous miRNA genes of Oryza sativa (japonica) from 10 different Oryza species were identified, and the evolutionary changes among these genes were analysed. Significant differences in the expansion of miRNA gene families were observed across the Oryza species...
September 11, 2017: BMC Genomics
Peterson Wambugu, Marie-Noelle Ndjiondjop, Agnelo Furtado, Robert Henry
Amylose content (AC) is a key quality trait in rice. A cross between Oryza glaberrima (African rice) and Oryza sativa (Asian rice) segregating for AC was analyzed by sequencing bulks of individuals with high and low AC. SNP associated with the granule bound starch synthase (GBSS1) locus on chromosome 6 were polymorphic between the bulks. In particular a G/A SNP that would result in an Asp to Asn mutation was identified. This amino acid substitution may be responsible for differences in GBSS activity as it is adjacent to a disulphide linkage conserved in all grass GBSS proteins...
May 12, 2017: Plant Biotechnology Journal
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
Evert Thomas, Eduardo Tovar, Carolina Villafañe, José Leonardo Bocanegra, Rodrigo Moreno
BACKGROUND: Crop wild relatives (CWRs) of rice hold important traits that can contribute to enhancing the ability of cultivated rice (Oryza sativa and O. glaberrima) to produce higher yields, cope with the effects of climate change, and resist attacks of pests and diseases, among others. However, the genetic resources of these species remain dramatically understudied, putting at risk their future availability from in situ and ex situ sources. Here we assess the distribution of genetic diversity of the four rice CWRs known to occur in Colombia (O...
December 2017: Rice
Anne-Sophie Petitot, Tina Kyndt, Rana Haidar, Alexis Dereeper, Myriam Collin, Janice de Almeida Engler, Godelieve Gheysen, Diana Fernandez
Background and Aims: The root-knot nematode Meloidogyne graminicola is responsible for production losses in rice ( Oryza sativa ) in Asia and Latin America. The accession TOG5681 of African rice, O. glaberrima , presents improved resistance to several biotic and abiotic factors, including nematodes. The aim of this study was to assess the cytological and molecular mechanisms underlying nematode resistance in this accession. Methods: Penetration and development in M...
March 1, 2017: Annals of Botany
Paloma Koprovski Menguer, Raul Antonio Sperotto, Felipe Klein Ricachenevsky
Oryza sativa, the common cultivated rice, is one of the most important crops for human consumption, but production is increasingly threatened by abiotic stresses. Although many efforts have resulted in breeding rice cultivars that are relatively tolerant to their local environments, climate changes and population increase are expected to soon call for new, fast generation of stress tolerant rice germplasm, and current within-species rice diversity might not be enough to overcome such needs. The Oryza genus contains other 23 wild species, with only Oryza glaberrima being also domesticated...
2017: Genetics and Molecular Biology
Cécile Monat, Bérengère Pera, Marie-Noelle Ndjiondjop, Mounirou Sow, Christine Tranchant-Dubreuil, Leila Bastianelli, Alain Ghesquière, Francois Sabot
Oryza glaberrima is one of the two cultivated species of rice, and harbors various interesting agronomic traits, especially in biotic and abiotic resistance, compared with its Asian cousin O. sativa. A previous reference genome was published but newer studies highlighted some missing parts. Moreover, global species diversity is known nowadays to be represented by more than one single individual. For that purpose, we sequenced, assembled and annotated de novo three different cultivars from O. glaberrima. After validating our assemblies, we were able to better solve complex regions than the previous assembly and to provide a first insight in pan-genomic divergence between individuals...
January 1, 2017: Genome Biology and Evolution
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
Hélène Pidon, Alain Ghesquière, Sophie Chéron, Souley Issaka, Eugénie Hébrard, François Sabot, Olufisayo Kolade, Drissa Silué, Laurence Albar
A new resistance gene against Rice yellow mottle virus was identified and mapped in a 15-kb interval. The best candidate is a CC-NBS-LRR gene. Rice yellow mottle virus (RYMV) disease is a serious constraint to the cultivation of rice in Africa and selection for resistance is considered to be the most effective management strategy. The aim of this study was to characterize the resistance of Tog5307, a highly resistant accession belonging to the African cultivated rice species (Oryza glaberrima), that has none of the previously identified resistance genes to RYMV...
April 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
Agnès Pinel-Galzi, Christine Dubreuil-Tranchant, Eugénie Hébrard, Cédric Mariac, Alain Ghesquière, Laurence Albar
Rice yellow mottle virus (RYMV) is one of the major diseases of rice in Africa. The high resistance of the Oryza glaberrima Tog7291 accession involves a null allele of the RYMV2 gene, whose ortholog in Arabidopsis, CPR5, is a transmembrane nucleoporin involved in effector-triggered immunity. To optimize field deployment of the RYMV2 gene and improve its durability, which is often a weak point in varietal resistance, we analyzed its efficiency toward RYMV isolates representing the genetic diversity of the virus and the molecular basis of resistance breakdown...
2016: Frontiers in Plant Science
Abdala Gamby Diedhiou, Fatou Kine Mbaye, Daouda Mbodj, Mathieu Ndigue Faye, Sarah Pignoly, Ibrahima Ndoye, Koffi Djaman, Souleymane Gaye, Aboubacry Kane, Laurent Laplaze, Baboucarr Manneh, Antony Champion
The overuse of agricultural chemicals such as fertilizer and pesticides aimed at increasing crop yield results in environmental damage, particularly in the Sahelian zone where soils are fragile. Crop inoculation with beneficial soil microbes appears as a good alternative for reducing agricultural chemical needs, especially for small farmers. This, however, requires selecting optimal combinations of crop varieties and beneficial microbes tested in field conditions. In this study, we investigated the response of rice plants to inoculation with arbuscular mycorrhizal fungi (AMF) and plant growth promoting bacteria (PGPB) under screenhouse and field conditions in two consecutive seasons in Senegal...
2016: PloS One
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