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Oryza glaberrima

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
No abstract text is available yet for this article.
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
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...
November 12, 2016: New Phytologist
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 to 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 3 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...
October 20, 2016: Genome Biology and Evolution
Tinde R van Andel, Rachel S Meyer, Saulo A Aflitos, Judith A Carney, Margaretha A Veltman, Dario Copetti, Jonathan M Flowers, Reinout M Havinga, Harro Maat, Michael D Purugganan, Rod A Wing, M Eric Schranz
African rice (Oryza glaberrima) and African cultivation practices are said to have influenced emerging colonial plantation economies in the Americas(1,2). However, the level of impact of African rice practices is difficult to establish because of limited written or botanical records(2,3). Recent findings of O. glaberrima in rice fields of Suriname Maroons bear evidence of the high level of knowledge about rice among African slaves and their descendants, who consecrate it in ancestor rituals(4,5). Here we establish the strong similarity, and hence likely origin, of the first extant New World landrace of O...
October 3, 2016: Nature Plants
Caijin Chen, Wenchuang He, Tondi Yacouba Nassirou, Wei Zhou, Yilong Yin, Xilong Dong, Quanqin Rao, Han Shi, Wubin Zhao, Andrew Efisue, Deming Jin
The introduction of closely related species genomic fragments is an effective way to enrich genetic diversity and creates new germplasms in crops. Here, we studied the genetic diversity of an introgression line (IL) population composed of 106 ILs derived from an interspecific tetra cross between O. glaberrima and O. sativa (RAM3/Jin23B//Jin23B///YuetaiB). The proportion of O. glaberrima genome (PGG) in the ILs ranged from 0.3% to 36.7%, with an average value of 12.32% which is close to the theoretically expected proportion...
2016: PloS One
Thomas Wicker, Yeisoo Yu, Georg Haberer, Klaus F X Mayer, Pradeep Reddy Marri, Steve Rounsley, Mingsheng Chen, Andrea Zuccolo, Olivier Panaud, Rod A Wing, Stefan Roffler
DNA (class 2) transposons are mobile genetic elements which move within their 'host' genome through excising and re-inserting elsewhere. Although the rice genome contains tens of thousands of such elements, their actual role in evolution is still unclear. Analysing over 650 transposon polymorphisms in the rice species Oryza sativa and Oryza glaberrima, we find that DNA repair following transposon excisions is associated with an increased number of mutations in the sequences neighbouring the transposon. Indeed, the 3,000 bp flanking the excised transposons can contain over 10 times more mutations than the genome-wide average...
2016: Nature Communications
Rachel S Meyer, Jae Young Choi, Michelle Sanches, Anne Plessis, Jonathan M Flowers, Junrey Amas, Katherine Dorph, Annie Barretto, Briana Gross, Dorian Q Fuller, Isaac Kofi Bimpong, Marie-Noelle Ndjiondjop, Khaled M Hazzouri, Glenn B Gregorio, Michael D Purugganan
African rice (Oryza glaberrima Steud.) is a cereal crop species closely related to Asian rice (Oryza sativa L.) but was independently domesticated in West Africa ∼3,000 years ago. African rice is rarely grown outside sub-Saharan Africa but is of global interest because of its tolerance to abiotic stresses. Here we describe a map of 2.32 million SNPs of African rice from whole-genome resequencing of 93 landraces. Population genomic analysis shows a population bottleneck in this species that began ∼13,000-15,000 years ago with effective population size reaching its minimum value ∼3,500 years ago, suggesting a protracted period of population size reduction likely commencing with predomestication management and/or cultivation...
September 2016: Nature Genetics
Kanako Bessho-Uehara, Diane R Wang, Tomoyuki Furuta, Anzu Minami, Keisuke Nagai, Rico Gamuyao, Kenji Asano, Rosalyn B Angeles-Shim, Yoshihiro Shimizu, Madoka Ayano, Norio Komeda, Kazuyuki Doi, Kotaro Miura, Yosuke Toda, Toshinori Kinoshita, Satohiro Okuda, Tetsuya Higashiyama, Mika Nomoto, Yasuomi Tada, Hidefumi Shinohara, Yoshikatsu Matsubayashi, Anthony Greenberg, Jianzhong Wu, Hideshi Yasui, Atsushi Yoshimura, Hitoshi Mori, Susan R McCouch, Motoyuki Ashikari
Domestication of crops based on artificial selection has contributed numerous beneficial traits for agriculture. Wild characteristics such as red pericarp and seed shattering were lost in both Asian (Oryza sativa) and African (Oryza glaberrima) cultivated rice species as a result of human selection on common genes. Awnedness, in contrast, is a trait that has been lost in both cultivated species due to selection on different sets of genes. In a previous report, we revealed that at least three loci regulate awn development in rice; however, the molecular mechanism underlying awnlessness remains unknown...
August 9, 2016: Proceedings of the National Academy of Sciences of the United States of America
Joseph Gayin, El-Sayed M Abdel-Aal, Massimo Marcone, John Manful, Eric Bertoft
Enzymatic hydrolysis in combination with gel-permeation and anion-exchange chromatography techniques were employed to characterise the composition of clusters and building blocks of amylopectin from two African rice (Oryza glaberrima) accessions-IRGC 103759 and TOG 12440. The samples were compared with one Asian rice (Oryza sativa) sample (cv WITA 4) and one O. sativa×O. glaberrima cross (NERICA 4). The average DP of clusters from the African rice accessions (ARAs) was marginally larger (DP=83) than in WITA 4 (DP=81)...
September 5, 2016: Carbohydrate Polymers
Zetao Bai, Jinfeng Chen, Yi Liao, Meijiao Wang, Rong Liu, Song Ge, Rod A Wing, Mingsheng Chen
BACKGROUND: Copy number variation (CNV), a complex genomic rearrangement, has been extensively studied in humans and other organisms. In plants, CNVs of several genes were found to be responsible for various important traits; however, the cause and consequence of CNVs remains largely unknown. Recently released next-generation sequencing (NGS) data provide an opportunity for a genome-wide study of CNVs in rice. RESULTS: Here, by an NGS-based approach, we generated a CNV map comprising 9,196 deletions compared to the reference genome 'Nipponbare'...
March 29, 2016: BMC Genomics
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
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