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Oryza glaberrima

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https://www.readbyqxmd.com/read/27907023/field-trials-reveal-ecotype-specific-responses-to-mycorrhizal-inoculation-in-rice
#1
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
https://www.readbyqxmd.com/read/27861933/a-single-base-change-explains-the-independent-origin-of-and-selection-for-the-nonshattering-gene-in-african-rice-domestication
#2
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
https://www.readbyqxmd.com/read/27797953/de-novo-assemblies-of-three-oryza-glaberrima-accessions-provide-first-insights-about-pan-genome-of-african-rices
#3
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
https://www.readbyqxmd.com/read/27694825/tracing-ancestor-rice-of-suriname-maroons-back-to-its-african-origin
#4
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
https://www.readbyqxmd.com/read/27603678/genetic-diversity-and-phenotypic-variation-in-an-introgression-line-population-derived-from-an-interspecific-cross-between-oryza-glaberrima-and-oryza-sativa
#5
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
https://www.readbyqxmd.com/read/27599761/dna-transposon-activity-is-associated-with-increased-mutation-rates-in-genes-of-rice-and-other-grasses
#6
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
https://www.readbyqxmd.com/read/27500524/domestication-history-and-geographical-adaptation-inferred-from-a-snp-map-of-african-rice
#7
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
https://www.readbyqxmd.com/read/27466405/loss-of-function-at-rae2-a-previously-unidentified-epfl-is-required-for-awnlessness-in-cultivated-asian-rice
#8
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
https://www.readbyqxmd.com/read/27185123/structure-of-clusters-and-building-blocks-in-amylopectin-from-african-rice-accessions
#9
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
https://www.readbyqxmd.com/read/27025496/the-impact-and-origin-of-copy-number-variations-in-the-oryza-species
#10
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'...
2016: BMC Genomics
https://www.readbyqxmd.com/read/26969003/mir2118-triggered-phased-sirnas-are-differentially-expressed-during-the-panicle-development-of-wild-and-domesticated-african-rice-species
#11
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
https://www.readbyqxmd.com/read/26687860/inconsistent-diversities-between-nuclear-and-plastid-genomes-of-aa-genome-species-in-the-genus-oryza
#12
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
https://www.readbyqxmd.com/read/26686152/unit-and-internal-chain-profile-of-african-rice-oryza-glaberrima-amylopectin
#13
Joseph Gayin, El-Sayed M Abdel-Aal, John Manful, Eric Bertoft
High-performance anion-exchange chromatography was used to study the unit chain profiles of amylopectins and their φ,β-limit dextrins from two African rice (Oryza glaberrima) accessions-TOG 12440 and IRGC 103759. The samples were compared with two Asian rice (Oryza sativa) samples (cv Koshihikari and cv WITA 4) and one O. sativa × O. glaberrima cross (NERICA 4). The ratio of short:long chains ranged between 12.1 and 13.8, and the ratio of A:B-chains was ∼ 1.0 in all samples. A significant difference was observed in the distribution of internal chains with regards to the proportion of short "fingerprint" B-chains (Bfp-chains), which in the φ,β-limit dextrins have a degree of polymerization (DP) 3-7...
February 10, 2016: Carbohydrate Polymers
https://www.readbyqxmd.com/read/26503287/genome-wide-survey-and-expression-analysis-of-the-osca-gene-family-in-rice
#14
Yunshuang Li, Fang Yuan, Zhaohong Wen, Yihao Li, Fang Wang, Tao Zhu, Wenqing Zhuo, Xi Jin, Yingdian Wang, Heping Zhao, Zhen-Ming Pei, Shengcheng Han
BACKGROUND: Reception of and response to exogenous and endogenous osmotic changes is important to sustain plant growth and development, as well as reproductive formation. Hyperosmolality-gated calcium-permeable channels (OSCA) were first characterised as an osmosensor in Arabidopsis and are involved in the perception of extracellular changes to trigger hyperosmolality-induced [Ca(2+)]i increases (OICI). To explore the potential biological functions of OSCAs in rice, we performed a bioinformatics and expression analysis of the OsOSCA gene family...
2015: BMC Plant Biology
https://www.readbyqxmd.com/read/26338659/convergent-loss-of-awn-in-two-cultivated-rice-species-oryza-sativa-and-oryza-glaberrima-is-caused-by-mutations-in-different-loci
#15
Tomoyuki Furuta, Norio Komeda, Kenji Asano, Kanako Uehara, Rico Gamuyao, Rosalyn B Angeles-Shim, Keisuke Nagai, Kazuyuki Doi, Diane R Wang, Hideshi Yasui, Atsushi Yoshimura, Jianzhong Wu, Susan R McCouch, Motoyuki Ashikari
A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from Oryza nivara, Oryza rufipogon, and Oryza glaberrima donors...
November 2015: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/26169392/fine-mapping-of-s37-a-locus-responsible-for-pollen-and-embryo-sac-sterility-in-hybrids-between-oryza-sativa-l-and-o-glaberrima-steud
#16
Yumin Shen, Zhigang Zhao, Hongyang Ma, Xiaofeng Bian, Yang Yu, Xiaowen Yu, Haiyuan Chen, Linglong Liu, Wenwei Zhang, Ling Jiang, Jiawu Zhou, Dayun Tao, Jianmin Wan
Hybrid sterility locus S37 between Oryza glaberrima and Oryza sativa results in both pollen and embryo sac sterility. Interspecific crossing between African cultivated rice Oryza glaberrima and Oryza sativa cultivars is hindered by hybrid sterility. To dissect the mechanism of interspecific hybrid sterility, we developed a near-isogenic line (NIL)-S37 using Dianjingyou1 (DJY1) as the recipient parent and an African cultivated rice variety as the donor parent. Empty pollen and embryo sac sterility were observed in F1 hybrids between DJY1 and NIL-S37...
November 2015: Plant Cell Reports
https://www.readbyqxmd.com/read/26050893/the-biosynthesis-structure-and-gelatinization-properties-of-starches-from-wild-and-cultivated-african-rice-species-oryza-barthii-and-oryza-glaberrima
#17
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
https://www.readbyqxmd.com/read/25985140/natural-alleles-of-a-proteasome-%C3%AE-2-subunit-gene-contribute-to-thermotolerance-and-adaptation-of-african-rice
#18
Xin-Min Li, Dai-Yin Chao, Yuan Wu, Xuehui Huang, Ke Chen, Long-Gang Cui, Lei Su, Wang-Wei Ye, Hao Chen, Hua-Chang Chen, Nai-Qian Dong, Tao Guo, Min Shi, Qi Feng, Peng Zhang, Bin Han, Jun-Xiang Shan, Ji-Ping Gao, Hong-Xuan Lin
Global warming threatens many aspects of human life, for example, by reducing crop yields. Breeding heat-tolerant crops using genes conferring thermotolerance is a fundamental way to help deal with this challenge. Here we identify a major quantitative trait locus (QTL) for thermotolerance in African rice (Oryza glaberrima), Thermo-tolerance 1 (TT1), which encodes an α2 subunit of the 26S proteasome involved in the degradation of ubiquitinated proteins. Ubiquitylome analysis indicated that OgTT1 protects cells from heat stress through more efficient elimination of cytotoxic denatured proteins and more effective maintenance of heat-response processes than achieved with OsTT1...
July 2015: Nature Genetics
https://www.readbyqxmd.com/read/25954322/genome-wide-comparison-of-asian-and-african-rice-reveals-high-recent-activity-of-dna-transposons
#19
Stefan Roffler, Thomas Wicker
BACKGROUND: DNA (Class II) transposons are ubiquitous in plant genomes. However, unlike for (Class I) retrotransposons, only little is known about their proliferation mechanisms, activity, and impact on genomes. Asian and African rice (Oryza sativa and O. glaberrima) diverged approximately 600,000 years ago. Their fully sequenced genomes therefore provide an excellent opportunity to study polymorphisms introduced from recent transposon activity. RESULTS: We manually analyzed 1,821 transposon related polymorphisms among which we identified 487 loci which clearly resulted from DNA transposon insertions and excisions...
2015: Mobile DNA
https://www.readbyqxmd.com/read/25842177/rapid-turnover-of-antimicrobial-type-cysteine-rich-protein-genes-in-closely-related-oryza-genomes
#20
Matthew R Shenton, Hajime Ohyanagi, Zi-Xuan Wang, Atsushi Toyoda, Asao Fujiyama, Toshifumi Nagata, Qi Feng, Bin Han, Nori Kurata
Defensive and reproductive protein genes undergo rapid evolution. Small, cysteine-rich secreted peptides (CRPs) act as antimicrobial agents and function in plant intercellular signaling and are over-represented among reproductively expressed proteins. Because of their roles in defense, reproduction and development and their presence in multigene families, CRP variation can have major consequences for plant phenotypic and functional diversification. We surveyed the CRP genes of six closely related Oryza genomes comprising Oryza sativa ssp...
October 2015: Molecular Genetics and Genomics: MGG
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