Dynamic Differential Evolution Schemes of WRKY Transcription
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Oryza Glaberrima Steud)
plants Review Advances in Molecular Genetics and Genomics of African Rice (Oryza glaberrima Steud) Peterson W. Wambugu 1, Marie-Noelle Ndjiondjop 2 and Robert Henry 3,* 1 Kenya Agricultural and Livestock Research Organization, Genetic Resources Research Institute, P.O. Box 30148 – 00100, Nairobi, Kenya; [email protected] 2 M’bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Ivory Coast; [email protected] 3 Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia * Correspondence: [email protected]; +61-7-661733460551 Received: 23 August 2019; Accepted: 25 September 2019; Published: 26 September 2019 Abstract: African rice (Oryza glaberrima) has a pool of genes for resistance to diverse biotic and abiotic stresses, making it an important genetic resource for rice improvement. African rice has potential for breeding for climate resilience and adapting rice cultivation to climate change. Over the last decade, there have been tremendous technological and analytical advances in genomics that have dramatically altered the landscape of rice research. Here we review the remarkable advances in knowledge that have been witnessed in the last few years in the area of genetics and genomics of African rice. Advances in cheap DNA sequencing technologies have fuelled development of numerous genomic and transcriptomic resources. Genomics has been pivotal in elucidating the genetic architecture of important traits thereby providing a basis for unlocking important trait variation. Whole genome re-sequencing studies have provided great insights on the domestication process, though key studies continue giving conflicting conclusions and theories. However, the genomic resources of African rice appear to be under-utilized as there seems to be little evidence that these vast resources are being productively exploited for example in practical rice improvement programmes. -
EFFECT of WEEDY RICE (Oryza Sativa L.)
EFFECT OF WEEDY RICE (Oryza sativa L.) ON THE YIELD OF CULTIVATED RICE (Oryza sativa L.) IN GREENHOUSE AND FIELD ENVIRONMENT SALMAH BINTI TAJUDDIN UNIVERSITI SAINS MALAYSIA 2014 EFFECT OF WEEDY RICE (Oryza sativa L.) ON THE YIELD OF CULTIVATED RICE (Oryza sativa L.) IN GREENHOUSE AND FIELD ENVIRONMENT by SALMAH BINTI TAJUDDIN Thesis submitted in fulfilment of the requirements for the degree of Master of Science AUGUST 2014 ACKNOWLEDGEMENTS My postgraduate (MSc) study at the Universiti Sains Malaysia (School of Biological Sciences) was a great challenge. It was made possible with the kind assistance of many individuals, either directly or indirectly, to whom I am indebted, not all of whom are mentioned in this page. First and foremost, my deepest appreciation goes to Prof. Mashhor Mansor for his strong support, unweary supervision and motivating guidance during the course of my study. In addition, I was also trained in writing scientific papers and had the opportunity to present scientific papers in seminars and conferences. Other academicians had also given support through inspirational motivations and guidance, particularly Dr. Azmi Man, Prof. Nashriyah Mat and Dr. Asyraf Mansor, my co-supervisors, to all of whom I am very grateful. I wish to thank the staff of the Malaysian Meteorological Department Pulau Pinang for providing me the necessary meteorological data needed for my thesis. The staff of MARDI (Seberang Perai) had been very helpful in my experimental work, especially En. Awang, En. Ebnil, En. Mustafa, Pn. Norhayati and Pn. Aqilah. The staff of USM for help me solve statistics analysis problems, particularly Dr. -
Invasive Plants of West Africa: Concepts, Overviews and Sustainable Management
& ling Wa yc s c te e M Noba et al., Adv Recycling Waste Manag 2017, 2:1 R a n n i a Advances in Recycling & Waste s g DOI: 10.4172/2475-7675.1000121 e e c m n e a n v t d A Management: Open Access Research Article Open Access Invasive Plants of West Africa: Concepts, Overviews and Sustainable Management Noba K1*, Bassene C1,2, Ngom A1, Gueye M1, Camara AA1, Kane M1, Ndoye F1,3, Dieng B1, Rmballo R1, Ba N1, Bodian M Y1, Sane S1, Diop D1,4, Gueye M1,5, Konta I S1,6, Kane A1,3, Mbaye MS1, and Ba AT1 1Laboratory of Botany and Biodiversity, Plant Biology Department, Faculty of Sciences and Technics, University Cheikh Anta Diop, Dakar-Fann, PB 5005, Senegal 2Section of Plant Production and Agriculture, Faculty of Science and Agriculture, Aquaculture and Food Technology, University Gaston Berger of Saint Louis, PB 234 Saint Louis, Senegal 3Common Microbiology Laboratory, Institute of Research for Development, Hann Bel Air Dakar, Senegal 4Laboratory of Botany, Fundamental Institute of Black Africa (IFAN), PB 5005 Dakar-Fann, Senegal 5Direction of National Parks of Senegal, PB 5135, Dakar-Fann, Senegal 6National Agency of Insertion and Agricultural Development (NAIAD), Ministry of Agriculture, Dakar, Senegal Abstract Invasive species are considered as one of the most environmental challenges of the 21st century. They constitute the second cause of biodiversity loss and lead to high economic disruption and public health. Despite significant, financial and human investments made by countries and world conservation of biodiversity agencies, there are not strategies that lead to appropriate measures for sustainable management and control. -
A Comparative Study of Genetic Relationships Among the AA-Genome Oryza Species Using RAPD and SSR Markers
____________________________________________________________________________www.paper.edu.cn Theor Appl Genet (2003) 108:113–120 DOI 10.1007/s00122-003-1414-x ORIGINAL PAPER Fugang Ren · Bao-Rong Lu · Shaoqing Li · Jingyu Huang · Yingguo Zhu A comparative study of genetic relationships among the AA-genome Oryza species using RAPD and SSR markers Received: 14 February 2003 / Accepted: 31 May 2003 / Published online: 19 September 2003 Springer-Verlag 2003 Abstract In order to estimate genetic relationships of the nome Oryza accessions. However, the RAPD analysis AA-genome Oryza species, RAPD and SSR analyses provides a more-informative result in terms of the overall were performed with 45 accessions, including 13 culti- genetic relationships at the species level compared to the vated varieties (eight Oryza sativa and five Oryza SSR analysis. The SSR analysis effectively reveals glaberrima) and 32 wild accessions (nine Oryza rufi- diminutive variation among accessions or individuals pogon, seven Oryza nivara, three Oryza glumaepatula, within the same species, given approximately the same four Oryza longistaminata, six Oryza barthii, and three number of primers or primer-pairs used in the studies. Oryza meridionalis). A total of 181 clear and repeatable bands were amplified from 27 selected RAPD primers, and 101 alleles were detected from 29 SSR primer pairs. Introduction The dendrogram constructed using UPGMA from a genetic-similarity matrix based on the RAPD data The genus Oryza L. is an economically valuable plant supported the clustering of distinct five groups with a group in the grass family (Poaceae), because it includes few exceptions: O. rufipogon/O. nivara/O. meridionalis, the world’s single most-important food crop, rice, that is a O. -
2178-IJBCS-Article-Chinyere Nwokeocha
Available online at http://ajol.info/index.php/ijbcs Int. J. Biol. Chem. Sci. 9(1): 35-47, February 2015 ISSN 1997-342X (Online), ISSN 1991-8631 (Print) Original Paper http://indexmedicus.afro.who.int Botanical indices of ploidy levels in some African accessions of Oryza punctata Kotschy ex Steud Chinyere Constance NWOKEOCHA Obafemi Awolowo University, Institute of Natural History Museum, Ile–Ife, Nigeria. E-mail: [email protected]; Tel: +234(0)8138338473 ABSTRACT Twenty-nine accessions of Oryza punctata Kotschy ex Steud, from local and other African habitats were studied to establish the attributes that can delineate the two ploidy levels based on agro-botanical, foliar epidermal and nodal anatomical characteristics. The diploid plants of O. punctata are early-maturing annuals with a small biomass, while the tetraploids are large, vigorous perennials. From the anatomical and morphological traits: the diploids have narrower leaves (0.95 - 1.36 cm wide) than the tetraploids (1.9 - 2.3 cm); the culms of diploids are generally thin (0.28 - 0.35 cm in diameter) compared to the tetraploids (0.37 - 0.57 cm); the diploids have longer spikelets (6.20 - 7.04 mm) with length/breadth > 3; longer awns (52 - 86 mm) than the tetraploids (20 - 31 mm). The basal cells of microhairs in the diploids are about twice the length of apical cells, but only slightly longer than the apical cells in the tetraploids; prickle hairs are sparse in the intercostal zone of diploids, but abundant in tetraploids; short cells are paired and abundant in the intercostal zone of diploids, but sparse and solitary in the tetraploids. -
Why Are Momilactones Always Associated with Biosynthetic Gene Clusters in Plants? COMMENTARY Juan Zhanga,B and Reuben J
COMMENTARY Why are momilactones always associated with biosynthetic gene clusters in plants? COMMENTARY Juan Zhanga,b and Reuben J. Petersa,1 There is an emerging realization that plant genomes intriguing hints about the distinct evolutionary pres- contain biosynthetic gene clusters (BGCs) for more sures leading to not only their assembly but also that specialized metabolism in certain cases (1). However, of BGCs in plants more generally. while horizontal gene transfer seems to drive the as- As labdane-related diterpenoids, the momilac- sembly of self-sufficient BGCs in microbes, the limita- tones require dual cyclization reactions (9). Notably, tions of strict vertical gene transmission necessitate a identification of the two relevant cyclases revealed distinct driving force for the assembly of BGCs in that the genes for these consecutively acting enzymes plants. The evidence for horizontal gene transfer of are close together in the rice genome (2). Moreover, BGCs in microbes is derived from the appearance of the only other genes in the region encode two closely homologous such loci, leading to biosynthesis of the related cytochrome P450 (CYP) monooxygenases same (or very closely related) natural products, in phy- (CYP99A2 and CYP99A3) and two short-chain alcohol logenetically distinct species. By contrast, there has dehydrogenases/reductases (SDRs) (10). The two been much less investigation of such occurrences in SDRs also are closely related, and both can catalyze plants. This is a result of many fewer examples of oxidation of the penultimate intermediate 3β-hydroxy- BGCs, as well as instances of natural products that skip syn-pimaradien-19,6β-olide to form the characteristic across phylogenetic distances in this kingdom. -
Table S1 PF00931 Species Abbreviated Species
Table S1 PF00931 Species_abbreviated Species Taxon Database 223 Acoerulea Aquilegia coerulea dicot phytozome12.1.6 152 Acomosus Ananas comosus monocot phytozome12.1.6 124 Ahalleri Arabidopsis halleri dicot phytozome12.1.6 119 Ahypochondriacus Amaranthus hypochondriacus dicot phytozome12.1.6 105 Ahypochondriacus_v2.1 Amaranthus hypochondriacus dicot phytozome12.1.6 177 Alyrata Arabidopsis lyrata dicot phytozome12.1.6 376 Aoccidentale_v0.9 Anacardium occidentale dicot phytozome12.1.6 35 Aofficinalis_V1.1 Asparagus officinalis monocot phytozome12.1.6 160 Athaliana Arabidopsis thaliana columbia dicot phytozome12.1.6 160 Athaliana_Araport11 Arabidopsis thaliana columbia dicot phytozome12.1.6 99 Atrichopoda Amborella trichopoda Amborellales phytozome12.1.6 16 Bbraunii_v2.1 Botryococcus braunii Chlorophyta phytozome12.1.6 308 Bdistachyon Brachypodium distachyon monocot phytozome12.1.6 331 BdistachyonBD21-3_v1.1 Brachypodium distachyon Bd21-3 monocot phytozome12.1.6 535 Bhybridum_v1.1 Brachypodium hybridum monocot phytozome12.1.6 114 Boleraceacapitata Brassica oleracea capitata dicot phytozome12.1.6 187 BrapaFPsc Brassica rapa FPsc dicot phytozome12.1.6 235 Bstacei Brachypodium stacei monocot phytozome12.1.6 297 Bstricta Boechera stricta dicot phytozome12.1.6 414 Bsylvaticum_v1.1 Brachypodium sylvaticum monocot phytozome12.1.6 766 Carabica_v0.5 Coffea arabica dicot phytozome12.1.6 99 Carietinum_v1.0 Cicer arietinum dicot phytozome12.1.6 342 Cclementina Citrus clementina dicot phytozome12.1.6 96 Cgrandiflora Capsella grandiflora dicot phytozome12.1.6 -
Why Are Momilactones Always Associated with Biosynthetic Gene Clusters in Plants?
Biochemistry, Biophysics and Molecular Biology Publications Biochemistry, Biophysics and Molecular Biology 6-2-2020 Why are momilactones always associated with biosynthetic gene clusters in plants? Juan Zhang Iowa State University Reuben J. Peters Iowa State University, [email protected] Follow this and additional works at: https://lib.dr.iastate.edu/bbmb_ag_pubs Part of the Biochemistry, Biophysics, and Structural Biology Commons, Genetics and Genomics Commons, and the Plant Sciences Commons The complete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ bbmb_ag_pubs/282. For information on how to cite this item, please visit http://lib.dr.iastate.edu/howtocite.html. This Article is brought to you for free and open access by the Biochemistry, Biophysics and Molecular Biology at Iowa State University Digital Repository. It has been accepted for inclusion in Biochemistry, Biophysics and Molecular Biology Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Why are momilactones always associated with biosynthetic gene clusters in plants? Abstract There is an emerging realization that plant genomes contain biosynthetic gene clusters (BGCs) for more specialized metabolism in certain cases (1). However, while horizontal gene transfer seems to drive the assembly of self-sufficient BGCs in microbes, the limitations of strict vertical gene transmission necessitates a distinct driving force for the assembly of BGCs in plants. The evidence for horizontal gene transfer of BGCs in microbes is derived from the appearance of homologous such loci, leading to biosynthesis of the same (or very closely related) natural products, in phylogenetically distinct species. -
Oryza Glaberrima): History and Future Potential
African rice (Oryza glaberrima): History and future potential Olga F. Linares* Smithsonian Tropical Research Institute, Box 2072, Balboa-Ancon, Republic of Panama Contributed by Olga F. Linares, October 4, 2002 The African species of rice (Oryza glaberrima) was cultivated long existed, the fact remains that African rice was first cultivated before Europeans arrived in the continent. At present, O. glaber- many centuries before the first Europeans arrived on the West rima is being replaced by the introduced Asian species of rice, African coast. Oryza sativa. Some West African farmers, including the Jola of The early Colonial history of O. glaberrima begins when the southern Senegal, still grow African rice for use in ritual contexts. first Portuguese reached the West African coast and witnessed The two species of rice have recently been crossed, producing a the cultivation of rice in the floodplains and marshes of the promising hybrid. Upper Guinea Coast. In their accounts, spanning the second half of the 15th century and all of the 16th century, they mentioned here are only two species of cultivated rice in the world: the vast fields planted in rice by the local inhabitants and TOryza glaberrima, or African rice, and Oryza sativa, or Asian emphasized the important role this cereal played in the native rice. Native to sub-Saharan Africa, O. glaberrima is thought to diet. The first Portuguese chronicler to mention rice growing in have been domesticated from the wild ancestor Oryza barthii the Upper Guinea Coast was Gomes Eanes de Azurara in 1446. (formerly known as Oryza brevilugata) by peoples living in the He described a voyage along the coast 60 leagues south of Cape floodplains at the bend of the Niger River some 2,000–3,000 Vert, where a handful of men, navigating down a river that was years ago (1, 2). -
The Sequenced Angiosperm Genomes and Genome Databases
REVIEW published: 13 April 2018 doi: 10.3389/fpls.2018.00418 The Sequenced Angiosperm Genomes and Genome Databases Fei Chen 1†, Wei Dong 1†, Jiawei Zhang 1, Xinyue Guo 1, Junhao Chen 2, Zhengjia Wang 2, Zhenguo Lin 3, Haibao Tang 1 and Liangsheng Zhang 1* 1 State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Life Sciences, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Ministry of Education Key Laboratory of Genetics, Breeding and Multiple Utilization of Corps, Fujian Agriculture and Forestry University, Fuzhou, China, 2 State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China, 3 Department of Biology, Saint Louis University, St. Louis, MO, United States Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive Edited by: review for three major types of angiosperm genome databases, including databases Santosh Kumar Upadhyay, Panjab University, India for a single species, for a specific angiosperm clade, and for multiple angiosperm Reviewed by: species. The scope, tools, and data of each type of databases and their features Sumit Kumar Bag, are concisely discussed. The genome databases for a single species or a clade of National Botanical Research Institute species are especially popular for specific group of researchers, while a timely-updated (CSIR), India Xiyin Wang, comprehensive database is more powerful for address of major scientific mysteries at North China University of Science and the genome scale. -
Genomes of 13 Domesticated and Wild Rice Relatives Highlight Genetic Conservation, Turnover and Innovation Across the Genus Oryza
ARTICLES https://doi.org/10.1038/s41588-018-0040-0 Corrected: Publisher Correction Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza Joshua C. Stein1, Yeisoo Yu2,21, Dario Copetti2,3, Derrick J. Zwickl4, Li Zhang 5, Chengjun Zhang 5, Kapeel Chougule1,2, Dongying Gao6, Aiko Iwata6, Jose Luis Goicoechea2, Sharon Wei1, Jun Wang7, Yi Liao8, Muhua Wang2,22, Julie Jacquemin2,23, Claude Becker 9, Dave Kudrna2, Jianwei Zhang2, Carlos E. M. Londono2, Xiang Song2, Seunghee Lee2, Paul Sanchez2,24, Andrea Zuccolo 2,25, Jetty S. S. Ammiraju2,26, Jayson Talag2, Ann Danowitz2, Luis F. Rivera2,27, Andrea R. Gschwend5, Christos Noutsos1, Cheng-chieh Wu10,11, Shu-min Kao10,28, Jhih-wun Zeng10, Fu-jin Wei10,29, Qiang Zhao12, Qi Feng 12, Moaine El Baidouri13, Marie-Christine Carpentier13, Eric Lasserre 13, Richard Cooke13, Daniel da Rosa Farias14, Luciano Carlos da Maia14, Railson S. dos Santos14, Kevin G. Nyberg15, Kenneth L. McNally3, Ramil Mauleon3, Nickolai Alexandrov3, Jeremy Schmutz16, Dave Flowers16, Chuanzhu Fan7, Detlef Weigel9, Kshirod K. Jena3, Thomas Wicker17, Mingsheng Chen8, Bin Han12, Robert Henry 18, Yue-ie C. Hsing10, Nori Kurata19, Antonio Costa de Oliveira14, Olivier Panaud 13, Scott A. Jackson 6, Carlos A. Machado15, Michael J. Sanderson4, Manyuan Long 5, Doreen Ware 1,20 and Rod A. Wing 2,3,4* The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. -
Exploring the Loci Responsible for Awn Development in Rice Through Comparative Analysis of All AA Genome Species
plants Article Exploring the Loci Responsible for Awn Development in Rice through Comparative Analysis of All AA Genome Species Kanako Bessho-Uehara 1,2, Yoshiyuki Yamagata 3 , Tomonori Takashi 4 , Takashi Makino 2, Hideshi Yasui 3, Atsushi Yoshimura 3 and Motoyuki Ashikari 1,* 1 Bioscience and Biotechnology Center, Nagoya University, Furo-cho, Chikusa, Nagoya, Aichi 464-8601, Japan; [email protected] 2 Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Miyagi 980-8578, Japan; [email protected] 3 Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan; [email protected] (Y.Y.); [email protected] (H.Y.); [email protected] (A.Y.) 4 STAY GREEN Co., Ltd., 2-1-5 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan; [email protected] * Correspondence: [email protected]; Tel.: +81-52-789-5202 Abstract: Wild rice species have long awns at their seed tips, but this trait has been lost through rice domestication. Awn loss mitigates harvest and seed storage; further, awnlessness increases the grain number and, subsequently, improves grain yield in Asian cultivated rice, highlighting the contribution of the loss of awn to modern rice agriculture. Therefore, identifying the genes regulating awn development would facilitate the elucidation of a part of the domestication process in rice and increase our understanding of the complex mechanism in awn morphogenesis. To identify the Citation: Bessho-Uehara, K.; novel loci regulating awn development and understand the conservation of genes in other wild rice Yamagata, Y.; Takashi, T.; Makino, T.; relatives belonging to the AA genome group, we analyzed the chromosome segment substitution Yasui, H.; Yoshimura, A.; Ashikari, M.