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Assessment of EST-SSR markers for genetic analisys on coffee
Missio, Robson Fernando;Caixeta, Eveline Teixeira;Zambolim, Eunize Maciel;Pena, Guilherme Ferreira;Ribeiro, Ana Paula;Zambolim, Laércio;Pereira, Ant?nio Alves;Sakiyama, Ney Sussumu;
Bragantia , 2009, DOI: 10.1590/S0006-87052009000300003
Abstract: est-ssr markers were used to investigate the genetic diversity among and within coffee populations, to explore the possibility of their use for fingerprinting of cultivars and to assist breeding programs. seventeen markers, developed from ests (expressed sequence tags) from the brazilian coffee genome project, were used. all markers showed polymorphism among the genotypes assessed. the average number of allele per primer was 5.1. the highest polymorphisms were found within c. canephora (88.2%) and rust-resistant varieties (35.3%). about 29.4% of the markers differentiated c. arabica from híbrido de timor; it was also possible to identify those closest and farthest from c. arabica . the analysis of population-grouped genotypes revealed a 64.0% genetic diversity among and a 36.0% genetic diversity within populations. the differentiation index was 0.637. six markers distinguished four rust-resistance varieties, showing their fingerprinting potential. these results demonstrate the usefulness of est-ssr markers for cross orientation, in diversity and introgression studies, and in genetic mapping.
Overview of Arabidopsis Resource Project in Japan  [cached]
Masatomo Kobayashi
Interdisciplinary Bio Central , 2011,
Abstract: Arabidopsis is well-known to the world’s plant research community as a model plant. Many significant resources and innovative research tools, as well as large bodies of genomic information, have been created and shared by the research community, partly explaining why so many researchers use this small plant for their research. The genome sequence of Arabidopsis was fully characterized by the end of the 20th century. Soon afterwards, the Arabidopsis research community began a 10-year international project on the functional genomics of the species. In 2001, at the beginning of the project, the RIKEN BioResource Center (BRC) started its Arabidopsis resource project. The following year, the National BioResource Project was launched, funded by the Japanese government, and the RIKEN BRC was chosen as a core facility for Arabidopsis resource. Seeds of RIKEN Arabidopsis transposon-tagged mutant lines, activation-tagged lines, full-length cDNA over-expresser lines, and natural accessions, as well as RIKEN Arabidopsis full-length cDNA clones and T87 cells, are preserved at RIKEN BRC and distributed around the world. The major resources provided to the research community have been full-length cDNA clones and insertion mutants that are suitable for use in reverse-genetics studies. This paper provides an overview of the Arabidopsis resources made available by RIKEN BRC and examples of research that has been done by users and developers of these resources.
Development of new genomic microsatellite markers from robusta coffee (Coffea canephora Pierre ex A. Froehner) showing broad cross-species transferability and utility in genetic studies
Prasad Hendre, Regur Phanindranath, V Annapurna, Albert Lalremruata, Ramesh K Aggarwal
BMC Plant Biology , 2008, DOI: 10.1186/1471-2229-8-51
Abstract: A small-insert partial genomic library of Coffea canephora, was probed for various SSR motifs following conventional approach of Southern hybridisation. Characterization of repeat positive clones revealed a very high abundance of DNRs (1/15 Kb) over TNRs (1/406 kb). The relative frequencies of different DNRs were found as AT >> AG > AC, whereas among TNRs, AGC was the most abundant repeat. The SSR positive sequences were used to design 58 primer pairs of which 44 pairs could be validated as single locus markers using a panel of arabica and robusta genotypes. The analysis revealed an average of 3.3 and 3.78 alleles and 0.49 and 0.62 PIC per marker for the tested arabicas and robustas, respectively. It also revealed a high cumulative PI over all the markers using both sib-based (10-6 and 10-12 for arabicas and robustas respectively) and unbiased corrected estimates (10-20 and 10-43 for arabicas and robustas respectively). The markers were tested for Hardy-Weinberg equilibrium, linkage dis-equilibrium, and were successfully used to ascertain generic diversity/affinities in the tested germplasm (cultivated as well as species). Nine markers could be mapped on robusta linkage map. Importantly, the markers showed ~92% transferability across related species/genera of coffee.The conventional approach of genomic library was successfully employed although with low efficiency to develop a set of 44 new genomic microsatellite markers of coffee. The characterization/validation of new markers demonstrated them to be highly informative, and useful for genetic studies namely, genetic diversity in coffee germplasm, individualization/bar-coding for germplasm protection, linkage mapping, taxonomic studies, and use as conserved orthologous sets across secondary genepool of coffee. Further, the relative frequency and distribution of different SSR motifs in coffee genome indicated coffee genome to be relatively poor in microsatellites compared to other plant species.Coffee tree, a member
An Italian functional genomic resource for Medicago truncatula
Andrea Porceddu, Francesco Panara, Ornella Calderini, Lorna Molinari, Paola Taviani, Luisa Lanfaloni, Carla Scotti, Maria Carelli, Laura Scaramelli, Gianluca Bruschi, Viviane Cosson, Pascal Ratet, Henri de Larembergue, Gerard Duc, Efisio Piano, Sergio Arcioni
BMC Research Notes , 2008, DOI: 10.1186/1756-0500-1-129
Abstract: Our report is on the production of three complementary mutant collections of the model species Medicago truncatula produced in Italy in the frame of a national genomic initiative. Well established strategies were used: Tnt1 mutagenesis, TILLING and activation tagging. Both forward and reverse genetics screenings proved the efficiency of the mutagenesis approaches adopted, enabling the isolation of interesting mutants which are in course of characterization. We anticipate that the reported collections will be complementary to the recently established functional genomics tools developed for Medicago truncatula both in Europe and in the United States.Medicago truncatula has emerged as one of the two model systems for legume species.The Medicago truncatula consortium (supported by US National Science Foundation and Samuel Roberts Noble Foundation in the USA, and in Europe, mainly by the European Union) has made significant achievements in genome and EST sequencing with a goal of completion of the gene space in 2008 [1]. The amount of information gained from the sequencing will assist studies related to gene function discovery. At the moment three complementary strategies have been chosen to create large mutant collections in M. truncatula: transposon tagging, fast neutron mutagenesis and TILLING. T-DNA tagging, one of the most popular strategies in Arabidopsis, did not represent the best option for M. truncatula because of the lack of a high throughput transformation system [2,3]. A population of more than 7600 Tnt1 lines was recently published [4] and is being developed as a public resource at the Samuel Roberts Noble Foundation http://www.noble.org webcite. Functional genomics platforms are also available in Europe at the John Innes Genome Laboratory http://jicgenomelab.co.uk/ webcite which, at the moment, provides access to a large population of deletion tilled lines and tilled lines for reverse genetic screening. Both resources were established during the course of
arrayMap: A Reference Resource for Genomic Copy Number Imbalances in Human Malignancies  [PDF]
Haoyang Cai, Nitin Kumar, Michael Baudis
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036944
Abstract: Background The delineation of genomic copy number abnormalities (CNAs) from cancer samples has been instrumental for identification of tumor suppressor genes and oncogenes and proven useful for clinical marker detection. An increasing number of projects have mapped CNAs using high-resolution microarray based techniques. So far, no single resource does provide a global collection of readily accessible oncogenomic array data. Methodology/Principal Findings We here present arrayMap, a curated reference database and bioinformatics resource targeting copy number profiling data in human cancer. The arrayMap database provides a platform for meta-analysis and systems level data integration of high-resolution oncogenomic CNA data. To date, the resource incorporates more than 40,000 arrays in 224 cancer types extracted from several resources, including the NCBI’s Gene Expression Omnibus (GEO), EBI’s ArrayExpress (AE), The Cancer Genome Atlas (TCGA), publication supplements and direct submissions. For the majority of the included datasets, probe level and integrated visualization facilitate gene level and genome wide data review. Results from multi-case selections can be connected to downstream data analysis and visualization tools. Conclusions/Significance To our knowledge, currently no data source provides an extensive collection of high resolution oncogenomic CNA data which readily could be used for genomic feature mining, across a representative range of cancer entities. arrayMap represents our effort for providing a long term platform for oncogenomic CNA data independent of specific platform considerations or specific project dependence. The online database can be accessed at http//www.arraymap.org.
POPcorn: An Online Resource Providing Access to Distributed and Diverse Maize Project Data  [PDF]
Ethalinda K. S. Cannon,Scott M. Birkett,Bremen L. Braun,Sateesh Kodavali,Douglas M. Jennewein,Alper Yilmaz,Valentin Antonescu,Corina Antonescu,Lisa C. Harper,Jack M. Gardiner,Mary L. Schaeffer,Darwin A. Campbell,Carson M. Andorf,Destri Andorf,Damon Lisch,Karen E. Koch,Donald R. McCarty,John Quackenbush,Erich Grotewold,Carol M. Lushbough,Taner Z. Sen,Carolyn J. Lawrence
International Journal of Plant Genomics , 2011, DOI: 10.1155/2011/923035
Abstract: The purpose of the online resource presented here, POPcorn (Project Portal for corn), is to enhance accessibility of maize genetic and genomic resources for plant biologists. Currently, many online locations are difficult to find, some are best searched independently, and individual project websites often degrade over time—sometimes disappearing entirely. The POPcorn site makes available (1) a centralized, web-accessible resource to search and browse descriptions of ongoing maize genomics projects, (2) a single, stand-alone tool that uses web Services and minimal data warehousing to search for sequence matches in online resources of diverse offsite projects, and (3) a set of tools that enables researchers to migrate their data to the long-term model organism database for maize genetic and genomic information: MaizeGDB. Examples demonstrating POPcorn’s utility are provided herein. 1. Introduction 1.1. Need for the POPcorn Resource In 1998, the National Science Foundation (NSF) launched the Plant Genome Research Program (PGRP), as part of the National Plant Genome Initiative. The establishment of PGRP coincided with an explosion of technologies that allowed large-scale genomic experiments to flourish, and PGRP grants fueled unprecedented advances in plant genomics research. This program was unique in that it strongly encouraged large collaborative projects and required project outcomes to be publicly available. Largely as the result of NSF’s forward thinking program, many independent online resources for plant research have been developed in the past 12 years. While this abundance of genomic data has transformed plant science in many ways, it has also created some problems: the plethora of independent websites requires researcher awareness of the various projects and what data each offers. Finding and using these resources is not always straightforward. Most sites use a variety of different tools that are often unique to that resource, each requiring that the researcher learn how to interact with them. In addition, it is also often difficult to use the results from one resource in another, and it is not generally possible to search multiple resources at the same time. Instead, researchers find themselves repeating the same search (e.g., BLAST [1]) at multiple sites in the hopes of locating all information relevant to their research. In addition, when funding for a project ends, the data generated often are not moved to long-term repositories. Thus, project sites degrade over time and sometimes disappear entirely. When the previously accessible data
Applying the DRC (Domestic Resource Cost) Index to Evaluate the Competitive Advantage of Dak Lak Coffee
Hoang Tuan Minh, Doan Thi Nhu Trang, Jiancheng Chen
Open Access Library Journal (OALib Journal) , 2016, DOI: 10.4236/oalib.1102727
Abstract:
In the past few years, the volatility of the world price market and the intrinsic weaknesses of production coupled with skepticism from experts as well as households had effects of coffee production [1], that’s why the purpose of the article is to use index DRC (Domestic Resource Cost) to confirm the effectiveness of the coffee plantations in Dak Lak, through DRC index we not only assess competitive advantage of the coffee over other crop products in Dak Lak but also can find agents that affect competitiveness and find a way to enhance the competitiveness of products. The result of the research confirms that comparative advantages of coffee products are very sensitive to fluctuations in the price of coffee exports.
PromBase: a web resource for various genomic features and predicted promoters in prokaryotic genomes
Vetriselvi Rangannan, Manju Bansal
BMC Research Notes , 2011, DOI: 10.1186/1756-0500-4-257
Abstract: Relative stability of DNA sequence has been used to predict promoter regions in 913 microbial genomic sequences with GC-content ranging from 16.6% to 74.9%. Irrespective of the genome GC-content the relative stability based promoter prediction method has already been proven to be robust in terms of recall and precision. The predicted promoter regions for the 913 microbial genomes have been accumulated in a database called PromBase. Promoter search can be carried out in PromBase either by specifying the gene name or the genomic position. Each predicted promoter region has been assigned to a reliability class (low, medium, high, very high and highest) based on the difference between its average free energy and the downstream region. The recall and precision values for each class are shown graphically in PromBase. In addition, PromBase provides detailed information about base composition, CDS and CG/TA skews for each genome and various DNA sequence dependent structural properties (average free energy, curvature and bendability) in the vicinity of all annotated translation start sites (TLS).PromBase is a database, which contains predicted promoter regions and detailed analysis of various genomic features for 913 microbial genomes. PromBase can serve as a valuable resource for comparative genomics study and help the experimentalist to rapidly access detailed information on various genomic features and putative promoter regions in any given genome. This database is freely accessible for academic and non- academic users via the worldwide web http://nucleix.mbu.iisc.ernet.in/prombase/ webcite.Controlling gene expression is the central process in all cellular processes. The synchronized control of gene expression is accomplished by the interplay of multiple regulatory mechanisms. Promoter elements are the key regulatory regions, which recruit the transcriptional machinery through the binding of a variety of regulatory proteins to the short oligonucleotide sequences occurring
Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains
Varani, Alessandro M.;Monteiro-Vitorello, Claudia B.;Almeida, Luiz G.P. de;Souza, Rangel C.;Cunha, Oberdan L.;Lima, Wanessa C.;Civerolo, Edwin;Sluys, Marie-Anne Van;Vasconcelos, Ana T.R.;
Genetics and Molecular Biology , 2012, DOI: 10.1590/S1415-47572012005000019
Abstract: the xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of xylella genomes. here we describe a database and tools for exploring the biology of this important plant pathogen. the hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. it is available from web site http://www.xylella.lncc.br.
Cytology, biochemistry and molecular changes during coffee fruit development
De Castro, Renato D.;Marraccini, Pierre;
Brazilian Journal of Plant Physiology , 2006, DOI: 10.1590/S1677-04202006000100013
Abstract: in commercial coffee species (coffea arabica and coffea canephora), fruit development is a lengthy process, characterized by tissue changes and evolutions. for example, soon after fecundation and up to mid development, the fruit is mainly constituted of the pericarp and perisperm tissue. thereafter, the perisperm gradually disappears and is progressively replaced by the endosperm (true seed). initially present in a "liquid" state, the endosperm hardens as it ripens during the maturation phase, as a result of accumulation of storage proteins, sucrose and complex polysaccharides representing the main reserves of the seed. the last step of maturation is characterized by the dehydration of the endosperm and the color change of the pericarp. important quantitative and qualitative changes accompany fruit growth, highlighting the importance of its study to better understand the final characteristics of coffee beans. following a description of the coffee fruit tissues, this review presents some data concerning biochemical, enzymatic and gene expression variations observed during the coffee fruit development. the latter will also be analyzed in the light of recent data (electronic expression profiles) arising from the brazilian coffee genome project.
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