Dear Colleagues, I would like to draw your attention to a Wiki site http://npgi-workshop.wetpaint.com/?mail=1128 that describes a summary of a recent workshop entitled: The National Plant Genome Initiative at Ten Years: A Community Workshop This site contains information (agenda, Rapporteurs summaries, session/Q&A notes, list of meeting participants and a meeting summary) related to the recent National Plant Genome Initiative Workshop held at the Arnold and Mabel Beckman Conference Center of the National Academies in Irvine California on August 26-28, 2008. The purpose of the meeting was to bring a broad group of stakeholders together to discuss the outcomes of the first ten years of the US National Plant Genome Initiative (NPGI) as well as the challenges and opportunities ahead for the next five to ten years. The NPGI started in 1998 and is managed by the Interagency Working Group on Plant Genomes (IWG-PG). The IWG-PG is currently in the process of developing a new five-year plan using a ...
There has been remarkably little attention to using the high resolution provided by genotyping-by-sequencing (i.e. RADseq and similar methods) datasets for assessing relatedness in wildlife populations. A major hurdle is the genotyping error, especially allelic dropout, often found in this type of dataset that could lead to downward-biased, yet precise, estimates of relatedness. Here we assess the applicability of genotyping-by-sequencing datasets for relatedness inferences given their relatively high genotyping error rates. Individuals of known relatedness were simulated under genotyping error, allelic dropout, and missing data scenarios based on an empirical ddRAD dataset, and their true relatedness was compared to that estimated by seven relatedness estimators. We found that an estimator chosen through such analyses can circumvent the influence of genotyping error, with the estimator of Ritland (1996) shown to be unaffected by allelic dropout and to be the most accurate when there is ...
The Materials Genome Initiative (MGI) is a U.S. Federal government multi-stakeholder initiative to develop an infrastructure to accelerate and sustain domestic materials discovery and deployment in the United States. MGI is distinct from "Materials Genome", which is a registered trademark of MaterialsGenome, Inc. (a Pennsylvania Corporation). The use of the term "Materials Genome Initiative" is not intended to serve as an endorsement of or an association with the trademarked term "Materials Genome ...
Genotyping-by-sequencing (GBS) approaches provide low-cost, high-density genotype information. However, GBS has unique technical considerations, including a substantial amount of missing data and a nonuniform distribution of sequence reads. The goal of this study was to characterize technical variation using this method and to develop methods to optimize read depth to obtain desired marker coverage. To empirically assess the distribution of fragments produced using GBS, ∼8.69 Gb of GBS data were generated on the Zea mays reference inbred B73, utilizing ApeKI for genome reduction and single-end reads between 75 and 81 bp in length. We observed wide variation in sequence coverage across sites. Approximately 76% of potentially observable cut site-adjacent sequence fragments had no sequencing reads whereas a portion had substantially greater read depth than expected, up to 2369 times the expected mean. The methods described in this article facilitate determination of sequencing depth in the ...
TY - JOUR. T1 - The First Plant Genome Sequence-Arabidopsis thaliana. AU - Feldmann, Kenneth A. AU - Goff, Stephen A. PY - 2014. Y1 - 2014. N2 - The Arabidopsis thaliana genome was the first plant genome to be sequenced. The substrates for sequencing consisted of a minimum tiling path of BAC, P1, YAC, TAC and cosmid clones, anchored to the genetic map. Using these substrates, 10 contigs were developed from 1569 clones. Annotation at the time the sequence was finished identified 25,498 protein-coding genes. With the continued development of software trained on Arabidopsis genes, along with the availability of large numbers of ESTs and additional plant genome sequences, the number of annotated genes has increased. The final TAIR (TAIR10) genome annotation release contains 27,202 nuclear protein-coding genes, 4827 pseudogenes and transposable element genes and 1359 noncoding RNAs. Gene density (kb/gene) is 4.35, with 5.89 exons/gene, an average exon length of 296. nt and an average intron length of ...
The PGSB plant genomics group focuses on the analysis of plant genomes, using bioinformatic techniques. To store and manage the data, we developed a database, PlantsDB, that aims to provide a data and information resource for individual plant species. In addition PlantsDB provides a platform for integrative and comparative plant genome research. ...
The PGSB plant genomics group focuses on the analysis of plant genomes, using bioinformatic techniques. To store and manage the data, we developed a database, PlantsDB, that aims to provide a data and information resource for individual plant species. In addition PlantsDB provides a platform for integrative and comparative plant genome research. ...
Diversity in plant genomes remains largely unexplored. The 10,000 Plant Genome Sequencing Project is a landmark effort to catalogue plant genomic variation, representing a major step in understanding the tree of life. The project offers new opportunities to study biological processes and address fundamental research questions.
As reference genome sequences are becoming available/undergoing for several crops, genotyping by sequencing (GBS) seems to be an option. Efforts are underway to offer GBS for Chickpea, Pigeonpea and Sorghum by using MiSeq. These efforts will be extended to other crops also. ...
The Genetics Society of America (GSA), founded in 1931, is the professional membership organization for scientific researchers and educators in the field of genetics. Our members work to advance knowledge in the basic mechanisms of inheritance, from the molecular to the population level.. Online ISSN: 1943-2631. ...
Yale is a founding member of the Genome-Wide RNAi Global Initiative a...The siRNA sequences have blueprints in DNA and are transcribed but no... Participation in this consortium gives us a cutting-edge technology t...The library will be available to the Yale University research communit...Founding members of the Global Initiative have a broad spectrum of bio...,Yale,participates,in,global,human,genome,initiative,biological,biology news articles,biology news today,latest biology news,current biology news,biology newsletters
AtSFP: The SIGnAL Arabidopsis Single Nuclutide Polymorphism (SNP), Deletion, and Single Feature Polymorphism (SFP) Database. Created and developed by Huaming Chen
AtSFP: The SIGnAL Arabidopsis Single Nuclutide Polymorphism (SNP), Deletion, and Single Feature Polymorphism (SFP) Database. Created and developed by Huaming Chen
Buy Plant Genome Analysis by Peter M. Gresshoff from Waterstones today! Click and Collect from your local Waterstones or get FREE UK delivery on orders over £20.
Not buying your argument Nick. Small plant genomes are very interesting and what a plant lineage such as this one did as its genome was reduced is also quite interesting. But many are overblowing the implications of this study. The fact that a plant can function without much non coding DNA really says nothing about the function or role of such non coding DNA in other species. All it says it that such non coding DNA is not absolutely essential for a plant to function. But this plant lineage could have evolved new means of regulation or other functions that were found in the non coding DNA of its ancestors. Or, in other words, a plant with a small genome says as much about non coding DNA in other plants and in humans as a fish with no eyes says about the role of eyes in vertebrates that see. Or should I try another? This says as much about the role of non coding DNA in other plants as the existence of snakes say about the role of legs. And so on. Delete ...
Dear Collegues, WHO has provided funds to its Schisto Genome Network to hold a Meeting to review progress in the Schisto Genome Initiative, to identify and resolve limitations arising from current strategies and to decide the future agenda for the Networks research. With respect to the future direction of research activities, WHO-TDRs Genome Committee, has indicated that it would like to see the initiation of post-genomic studies and that it is willing to receive applications for such projects in the next funding round (deadline for new applications, 15th July 1998). This potential shift in emphasis of Network activity may make participation in the Genome Network more attractive to various research groups. WHO defines post-genomic initiatives as projects investigating DNA sequence information for the identification of molecules important for parasite virulence and host survival. Since this is a relatively new area, the Committee does not wish to restrict the scope of such proposals but ...
What is the consensus, and what is your take on the UCS critique?. Professor Fedoroff: The board statement is pretty careful. It says, as the UCS attack quotes: "Indeed, the science is quite clear: crop improvement by the modern molecular techniques of biotechnology is safe." Youll notice that the AAAS Board statement DOESNT say that "all plants genetically modified by modern molecular techniques are safe," nor did it say what he [Doug Gurian-Sherman from UCS] claims it does: "a blanket statement that GE crops are "safe" is misleading." There is no evidence that modifying plants by molecular techniques causes problems to the plants, people, or nature. In fact, everything weve learned says that plant genomes are much less disturbed and altered when genes are introduced by molecular techniques than when changes are made by genetic crosses, or mutations are made by chemicals or radiation or by putting plant tissues into culture, then regenerating the plants. Whether a human crop plant causes ...
Do you have any idea what causes wild Pacific salmon to have its color? It is one of the hottest new nutrient discoveries from an algae called astaxanthin.
Pharos is the web interface for data collected by the Illuminating the Druggable Genome initiative. Target, disease and ligand information are collected and displayed.
As part of NISTs response to the Materials Genome Initiative (MGI), this project provides resources to address some of the challenges to the wider use of ...
Several studies have found that, even when increased CO2 makes plants grow bigger and faster, it reduces proteins and other nutrients in important food crops.
The nutrient and the diet that affects your blood sugar the most is carbohydrate. It is the nutrient that does raise blood sugar more than protein and certainly more than fat. It is, however, a nutrient that is contained in many, many important foods in our diet.
AFLP protocol using IRDye infrared fluorescent dyes for large plant genome analysis. Manuals for 4300 DNA Analyzer and 4300 DNA Analysis system Brochure
The first hints of the complex organization of the maize genome came from cytological studies. Although maize is diploid, early studies by McClintock (3, 4) demonstrated the association of nonhomologous chromosomes during meiosis. Later studies documented the formation of bivalents and multivalents in maize haploids (5, 6). Altogether, cytological observations suggested that the maize genome contains extensive regions of homology, probably reflecting chromosomal duplications.. Evidence for chromosomal duplication also came from linkage information. In 1951, Rhoades (7, 8) noted that some regions of linkage maps did not contain mutants, and he proposed that the lack of mutants reflected genetic redundancy caused by chromosomal duplication. Rhoades proposal has since been supported by molecular data. For example, isozyme studies have documented the presence of duplicated, linked loci in maize (9-12), and restriction fragment length polymorphism mapping studies have shown that many markers map to ...
Development of a high quality reference sequence is a daunting task in crops like wheat with large (~17Gb), highly repetitive (>80%) and polyploid genome. To achieve complete sequence assembly of such genomes, development of a high quality physical map is a necessary first step. However, due to the lack of recombination in certain regions of the chromosomes, genetic mapping, which uses recombination frequency to map marker loci, alone is not sufficient to develop high quality marker scaffolds for a sequence ready physical map. Radiation hybrid (RH) mapping, which uses radiation induced chromosomal breaks, has proven to be a successful approach for developing marker scaffolds for sequence assembly in animal systems. Here, the development and characterization of a RH panel for the mapping of D-genome of wheat progenitor Aegilops tauschii is reported. Radiation dosages of 350 and 450 Gy were optimized for seed irradiation of a synthetic hexaploid (AABBDD) wheat with the D-genome of Ae. tauschii accession
Hexaploid oat (Avena sativa L., 2n = 6x = 42) is a member of the Poaceae family and has a large genome (similar to 12.5 Gb) containing 21 chromosome pairs from three ancestral genomes. Physical rearrangements among parental genomes have hindered the development of linkage maps in this species. The objective of this work was to develop a single high-density consensus linkage map that is representative of the majority of commonly grown oat varieties. Data from a cDNA-derived single-nucleotide polymorphism (SNP) array and genotyping-by-sequencing (GBS) were collected from the progeny of 12 biparental recombinant inbred line populations derived from 19 parents representing oat germplasm cultivated primarily in North America. Linkage groups from all mapping populations were compared to identify 21 clusters of conserved collinearity. Linkage groups within each cluster were then merged into 21 consensus chromosomes, generating a framework consensus map of 7202 markers spanning 2843 cM. An additional ...
Historically, potato has been notoriously difficult to work with. It is a tetraploid, meaning its cells contain four copies of each chromosome, which makes it difficult to breed. Despite decades of improvement work, the crop remains susceptible to pests, pathogens and inbreeding depression (where new potato lines are weaker than their parents). Sequencing of the potato genome should speed efforts to address these issues. "It will take researchers awhile to use the genome information to improve its agronomic traits, such as improved quality, yield, drought tolerance and disease resistance. But our most recent research will accelerate efforts to improve potato varieties and help close the gap in bringing a better potato to the farmer," says Robin Buell, a plant biologist at Michigan State University, one of three co-leaders of the potato genome project. Jiang says the availability of potatos genetic code will get him back in the game of hunting-or cloning-genes of value to the potato industry. He ...
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BACKGROUND: The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to these collections is that most of these rice varieties have long life cycles, and/or low transformation efficiencies, which limits their usefulness as model organisms for functional genomics studies. In contrast, the rice variety Kitaake has a rapid life cycle (9 weeks seed to seed) and is easy to transform and propagate. For these reasons, Kitaake has emerged as a model for studies of diverse monocotyledonous species. RESULTS: Here, we report the de novo genome sequencing and analysis of Oryza sativa ssp. japonica variety KitaakeX, a Kitaake plant carrying the rice XA21 immune receptor. Our KitaakeX sequence assembly contains 377.6 Mb, consisting of 33 scaffolds (476 contigs) with a contig N50 of 1.4 Mb. Complementing the assembly are detailed gene annotations of 35,594 protein coding genes. We ...
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Many recent studies have emphasized the important role of structural variation (SV) in determining human genetic and phenotypic variation. In plants, studies aimed at elucidating the extent of SV are still in their infancy. Evidence has indicated a high presence and an active role of SV in driving plant genome evolution in different plant species.With the aim of characterizing the size and the composition of the poplar pan-genome, we performed a genome-wide analysis of structural variation in three intercrossable poplar species: Populus nigra, Populus deltoides, and Populus trichocarpa We detected a total of 7,889 deletions and 10,586 insertions relative to the P. trichocarpa reference genome, covering respectively 33.2 Mb and 62.9 Mb of genomic sequence, and 3,230 genes affected by copy number variation (CNV). The majority of the detected variants are inter-specific in agreement with a recent origin following separation of species.Insertions and deletions (INDELs) were preferentially located in ...
Background: Mapping and map-based cloning of genes that control agriculturally and economically important traits remain great challenges for plants with complex highly repetitive genomes such as those within the grass tribe, Triticeae. Mapping limitations in the Triticeae are primarily due to low frequencies of polymorphic gene markers and poor genetic recombination in certain genetic regions. Although the abundance of repetitive sequence may pose common problems in genome analysis and sequence assembly of large and complex genomes, they provide repeat junction markers with random and unbiased distribution throughout chromosomes. Hence, development of a high-throughput mapping technology that combine both gene-based and repeat junction-based markers is needed to generate maps that have better coverage of the entire genome. Results: In this study, the available genomics resource of the diploid Aegilop tauschii, the D genome donor of bread wheat, were used to develop genome specific markers that ...
Citation: Ling, P., Garland Campbell, K.A., Little, L.M., Skinner, D.Z. 2006. Service and research for molecular marker development in the usda-ars western regional small grains genotyping laboratory. Plant and Animal Genome Abstracts, page 14, #P203. Plant Animal Genome Conference XIV. January 14-18, 2006. San Diego, CA. Interpretive Summary: Technical Abstract: The Western Regional Small Grain Genotyping Laboratory is offering collaborative genotyping services to assist the marker assisted selection for wheat and barley cultivar development in Western region. Commonly known molecular markers are routinely used. Effective and versatile genomic technology is used to develop robust high-density and high-throughput markers that can be effectively deployed for closely related elite germplasm. Affymetrix Wheat GeneChips was used to identify Single Feature Polymorphisms (SFPs), which would allow us to screening the whole gene rich space for Single Nucleotide Polymorphisms (SNPs) in parallel, ...
Nearly 150 scientists and industrialists attended a recent meeting outside Cambridge to review progress in the application of genomics to crop plant improvement. The meeting covered a wide range of topics, from genome sequencing methods to marker-assisted breeding for wheat improvement. In her opening address, Julia Goodfellow (Biotechnological and Biological Sciences Research Council, Swindon, UK) described the increasing need for more healthy and nutritious food produced in environmentally sustainable ways and the need to translate the fruits of basic research in model species into crop improvement. The meeting established that such a research pipeline is a high priority and that genomics provides the means to achieve it.. Crop plants often have large and complex genomes; the maize genome, for example, is around 2.5 gigabase pairs (109 base pairs), approximately the same size as that of humans. Richard McCombie (Cold Spring Harbor Laboratory, New York, USA) described the remarkable progress ...
Since our doors first opened in 1910, the National Museum of Natural History has inspired curiosity and learning about the natural world and our place in it.
Crop plants have always been adapted to the needs of man by breeding for them to carry more fruit, survive droughts, or resist pests. Green biotechnology now adds new tools to the classical breeding methods for a more rapid and efficient improvement of plant properties. A biotechnological technique developed by KIT botanists to more precisely and reliably install or modify genetic information in the plant genome is now presented by the expert journal PNAS.
Find Latest Updates on Plant Science Conferences and Plant Biology Conferences happening in USA, Europe, Asia, Canada, Australia and Spain 2018. Trends in Plant Science, Frontier of Plant Science
Eukaryotic cells contain DNA in different compartments, i.e., the nucleus, mitochondria, and, in plant or algal cells, chloroplasts. The genomes of chloroplasts and mitochondria encode proteins essential for photosynthesis (Sato et al., 1999) or in the electron transport chain (Unseld et al., 1997). Plants, in contrast to animals, are sessile organisms that develop organs throughout their life cycle and usually only produce reproductive cells from meristems late in their development. Therefore, plant genomes are exposed to harmful mutations throughout their life cycle. Maintaining the stability of plant genomes is essential for development and requires accurate replication and efficient repair mechanisms. In addition to replication errors, many endogenous and exogenous factors, such as reactive species of oxygen or nitrogen, alkylating products, and genotoxic chemicals, but also environmental conditions, such as UV radiation, can cause DNA damage (De Bont and van Larebeke, 2004; Boesch et al., ...
The Hickey lab conducts discovery and applied research on Australias most important cereal crops - wheat and barley. The group is situated within the Queensland Alliance for Agriculture and Food Innovation at The University of Queensland, Brisbane, Australia. Our research is focused on key abiotic and biotic factors that limit grain production, as well as development of novel breeding tools and methodologies.. Our germplasm pipeline takes advantage of large nested-association mapping (NAM) populations, speed breeding technology, high-throughput phenotyping methods, and genotyping-by-sequencing (GBS) marker platforms. We develop novel pre-breeding germplasm with adapted genetic backgrounds, along with validated marker-trait associations. Our genetic studies improve understanding of gene effects, trait interactions, and interactions with specific environments. Such information and tools better equip breeders to assemble improved cultivars for farmers.. ...
The Hickey lab conducts discovery and applied research on Australias most important cereal crops - wheat and barley. The group is situated within the Queensland Alliance for Agriculture and Food Innovation at The University of Queensland, Brisbane, Australia. Our research is focussed on key abiotic and biotic factors that limit grain production, as well as development of novel breeding tools and methodologies. Our germplasm pipeline takes advantage of large nested-association mapping (NAM) populations, speed breeding technology, high-throughput phenotyping methods, and genotyping-by-sequencing (GBS) marker platforms. We develop novel pre-breeding germplasm with adapted genetic backgrounds, along with validated marker-trait associations. Our genetic studies improve understanding of gene effects, trait interactions, and interactions with specific environments. Such information and tools better equip breeders to assemble improved cultivars for farmers ...
One third of all the food produced in the world today is wasted, enough to feed 3 billion people-a shocking number in a world full of hunger and volatile food prices. In the United States alone, an estimated 40 percent of all the food produced is wasted
Heat author Bill Buford finds his McGee indispensable - that is, Harold McGees essential tome On Food and Cooking. McGee is the most important person alive writing about food, Buford says.
The sheer size of the wheat genome has been daunting in terms of whole genome sequencing. The Wheat genome is about five times the size of the human genome and hence was considered close to impossible to sequence. In Comparison to other important crop plants such as Soyabean and Rice, the difficulty of working with such a large genome has left wheat lagging behind in the race of genome sequencing. However, using advanced sequencing techniques employed by Roches 454 sequencers, the effort has managed to cover about 95% of the known wheat genes. The results of the study are now available for public use via Genbank, EMBL and CerealsDB. Nevertheless, there are those who warn that the gene map is far from complete and that the first high quality complete map data will be available only within five years. The full sequenced genome requires further read-throughs, assembly of the data into chromosomes and significant work to fully annotate the sequence data.. According to Dr. Neil Hall of the ...
was coordinating WPI and plays a leading role in examining the organisation and diversity of EPRV and related sequences in the host plant nuclear genome. Together with other partners, we are developing universal tools to isolate EPRVs from a limited number of crops where EPRV activation has already been observed, and investigate the biodiversity represented in EPRV sequences. By examination of short and long clones, and by PCR, we plan to determine the nature, organisation and sequence relationships of EPRVs between accessions of two target species groups, examining the copy numbers and chromosomal arrangement, long-range organisation and fine structure of EPRVs. Partners will develop evolutionary and structural models of EPRVs that will allow us to predict infection and expression routes. In the final task, partners will design molecular tools for identifying candidate EPRVs in any species, concentrating on five major European crops and, attempt implement them for routine screening; results, ...
Now comes the difficult part of sifting through the data to find the best models. The folding algorithm is noise and there will be many inaccurate models. We need to find the best models from the almost 7 billion models generated. This should take approximately 3-6 months using our fastest methods. After identifying the most accurate models, we then will use the information to figure out what functions these proteins perform in the rice organism. This involves comparing the structure and sequence to known proteins and is also a time consuming process. The plant genomes are not nearly as well studied as the human and mammalian genomes which makes the process all the more difficult ...
Background The availability of thousands of complete rice genome sequences from diverse varieties and accessions has laid the foundation for in-depth exploration of the rice genome. One drawback to...
What is the difference between Autopolyploidy and Allopolyploidy? Autopolyploidy and Allopolyploidy are two main types of polyploidy. Autopolyploidy is the...
Name: Altenb-2. ABRC stock number: CS76353. Description: Natural accession resequenced using the Illumina GA platform by the D. Weigel laboratory at the Max Planck Institute for Developmental Biology - Germany as part of the 1001 Genomes Project; single plant propagation from the sequenced plant.. Donation Date: 2010-01-29. ...
Accelerating the discovery of advanced materials is essential for human beings. However, the traditional trial-and-error way of developing materials is often very empirical and time- consuming. In 2011, the launch of Materials Genome Initiative marked a large-scale collaboration between computer scientists and materials scientists to deploy proven computational methods to predict, screen, and optimize materials at an unparalleled scale and rate. This thesis is based on this idea. Finding a suitable cathode material for Mg batteries has been one of the key challenges to the next-generation multi-valent battery technology. In this thesis, a high-throughput computation system is proposed to solve such problem. I tested the high-throughput structures applying traditional NEB calculations schemes and find out it is very different to scale traditional NEB method to a high-throughput application. Then I proposed a new scheme for estimating migration minimum- energy path (MEP) geometry and energetics ...