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 ...
The scientific revolution that started with the human-genome sequencing project, carried out with first-generation sequencing technology, has initiated other sequencing projects, including those for plant species. Different technologies have been developed together with the second- and third-generation sequencing platforms called next-generation sequencing. This review deals with the most relevant second-generation sequencing platforms, advanced analysis tools, and sequenced plant genomes. To date, a number of plant genomes have been sequenced, with many more projected for the near future. Using the new techniques and developed advanced bioinformatics tools, several studies including both plant genomics and transcriptomics were carried out. Likewise, completion of reference genome sequences and high-throughput resequencing projects presented opportunities to better understand the genomic nature of plants and accelerated the process of crop improvement. Modern sequencing and bioinformatics ...
2016 Tinker et al. Genotyping-by-sequencing (GBS), and related methods, are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of single nucleotide polymorphisms (SNPs) within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. However, due to the complexity of analyzing large data sets, applications of GBS may require substantial time, expertise, and computational resources. Haplotag, the novel GBS software described here, is freely available, and operates with minimal user-investment on widely available computer platforms. Haplotag is unique in fulfilling the following set of criteria: (1) operates without a reference genome; (2) can be used in a polyploid species; (3) provides a discovery mode, and a production mode; (4) discovers polymorphisms based on a model of tag-level haplotypes within sequenced tags; (5) reports ...
2016 Tinker et al. Genotyping-by-sequencing (GBS), and related methods, are based on high-throughput short-read sequencing of genomic complexity reductions followed by discovery of single nucleotide polymorphisms (SNPs) within sequence tags. This provides a powerful and economical approach to whole-genome genotyping, facilitating applications in genomics, diversity analysis, and molecular breeding. However, due to the complexity of analyzing large data sets, applications of GBS may require substantial time, expertise, and computational resources. Haplotag, the novel GBS software described here, is freely available, and operates with minimal user-investment on widely available computer platforms. Haplotag is unique in fulfilling the following set of criteria: (1) operates without a reference genome; (2) can be used in a polyploid species; (3) provides a discovery mode, and a production mode; (4) discovers polymorphisms based on a model of tag-level haplotypes within sequenced tags; (5) reports ...
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 ...
Advances in next generation technologies have driven the costs of DNA sequencing down to the point that genotyping-by-sequencing (GBS) is now feasible for high diversity, large genome species. Here, we report a procedure for constructing GBS libraries based on reducing genome complexity with restric …
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. ...
During the last decade, plant biotechnological laboratories have sparked a monumental revolution with the rapid development of next sequencing technologies at affordable prices. Soon, these sequencing technologies and assembling of whole genomes will extend beyond the plant computational biologists and become commonplace within the plant biology disciplines. The current availability of large-scale genomic resources for non-traditional plant model systems (the so-called orphan crops) is enabling the construction of high-density integrated physical and genetic linkage maps with potential applications in plant breeding. The newly available fully sequenced plant genomes represent an incredible opportunity for comparative analyses that may reveal new aspects of genome biology and evolution. The analysis of the expansion and evolution of gene families across species is a common approach to infer biological functions. To date, the extent and role of gene families in plants has only been partially addressed
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. ...
By Ken G. Dodds, John C. McEwan, Rudiger Brauning, Rayna M. Anderson, Tracey C. van Stijn, Theodor Kristjánsson and Shannon M. Clarke ...
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
There is great potential for the genetic improvement of oil palm yield. Traditional progeny tests allow accurate selection but limit the number of individuals evaluated. Genomic selection (GS) could overcome this constraint. We estimated the accuracy of GS prediction of seven oil yield components using A × B hybrid progeny tests with almost 500 crosses for training and 200 crosses for independent validation. Genotyping-by-sequencing (GBS) yielded +5000 single nucleotide polymorphisms (SNPs) on the parents of the crosses. The genomic best linear unbiased prediction method gave genomic predictions using the SNPs of the training and validation sets and the phenotypes of the training crosses. The practical impact was illustrated by quantifying the additional bunch production of the crosses selected in the validation experiment if genomic preselection had been applied in the parental populations before progeny tests. We found that prediction accuracies for cross values plateaued at 500 to 2000 SNPs, with
Despite several efforts in the last decade toward development of simple sequence repeat (SSR) markers in peanut, there is still a need for more markers for conducting different genetic and breeding studies. With the effort of the International Peanut Genome Initiative, the availability of reference genome for both the diploid progenitors of cultivated peanut allowed us to identify 135,529 and 199,957 SSRs from the A (Arachis duranensis) and B genomes (Arachis ipaensis), respectively. Genome sequence analysis showed uneven distribution of the SSR motifs across genomes with variation in parameters such as SSR type, repeat number, and SSR length. Using the flanking sequences of identified SSRs, primers were designed for 51,354 and 60,893 SSRs with densities of 49 and 45 SSRs per Mb in A. duranensis and A. ipaensis, respectively. In silico PCR analysis of these SSR markers showed high transferability between wild and cultivated Arachis species. Two physical maps were developed for the A genome and the B
EST sequences are valuable data for gene discovery, especially for plant species with large genomes that have not been fully sequenced, and they provide a convenient means of accessing the transcriptome of a given species. However, ESTs generally correspond to only partial cDNA sequences, and EST samples are typically highly redundant (especially if EST sets are not derived from normalized EST libraries). Therefore, the assembly of overlapping ESTs into putative unique transcript contigs on a frequent and regular basis constitutes the first step for all EST analyses performed at PlantGDB (for more details, see http://www.plantgdb.org/prj/ESTCluster/progress.php). A similar analysis is provided by the TIGR gene indices for selected species with sufficiently large numbers of ESTs (http://www.tigr.org/tdb/tgi/plant.shtml; Lee et al., 2005).. EST assembly remains a computational challenge given the large number of EST sequences currently available. For example, with more than 400,000 maize ESTs, ...
Announcing the availability of the Plant Genome Database CD-ROM, a compilation of plant genome databases, which have been dumped as text from their ACEDB versions and marked up with hypertext links. The data are browsable from the Sun UNIX X-Windows, PC Windows, and Mac Mosaic hypertext browsers. In addition, the genome data have been indexed to allow full-text Boolean searching for Mac, Sun, Windows, and DOS. Where images exist, they have been linked to their respective databases. Databases include information on: Arabidopsis, soybean, Chlamydomonas, small grains (wheat, barley, etc.), maize, rice, tomato, potato, pepper, and forest trees. Also included, are various related documents: newsletters for Arabidopsis (Weeds World), forest trees (Dendrome), rice (The Rice Genetics Newsletter), and tomato (Report of the Tomato Genetic Cooperative); plant genome thesauri for cytogenetics, morphology, and references; a controlled genetic vocabulary; and a listing of the Agricultural Genome curators. The ...
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 ...
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 ...
Domain architecture and assignment details (superfamily, family, region, evalue) for LOC_Os08g25060.1|13108.m02571|protein from Oryza sativa ssp. japonica 5.0. Plus protein sequence and external database links.
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 ...
Oryzias latipes can be divided into five groups (N.JPN, S.JPN, E.KOR, W.KOR and Tajima-Tango) by mtDNA sequences and allozymic electrophoresis patterns (Sakaizumi 1984; Takehana et al. 2003). In this study, based on chromosomal SNPs, the genetic clustering analysis showed that K = 4 was the most supportive because it presented the lowest fivefold cross-validation error, indicating that N.JPN and S.JPN were divided into three ancestral clusters. When the K values increased, only S.JPN divided into more subgroups, which suggests that the S.JPN group was composed of more divergent groups than the other groups. Considering together with the results of the ML tree analysis, it is possible to redefine subgroups composed of each major group for our wild lab-stocks originated from the Japanese archipelago as follows. First, Tajima-Tango, which had been considered a hybridization group, should be included under the N.JPN group because it shows almost the same ancestral component as N.JPN, for which we ...
The IWGSC produced a survey of the gene content and composition of all 21 chromosomes and identified 124,201 gene loci, with more than 75,000 positioned along the chromosomes. Comparing the bread wheat gene sequences with gene repertoires from its closest extant relatives (representing the species that donated the A, B, and D progenitor genomes) showed limited gene loss during the evolution of the hexaploid wheat genome but frequent gene duplications after these genomes came together. Gene expression patterns revealed that none of the subgenomes dominated gene expression.. Choulet et al. describe the sequencing, assembly, annotation, and analysis of the reference sequence of the largest wheat chromosome, 3B, which at nearly 1 gigabase is more than seven times larger than the entire sequence of the model plant Arabidopsis thaliana. Relying on a physical map derived from the chromosome 3B-specific bacterial artificial chromosome (BAC) library (1), more than 8000 BAC clones were sequenced and ...
Mayer, K.F.X., Martis, M., Hedley, P.E. et al. 2011. Unlocking the Barley Genome by Chromosomal and Comparative Genomics. Plant Cell 23, 1249-1263. (doi:10.1105/tpc.110.082537 ...
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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 ...
The majority of diploid organisms have polyploid ancestors. The evolutionary process of polyploidization (and subsequent re-diploidization) is poorly understood, but has frequently been conjectured to involve some form of genome shock - partly inspired by studies in crops, where polyploidy has been linked to major genomic changes such as genome reorganization and subgenome expression dominance. It is unclear, however, whether such dramatic changes would be characteristic of natural polyploidization, or whether they are a product of domestication. Here, we study polyploidization in Arabidopsis suecica (n = 13), a post-glacial allopolyploid species formed via hybridization of A. thaliana (n = 5) and A. arenosa (n = 8). We generated a chromosome-level genome assembly of A. suecica and complemented it with polymorphism and transcriptome data from multiple individuals of all species. Despite a divergence of ∼6 Mya between the two ancestral species and appreciable differences in their genome ...
The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the Oryza Map Alignment Project (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Projects finished reference genome--O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice ...
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摘要】:[Background] Eating and cooking qualities(ECQs) of rice(Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. Genetic factors are required for development of rice varieties with excellent ECQs and association mapping is one of the promising approaches for discovering such associated genetic factors. [Material and method] A genome-wide association mapping was performed on a set of 253 non-glutinous rice accessions consisting of 83 indica and 170 japonica Asian cultivated rice varieties through phenotyping for 11 ECQ traits in two consecutive years and genotyping with 210 polymorphic SSR and candidate-gene markers. [Results] These markers amplified 747 alleles with an average of 3.57 alleles per locus. The structure, phylogenetic relationship, and principal component analysis indicated a strong population differentiation between indica and japonica accessions and association mapping was thus undertaken within indica and japonica subpopulations. All ...
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 ...
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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.
TY - JOUR. T1 - Construction of reference chromosome-scale pseudomolecules for potato. T2 - Integrating the potato genome with genetic and physical maps. AU - Sharma, Sanjeev Kumar. AU - Bolser, Daniel. AU - de Boer, Jan. AU - Sønderkær, Mads. AU - Amoros, Walter. AU - Carboni, Martin Federico. AU - DAmbrosio, Juan Martín. AU - de la Cruz, German. AU - Di Genova, Alex. AU - Douches, David S.. AU - Eguiluz, Maria. AU - Guo, Xiao. AU - Guzman, Frank. AU - Hackett, Christine A.. AU - Hamilton, John P.. AU - Li, Guangcun. AU - Li, Ying. AU - Lozano, Roberto. AU - Maass, Alejandro. AU - Marshall, David. AU - Martinez, Diana. AU - McLean, Karen. AU - Mejía, Nilo. AU - Milne, Linda. AU - Munive, Susan. AU - Nagy, Istvan. AU - Ponce, Olga. AU - Ramirez, Manuel. AU - Simon, Reinhard. AU - Thomson, Susan J.. AU - Torres, Yerisf. AU - Waugh, Robbie. AU - Zhang, Zhonghua. AU - Huang, Sanwen. AU - Visser, Richard G.F.. AU - Bachem, Christian W.B.. AU - Sagredo, Boris. AU - Feingold, Sergio E.. AU - ...
The Ingvarsson research group is focused on understanding what factors govern the distribution of genetic variation across plant genomes, and how this drives phenotypic variation in traits that are of adaptive or economic importance. We mainly rely on computational analyses of large-scale DNA sequencing data sets but also use data on gene expression and traditional genetic mapping in combination with field and greenhouse experiments. We are especially interested in understanding the genetic architecture of local adaptation in phenology and the relative importance of genetic drift, recombination and natural selection in driving genome-wide patterns of genetic diversity.. The Ingvarsson research group is located at the Department of Plant Biology, Swedish University of Agricultural Sciences in Uppsala, Sweden, although a few people remain at the Department of Ecology and Environmental Sciences, Umeå University where we were located from 2002 to 2016.. ...
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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., ...
In this study a mapping population (F8) of ca 200 progeny from a cross between the commercial rice varieties Apo and IR64 has been both genotyped and phenotyped. A genotyping-by-sequencing approach was first used to identify 2,681 polymorphic SNP markers which gave dense coverage of the genome with a good distribution across all 12 chromosomes. The coefficient of parentage was also low, at 0.13, confirming that the parents are genetically distant from each other. The progeny, together with both parents, were grown under irrigated and water restricted conditions in a randomised block design. All grain was harvested to determine variation in yield across the population. The grains were then polished following standard procedures prior to performing the phenotyping analyses. A Gas Chromatography-Mass Spectrometry approach was used to determine the volatile biochemical profiles of each line and after data curation and processing, discriminatory metabolites were putatively identified based on in-house and
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 ...
The cultivated peanut is an allotetraploid (2n=4x=40) that carries both the A and B genomes and A. duranensis (2n=2x=20) has likely contributed the A genome, the smaller set of chromosomes in the karyotype. These two ancestral diploids separated from each other about 3 million years ago. The genome merger, allopolyploidy event, ocurred relatively very recently, five to ten thousand years ago, followed by domestication in South America from where it appeared in most part of the world by 1600 ...
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.
First we should know what is edema? Edema is also known as the bodys immersion. It is a condition that can create bloating in the body.
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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 ...
Plant genome research is already revolutionizing the field of biology. Currently, scientists are unlocking the secrets of some of the most important plants in our lives, including corn, cotton and potatoes. Secrets of Plant Genomes: Revealed! takes viewers on a lively, upbeat journey that explores how these plants got to be the way they are and investigates how we can make better use of them in the future. Plant scientists are hard at work--in the lab, in the field and at the computer--to increa ...
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 ...
Scientists have discovered that two different approaches to identifying the non-repetitive regions of the maize genome together provide a complementary and cost-effective alternative to sequencing the entire genome.
Name: RRS-7. ABRC stock number: CS76593. Description: Natural accession targeted for sequencing using the Illumina HiSeq2000 platform by the J. Ecker laboratory at the Salk Institute-USA as part of the 1001 Genomes Project. Bulk seed were collected from siblings of a single sequenced plant.. Donation Date: 2010-07-08. ...
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