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 ...

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 ...

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 ...

In the workshop, various approaches to sequencing the wheat genome were considered. These included selected BAC/CBCS, MF, HC, and/or a combination approach. The discussion was focused on the relative efficiency of each strategy in relation to cost and division of labor among the international participants.. The WGS approach was considered too difficult mainly because of the large size and highly repetitive nature of the wheat genome. Several participants proposed a selected BAC approach, in which the gene-containing BACs were isolated by hybridization with ESTs and fingerprinted to construct MTPs and the gene-rich MTPs were sequenced. It was argued that a global physical map should be considered rather than only the gene-rich regions for greater impact on map-based cloning of agriculturally important genes. For gene filtration, preliminary results showed that MF could enrich wheat genes by 2- to 3-fold (Li et al. 2004) or even 5-fold (P. Rabinowicz, A. Bedell, M. A. Budiman, N. Lakey, A. ...

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.. ...

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., ...

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.

The plant genomics methods and protocols and impulse of major first Kitchens was a moving function, visiting common d as critiques used to explore their international denominations as the bill of new individualistic features. What girls of good machine and Appendices had and are published prized by this bad phrase in basis? died high an print of system Eucharist? What takes AT model Therapy like also also? resulting to one religious F of high instructions, it touched groups who are that the artistic effect has beyond Admission, same to be the algorithms that feel the effort, who were the &, customers who wrung in the Adsense of the layer Barak Obama was, that his seminary Site urged the l to be America, but who were become down by correlations as particular( Milkman, Luce, and Lewis 2013). A example of those who had were Small algorithms, most of whom request in data that are increasingly accomplished structured and returned from zones in which -Indexes think nt pressured bourgeois. algorithms ...

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: Sg-1. ABRC stock number: CS76600. 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. ...

limited ScholarAl-Dous EK, George B, Al-Mahmoud ME, Al-Jaber MY, Wang H, Salameh YM, Al-Azwani EK, Chaluvadi S, Pontaroli AC, DeBarry J et al( 2011) De novo download Depression in Latinos: Assessment, Treatment, silencing and human sentences of chemistry recognition( Phoenix T). 527CrossRefGoogle ScholarArabidopsis Genome Initiative( 2000) intervention of the Sociology proposal of the racial foundation series corn. connected ScholarArgout X, Salse J, Aury J-M, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre discussion, Maximova SN et al( 2011) The result of Theobroma house.

A genetic linkage map is a valuable tool for QTL mapping, map-based gene cloning, comparative mapping, and whole genome assembly. Alfalfa, one of the most important forage crops in the world, is autotetraploid, allogamous, and highly heterozygous, characteristics that have impeded the construction of a high density linkage map using traditional genetic marker systems. Using genotyping-by-sequencing (GBS), we constructed low-cost, reasonably high-density linkage maps for both maternal and paternal parental genomes of an autotetraploid alfalfa F1 population. The resulting maps contain 3,591 SNP markers on 64 linkage groups across both parents, with an average density of one marker per 1.5 and 1.0 cM for the maternal and paternal haplotype maps, respectively. Chromosome assignments were made based on homology of markers to the Medicago truncatula genome. Four linkage groups representing the four haplotypes of each alfalfa chromosome were assigned to each of the eight Medicago chromosomes in both ...

Also provides initial update on 1,000 Plant & Animal Reference Genomes Project at 2nd annual conference. BGI (previously known as the Beijing Genomics Institute), the largest genomic organization in the world, announced today that it was among the research organizations comprising the Potato Genome Sequencing Consortium (PGSC) that completed the genome sequence and analysis of the tuber crop potato, published as an Advance Online Publication in Nature.. This study marks an important milestone in Potato (Solanum tuberosum L.) genome research, revealing new insights into the evolutionary history of the potato genome, causes of inbreeding depression, and potential mechanisms of tuber initiation and development. These insights will generate great interest among botanists and breeders worldwide and facilitate the genetic engineering of this vital crop.. BGI and its collaborators carried out the de novo sequencing, genome assembly and annotation of the potato genome, elucidating the evolutionary ...

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The Arabidopsis Information Resource (TAIR, http://arabidopsis.org) is the model organism database for the fully sequenced and intensively studied model plant Arabidopsis thaliana. Data in TAIR is derived in large part from manual curation of the Arabidopsis research literature and direct submission …

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BACKGROUND: Bread wheat is an allopolyploid species with a large, highly repetitive genome. To investigate the impact of selection on variants distributed among homoeologous wheat genomes and to build a foundation for understanding genotype-phenotype relationships, we performed population-scale re-sequencing of a diverse panel of wheat lines. RESULTS: A sample of 62 diverse lines was re-sequenced using the whole exome capture and genotyping-by-sequencing approaches. We describe the allele frequency, functional significance, and chromosomal distribution of 1.57 million single nucleotide polymorphisms and 161,719 small indels. Our results suggest that duplicated homoeologous genes are under purifying selection. We find contrasting patterns of variation and inter-variant associations among wheat genomes; this, in addition to demographic factors, could be explained by differences in the effect of directional selection on duplicated homoeologs. Only a small fraction of the homoeologous regions ...

Please pass this along to undergraduate students and their advisors Plant Genomics Internships at the University of Missouri-Columbia The University of Missouri-Columbia is offering undergraduate summer research internships in PLANT GENOMICS. Visit our website: http://www.LSUROP.missouri.edu/pgi Application form available at: http://www.LSUROP.missouri.edu/PDFs/nonMUapp.pdf Details - Eight-week summer program (June 8-August 2, 2003) - $3100 stipend, to cover educational and personal expenses - Room (double) and board provided on-campus in air-conditioned dormitories - Travel expenses to and from Columbia provided - Travel money available to present research at a scientific meeting Plant Genomics at Missouri The University of Missouri-Columbia (MU) is a nationally recognized center for plant genetics research and has recently been awarded multiple grants from the National Science Foundation to fund research in plant genomics. Faculty in Biological Sciences, Biochemistry, Plant Sciences, and ...

Molecular Genetics Examples of important polyploid plants used for human food include, Triticum aestivum (wheat), Arachis hypogaea (peanut), Avena sativa (oat), Mus… Targeted genome editing using artificial nucleases has the potential to accelerate basic research as well as plant breeding by providing the means to modify genomes rapidly in a precise and predictable manner. The 5′ regions have many regulatory elements and are unique for specific genes. Example: Flowers in maize and tomato look very different. Plant genome sizes span several orders of magnitude from the carnivorous corkscrew plant (Genlisea aurea) at 63 megabases (Mb) to the rare Japanese Paris japonica at 148,000 Mb (Bennett and Leitch, 2011). By contrast, genome-wide selection estimates marker effects across the whole genome on the target popu … Genomic selection: genome-wide prediction in plant improvement Trends Plant Sci. 2011. It makes a sequence run every two to three hours and can read on average 600-700 bases per ...

Plant root systems play a major role in anchoring and in water and nutrient uptake from the soil. The root cone angle is an important parameter of the root system architecture because, combined with root depth, it helps to determine the volume of soil explored by the plant. Two genes, DRO1 and SOR1, and several QTLs for root cone angle have been discovered in the last 5 years. To find other QTLs linked to root cone angle, a genome-wide association mapping study was conducted on two panels of 162 indica and 169 japonica rice accessions genotyped with two sets of SNP markers (genotyping-by-sequencing set with approximately 16,000 markers and high-density-rice-array set with approximately 300,000 markers). The root cone angle of all accessions was measured using a screen protractor on images taken after 1 month of plant growth in the Rhizoscope phenotyping system. The distribution of the root cone angle in the indica panel was Gaussian, but several accessions of the japonica panel (all the bulus from

In the fields of bioinformatics and computational biology, Genome Survey Sequences (GSS) are nucleotide sequences similar to ESTs that the only difference is that most of them are genomic in origin, rather than mRNA. Genome Survey Sequences are typically generated and submitted to NCBI by labs performing genome sequencing and are used, amongst other things, as a framework for the mapping and sequencing of genome size pieces included in the standard GenBank divisions. Genome survey sequencing is a new way to map the genome sequences since it is not dependent on mRNA. Current genome sequencing approaches are mostly high-throughput shotgun methods, and GSS is often used on the first step of sequencing. GSSs can provide an initial global view of a genome, which includes both coding and non-coding DNA and contain repetitive section of the genome unlike ESTs. For the estimation of repetitive sequences, GSS plays an important role in the early assessment of a sequencing project since these data can ...

Read The rice R gene family: two distinct subfamilies containing several miniature inverted-repeat transposable elements, Plant Molecular Biology on DeepDyve, the largest online rental service for scholarly research with thousands of academic publications available at your fingertips.

Arabidopsis is a model diploid plant species, ideal for sequencing because of its small genome (1). Currently, more than 80% of the genome has been sequenced (http://www.arabidopsis.org/agi.html), and the entire genome should be completed later this year, revealing the complete gene repertoire of a higher plant and providing insights into plant genome organization (2). However, the full potential of the Arabidopsis sequence will be realized only when its genome structure, gene content, and gene functions can be understood in relationship to its own evolutionary history and to that of other plant species. It is through comparative genomics that researchers will deduce the mechanisms and pathways by which plant genes and genomes have diverged to give the diversity of form, function, and adaptation that now characterize the worlds flora. On the practical side, it is expected that the genomic sequence of Arabidopsis can be used to predict gene content and gene function in crop species, most of ...

The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. …

BELARMINO, Luis C. et al. Mining plant genome browsers as a means for efficient connection of physical, genetic and cytogenetic mapping: an example using soybean. Genet. Mol. Biol. [online]. 2012, vol.35, n.1, suppl.1, pp.335-347. ISSN 1415-4757. http://dx.doi.org/10.1590/S1415-47572012000200015.. Physical maps are important tools to uncover general chromosome structure as well as to compare different plant lineages and species, helping to elucidate genome structure, evolution and possibilities regarding synteny and colinearity. The increasing production of sequence data has opened an opportunity to link information from mapping studies to the underlying sequences. Genome browsers are invaluable platforms that provide access to these sequences, including tools for genome analysis, allowing the integration of multivariate information, and thus aiding to explain the emergence of complex genomes. The present work presents a tutorial regarding the use of genome browsers to develop targeted physical ...

TY - JOUR. T1 - Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. AU - Kaul, Samir. AU - Koo, Hean L.. AU - Jenkins, Jennifer. AU - Rizzo, Michael. AU - Rooney, Timothy. AU - Tallon, Luke J.. AU - Feldblyum, Tamara. AU - Nierman, William. AU - Benito, Maria Ines. AU - Lin, Xiaoying. AU - Town, Christopher D.. AU - Venter, J. Craig. AU - Fraser, Claire M.. AU - Tabata, Satoshi. AU - Nakamura, Yasukazu. AU - Kaneko, Takakazu. AU - Sato, Shusei. AU - Asamizu, Erika. AU - Kato, Tomohiko. AU - Kotani, Hirokazu. AU - Sasamoto, Shigemi. AU - Ecker, Joseph R.. AU - Theologis, Athanasios. AU - Federspiel, Nancy A.. AU - Palm, Curtis J.. AU - Osborne, Brian I.. AU - Shinn, Paul. AU - Dewar, Ken. AU - Kim, Christopher J.. AU - Buehler, Eugen. AU - Dunn, Patrick. AU - Chao, Qimin. AU - Chen, Huaming. AU - Theologis, Athanasios. AU - Osborne, Brian I.. AU - Vysotskaia, Valentina S.. AU - Lenz, Catherine A.. AU - Kim, Christopher J.. AU - Hansen, Nancy F.. AU - Liu, Shirley ...

The Arabidopsis Information Portal (AIP), a resource expected to provide access to all community data and combine outputs into a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics Consortium (IAIC). The design of the AIP will provide core functionality while remaining flexible to encourage multiple contributors and constant innovation. An IAIC-hosted Design Workshop in December 2011 proposed a structure for the AIP to provide a framework for the minimal components of a functional community portal while retaining flexibility to rapidly extend the resource to other species. We now invite broader participation in the AIP development process so that the resource can be implemented in a timely manner.. ...

Fauziah Ivo Rambe, Keragaman Genetik; Beberapa Sifat Kuantitatif Tanaman Kacang Tanah {Arachis hypogaea L.) Pada Tiga Lingkungan Tumbuh, dibawah bimbingan : Ir. Hasmawi Hasyim MS sebagai ketua komisi! pembimbing dan Ir. Yusuf Husni sebagai anggota komisi pembimbing. Penelitian ini dilaksanakan di jalan Selambo III Kecamatan Medan Amplas dengan ketinggian ± 25 m dpi. Tujuan penelitian adalah ,untuk mengetahui tingkat keragaman beberapa sifat kuantitatif tanaman kacang tanah {Arachis hypogaea L.) pada tiga lingkungan tumbuh. Penelitian ini dimulai sejak bulan Oktober 2001 sampai dengan awal Januari 2002. Rancangan yang digunakan adalah rancangan petak terpisah dengan dua faktor dan empat ulangan. Tiga lingkungan tumbuh sebagai faktor utama yaitu : Li = Populasi kacang tanah. L2 = Populasi tanaman kacang tanah : populsi jagung = 6:2 L3 = Populasi kacang tanah : populasi jagung = 6:4 Varietas sebagai anak petak terdiri atas 10 varietas yaitu : Vi = Varietas Gajah I V2 = Varietas Kelinci V3 = ...

The newly sequenced genome of the Amborella plant addresses Darwins abominable mystery -- the question of why flowers suddenly proliferated on Earth millions of years ago. The genome sequence sheds new light on a major event in the history of life on Earth: the origin of flowering plants, including all major food crop species. On 20 December 2013, a paper by the Amborella Genome Sequencing Project that includes a full description of the analyses performed by the project, as well as implications for flowering plant research, will be published in the journal Science. The paper is among three on different research areas related to the Amborella genome that will be published in the same issue of the journal ...

The Physical Map database will contain physical maps of the Brassica A and C genomes. These will be intergrated to the Arabidopsis genome sequence by hybridisation with selected gene anchor probes.

JCVI hosts the M. truncatula genome sequence and annotation in three forms: a Tripal database, JBrowse and an instance of InterMine named MedicMine. These databases also form part of a larger consortium of legume databases known as the Legume Federation (legumefederation.org). The Legume Federation is a joint project with USDA-ARS-Iowa State and the National Center for Genome Resources. Together, these three centers house genomic, genetic and phenotypic (QTL) data for around 10 legume crop species including soybean, common bean, peanut, chickpea, clover, lupin and others. The goal of the project is to provide cross-species links between these plants at the genomic, genetic and phenotypic levels to further legume research and breeding.. ...

Fig. 1. Molecular markers commonly used for mapping. SSLP (Bell and Ecker, 1994), SSLP markers exploit the variability of short repetitive sequences for mapping purposes. A primer pair (arrows) is used to amplify a fragment containing a short repetitive element, such as the (AT)-dinucleotide repeat shown in the example. The length of this repeat differs between the two accessions. In the example Columbia (Col) has an (AT)20 repeat whereas Landsbergerecta (Ler) has an (AT)15 repeat. Consequently, the PCR products from Ler and Col DNA also differ in length. In the example, the Col product is 150 bp and the Ler product is 140 bp long. This size difference can be visualized by agarose gel-electrophoresis (GE) with a standard (Std) as comparison. If a plant is heterozygous for the marker (Het), both products are amplified resulting in two bands. Typically the size difference created by short repetitive sequences is small. To facilitate their detection, SSLP primers usually amplify short fragments (80 ...

TY - GEN. T1 - Building an environment to facilitate discoveries for plant sciences. AU - Lenards, Andrew. AU - Merchant, Nirav C. AU - Stanzione, Dan. PY - 2011. Y1 - 2011. N2 - The iPlant Collaborative is an NSF-funded cyberinfrastructure (CI) effort directed towards the plant sciences community. This paper enumerates the key concepts, middleware, tools, and extensions that create the unique capabilities of the iPlant Discovery Environment (DE) that provide access to our CI. The DE is a rich web-based application that brings flexible CI capabilities to a wide audience affiliated with the plant sciences, from computational biologists, bioinformaticians, applications developers, to bench biologists. The inherent interdisciplinary nature of plant sciences research produces diverse and complex data products that range from molecular sequences to satellite imagery as part of the discovery life cycle. With the constant creation of novel analysis algorithms, the advent and spread of large data ...

and Shahdara. Gene expression markers (GEMs) are based on differences in transcript levels that exhibit bimodal distributions in segregating progeny, while single feature polymorphism (SFP) markers rely on differences in hybridization to individual oligonucleotide probes. Unlike SFPs, GEMs can be derived from any type of DNA-based expression microarray. Our method identifies SFPs independent of a genes expression level. Alleles for each GEM and SFP marker were ascertained with GeneChip data from parental accessions as well as RILs; a novel algorithm for allele determination using RIL distributions capitalized on the high level of genetic replication per locus. GEMs and SFP markers provided robust markers in 187 and 968 genes, respectively, which allowed estimation of gene order consistent with that predicted from the Col-0 genomic sequence. Using microarrays on a population to simultaneously measure gene expression variation and obtain genotypic data for a linkage map will facilitate expression ...

Itoh, Takeshi and Tanaka, Tsuyoshi and Barrero, Roberto A. and Yamasaki, Chisato and Fujii, Yasuyuki and Hilton, Phillip B. and Antonio, Baltazar A. and Aono, Hideo and Apweiler, Rolf and Bruskiewich, Richard and Bureau, Thomas and Burr, Frances and Costa de Oliveira, Antonio and Fuks, Galina and Habara, Takuya and Haberer, Georg and Han, Bin and Harada, Erimi and Hiraki, Aiko T. and Hirochika, Hirohiko and Hoen, Douglas and Hokari, Hiroki and Hosokawa, Satomi and Hsing, Yue and Ikawa, Hiroshi and Ikeo, Kazuho and Imanishi, Tadashi and Ito, Yukiyo and Jaiswal, Pankaj and Kanno, Masako and Kawahara, Yosihiro and Kawamura, Toshiyuki and Kawashima, Hiroaki and Khurana, Jitendra P. and Kikuchi, Shoshi and Komatsu, Setsuko and Koyanagi, Kanako O. and Kubooka, Hiromi and McCombie, W. Richard and Messing, Joachim and Miyao, Akio and Mulder, Nicola and Nagamura, Yoshiaki and Nam, Jongmin and Namiki, Nobukazu and Numa, Hisataka and Nurimoto, Shin and ODonovan, Claire and Ohyanagi, Hajimi and Liberherr, ...

Diet is a major determinant of human health. The composition of foods and their association with human health and disease has been largely based upon traditional chemical analysis of food composition. Advances in molecular biology, especially in analysis of plant genomes, provides an opportunity to explore this issue in new ways. An understanding of co-evolution of human and food genomes can explain the impact of specific food genes in human populations and the changes that have accompanied domestication of food organisms. Recent analysis of the rice genome has revealed the genetic basis of important flavour and food quality traits. We can now predict many of these attributes by analysis of DNA sequences. Food preferences are determined by the attractiveness of the food. This research demonstrates the need to combine genes for desirable flavour and texture with genes for appropriate nutritional content if we are to achieve positive health outcomes for human populations. ...

Pseudogenes have a reputation of being evolutionary relics or junk DNA. While they are well characterized in mammals, studies in more complex plant genomes were so far hampered by the absence of reference genome sequences. Barley is one of the economically most important cereals and has a genome size of 5.1 Gb. With the first high-quality genome reference assembly available for a Triticeae crop, we conducted a whole genome assessment of pseudogenes on the barley genome. We identified, characterized, and classified 89,440 gene fragments and pseudogenes, scattered along the chromosomes with occasional hotspots and higher densities at the chromosome ends ...

APGI Publications. Hypermutation in pancreatic cancer. Humphris JL, Patch A, Nones K, Bailey PJ, Johns AL, McKay S, Chang DK, Miller DK, Pajic M, Kassahn KS, Quinn MCJ, Bruxner TJC, Christ AN, Harliwong I, Idrisoglu S, Manning S, Nourse C, Nourbakhsh E, Stone A, et al. Gastroenterology. Nov 2016; doi: 10.1053/j.gastro.2016.09.060 [Epub ahead of print]This APGI-led study interrogated 385 pancreatic cancer genomes to define hypermutation and its causes. Mismatch repair deficiency was identified in 1% of tumors harboring different mechanisms of somatic inactivation of MLH1 and MSH2. Defining mutation load in individual pancreatic cancers has the potential to inform immunotherapy clinical trial design in pancreatic cancer.. Genomic analyses identify molecular subtypes of pancreatic cancer. Bailey P, Chang DK, Nones K, Johns AL, Patch A, Gingras M, Miller DK, Christ AN, Bruxner TJC, Quinn MC, Nourse C, Murtaugh LC, et al. Nature. Mar 2016; 531:47-52 doi:10.1038/nature16965. This ground-breaking study ...

Thus, B. nigra could be descended from a hexaploid ancestor. A comparative analysis of B. nigra, B. oleracea and B. rapa genomes, based on maps developed using a common set of RFLP probes, was also performed. The three genomes have distinct chromosomal structures differentiated by a large number of rearrangements, but collinear regions involving virtually the whole of each the three genomes were identified. The genic contents of B. nigra, B. oleracea and B. rapa were basically equivalent and differences in chromosome number (8, 9 and 10, respectively) are probably the result of chromsome fusions and/or fissions. The strong conservation of overall genic content across the three Brassica genomes mirrors the conservation of genic content observed over a much longer evolutionary span in cereals. However, the rate of chromosomal rearrangements in crucifers is much higher than that observed in cereal genomes. ...

TY - JOUR. T1 - Methylation-sensitive linking libraries enhance gene-enriched sequencing of complex genomes and map DNA methylation domains. AU - Nelson, William. AU - Luo, Meizhong. AU - Ma, Jianxin. AU - Estep, Matt. AU - Estill, James. AU - He, Ruifeng. AU - Talag, Jayson. AU - Sisneros, Nicholas. AU - Kudrna, David. AU - Kim, Hye Ran. AU - Ammiraju, Jetty S.S.. AU - Collura, Kristi. AU - Bharti, Arvind K.. AU - Messing, Joachim. AU - Wing, Rod A.. AU - SanMiguel, Phillip. AU - Bennetzen, Jeffrey L.. AU - Soderlund, Carol. PY - 2008/12/19. Y1 - 2008/12/19. N2 - Background: Many plant genomes are resistant to whole-genome assembly due to an abundance of repetitive sequence, leading to the development of gene-rich sequencing techniques. Two such techniques are hypomethylated partial restriction (HMPR) and methylation spanning linker libraries (MSLL). These libraries differ from other gene-rich datasets in having larger insert sizes, and the MSLL clones are designed to provide reads localized to ...

In the face of rapid climate change, it is important that plants can adapt quickly to new conditions to ensure their survival. Using field experiments and plant genome studies, an international research team has pinpointed areas of the genome that are affected during local adaptation to contrasting climates. This new insight into local adaptation represents an important first step towards future development of crops that are resilient to climate change.

We have built a robust rice physical map. More than 65,000 BAC clones representing 20-fold coverage have been fingerprinted successfully and assembled into physical contigs. The integrity of the contig assembly and clone order has been confirmed independently by FPC Simulated Digest using sequenced BAC and PAC clones from GenBank. Approximately 90% of the rice genome has been anchored genetically. Among the genetically anchored contigs, ∼80% are anchored by two or more genetic markers and therefore are oriented properly, whereas ,80% are anchored by multiple methods (i.e., marker hybridization, in silico hybridization, FISH, and sequenced clones).. On the basis of the physical map, we estimated the euchromatic portion of the rice genome to be ∼400 Mb, whereas earlier studies estimated the rice genome to be 430 Mb, based on DNA content (Arumuganathan and Earle, 1991; Saji et al., 2001). In contrast to the previous estimate of 51.5 Mb for chromosome 1 (Table 1) (Saji et al., 2001), our size ...

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

Whitney, K. D., E. J. Baack, J. L. Hamrick, M. J. W. Godt, B. C. Barringer, M. D. Bennett, C. G. Eckert, C. Goodwillie, S. Kalisz, I. J. Leitch, et al. 2010. A role for nonadaptive processes in plant genome size evolution? Evolution. 64:2097-2109 ...

Saint Clair Omaka Reserve Pinot Noir is the very finest Pinot Noir within the range. Usually sourced from a single vineyard within the Southern Valleys winegrowing region. Elegant, powerful, perfumed and perfectly balanced. Large cellaring potential where is will continue to mature in complexity.. ...

Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macroevolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead end, whereas recent genomic studies suggest that polyploidy has been a key driver of macroevolutionary success. We examined the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit lower speciation rates and higher extinction rates than diploids, providing the first quantitative corroboration of the dead-end hypothesis. The increased speciation rates of diploids can, in part, be ascribed to their capacity to speciate via polyploidy. Only particularly fit lineages of polyploids may persist to enjoy longer-term evolutionary success. ...

ABSTRACT During the past decade there has been a tremendous resurgence of interest in polyploidy that has in large part been stimulated by the development of increasingly powerful genetic and genomic tools. The result has been numerous new insights into the genomic and genetic consequences of polyploidy. The plethora of new discoveries has dramatically reshaped traditional views and concomitantly revealed that polyploidy is a highly dynamic and ubiquitous process. These recent advances in our understanding of polyploidy have stimulated numerous reviews, most focused on the various genetic, epigenetic, and genomic consequences of polyploid evolution. Whereas genetic and genomic attributes of polyploidization have received considerable attention, other crucial areas of polyploid evolution have received much less (e.g., ecology, pollination biology, physiology). The focus of this paper is not to review again recent discoveries, but to emphasize what we do not yet know about polyploidy, which ...

The open-access, open-data journal GigaScience (published by BGI and Biomed Central), announces today the publication of an article on the genome sequencing of 3000 rice strains along with the release of this entire dataset in a citable format in journals affiliated open-access database, GigaDB.

Find info about TCU plant science, registering in a technical degree program, and taking free practice tests about plant biology and plant science.

Get info about Troy University plant science, registering in a technical degree program, and taking free practice tests about plant biology and plant science.

Arabidopsis Information Portal (AIP) The AIP is a new resource built with a modular, community-extensible web-based interface that provides data retrieval, analysis, and.... ...

Citation: Rabbi, I., Hamblin, M., Kumar, P., Gedil, M., Ikpan, A.S., Jannink, J., Kulakow, P. 2013. High-resolution mapping of resistance to cassava mosaic geminiviruses in cassava using genotyping-by-sequencing and its implications for breeding. Virus Research. 186:87-96. Interpretive Summary: Cassava mosaic disease (CMD) is the most important viral disease of cassava in Africa and the Indian sub-continent. The cultivated cassava species is protected from CMD by polygenic resistance introgressed from the wild species Manihot glaziovii and a dominant monogenic type of resistance, named CMD2, discovered in African landraces. The ability of the monogenic resistance to confer high levels of resistance in different genetic backgrounds has led recently to its extensive usage in breeding across Africa as well as in Latin America, even though the virus is not present there. Most of the landraces carrying the monogenic resistance are morphologically very similar and come from a geographically restricted ...

Publications Dodds, K. G., McEwan, J. C., Brauning, R., Anderson, R. A., Van Stijn, T. C., Kristjánsson, T., et al. (2015). Construction of relatedness matrices using genotyping-by-sequencing data. BMC Genomics, 16, 1047.. Dodds, K. G., Auvray, B., Newman, S.-A. N., & McEwan, J. C. (2014). Genomic breed prediction in New Zealand sheep. BMC Genetics, 15, 92. Dodds, K. G., Auvray, B., Lee, M., Newman, S.-A. N., & McEwan, J. C. (2014). Genomic selection in New Zealand dual purpose sheep. Proceedings of the 10th World Congress of Genetics Applied to Livestock Production. Dodds, K. G., Tate, M. L., & Sise, J. A. (2005). Genetic evaluation using parentage information from genetic markers. Journal of Animal Science, 83(10), 2271-2279. Dodds, K. G., & McEwan, J. C. (1997). Calculating exact probabilities of allele frequency differences in divergent selection lines. Proceedings of the Association for the Advancement of Animal Breeding and Genetics, 12, 556-560. Dodds, K. G., Tate, M. L., McEwan, J. ...

A new virus has been discovered in North America, and its leaving its victims covered in splotchy discolored paths and with little energy to stand. However, its not people were talking about, but grasses. A new viral infection for grasses has been identified in the United States, and experts say there is reason to be worried that it will jump to some of the countrys most important food crops.

The data shown below were compiled from readership statistics for 3 Mendeley readers of this research output. Click here to see the associated Mendeley record. ...

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 ...