1,721,041 research outputs found
Two genomic regions contribute disproportionately to geographic differentiation in wild barley
Full text linkGenetic differentiation in natural populations is driven by geographic distance and by
ecological or physical features within and between natural habitats that reduce migration. The primary
population structure in wild barley differentiates populations east and west of the Zagros Mountains.
Genetic differentiation between eastern and western populations is uneven across the genome and is
greatest on linkage groups 2H and 5H. Genetic markers in these two regions demonstrate the largest
difference in frequency between the primary populations and have the highest informativeness for
assignment to each population. Previous cytological and genetic studies suggest there are chromosomal
structural rearrangements (inversions or translocations) in these genomic regions. Environmental association
analyses identified an association with both temperature and precipitation variables on 2H and with
precipitation variables on 5H.Fang, Zhou; Gonzales, Ana M; Clegg, Michael T; Smith, Keven P; Muehlbauer, Gary J; Steffenson, Brian; Morrell, Peter L. (2014). Two genomic regions contribute disproportionately to geographic differentiation in wild barley. Retrieved from the University Digital Conservancy, https://doi.org/10.1534/g3.114.010561
SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley"
No full textThe 318 sampled wild barley accensions, known as the Wild Barley Diversity Collection (WBDC), were genotyped using the Illumina Golden Gate Genotyping Assay with two Barley Oligo Pool assay chips (BOPA1 and BOPA2). The genotype calls were based on machine-scored data using the program ALCHEMY and the SNPs were annotated using the program SNPMeta. The BOPA1 & 2 files contains the output of the ALCHEMY program.
Finally the original individual SSR for barley are publicly available at the website called GrainGenes and the sample used in this dataset are included as a txt file. All three files (tsv and txt) can be opened by text editors.Two Barley Oligo Pool Assay chips (BOPA 1 and 2) were genotyped from the Wild Barley Diversity Collection. Due to its broad geographic distribution and ecological adaptation, this collection is a valuable source of potentially useful genes.USDA NIFA 2011-68002-30029University of Minnesota Doctoral Dissertation FellowshipLieberman-Okinow Endowment at the University of MinnesotaUSAID-funded Cereals Comparative Genomics InitiativeFang, Zhou; Gonzales, Ana M; Clegg, Michael T; Smith, Kevin P; Muehlbauer, Gary J; Steffenson, Brian J; Morrell, Peter L. (2016). SNP Genotyping Data from the Barley Experimental Population from "Two Genomic Regions Contribute Disproportionately to Geographic Differentiation in Wild Barley". Retrieved from the University Digital Conservancy, http://doi.org/10.13020/D6B59N
Barley Proteomics
No full textThe present chapter summarizes the current status of proteome research on barley. The importance of barley as a model for cereals and as a major crop is reflected by a large number of publications using proteomics as an approach to address fundamental or applied research questions. Progress through technological developments in mass spectrometry, the central analytical technique in proteomics, forms the background methodology applied for protein or peptide separation and protein identification as outlined in the first section. The grain is of central relevance for the use of barley as a crop and seed biology is a central topic in plant science. Hence, a large number of studies focus on the grain proteome as well as the changes in proteome composition during grain maturation and germination. Separate sections cover research on abiotic and biotic stress defence responses. The next section is dedicated to subcellular proteomics, isolation of organelles or subcellular fractions being a powerful strategy to cope with the complexity of the plant proteome. Typical current analytical tools can cover only a small fraction of the complete proteome. With regard to the number of genes, any proteome is increased in complexity by a high number of post-translational modifications and many potential splicing variants. In addition, the dynamic range of the individual protein abundance covers many orders of magnitude exceeding the limits of current detection methods. Although this complexity of the proteome is demanding for in-depth protein analysis, information on, e.g. post-translational modifications cannot be derived from other approaches such as transcriptomics. These aspects and potential developments are addressed in the final section of our contribution
Barley Inflorescence Architecture
No full textCultivated barley, Hordeum vulgare ssp. vulgare, is the fourth most abundantly grown cereal in the world (www.fao.org/faostat) and is long associated with human civilisations. Although most barley grain grown today is destined for animal feed and malting, barley remains an important source of primary calories in many parts of the world. Increasing barley yield in the face of challenges posed by increasing world population and climate change is a major goal of current research efforts. Grain is the ultimate product of inflorescence development and maturation. As such, understanding the genetics underlying inflorescence architecture in barley and then learning how to apply this knowledge to manipulate inflorescence development are important steps towards improving yield. The barley reference genome sequence represents an invaluable resource to support the identification and functional characterization of genes controlling inflorescence architecture. Resolving the relationships between gene and inflorescence traits are critical to support breeding as well as to provide insight about fundamental questions in cereal developmental biology. In this chapter, we first provide an overview of inflorescence development in cereals, highlighting the transitions in meristem identity associated with species-specific architectures. From here, we describe the development of key morphological features associated with the barley spike, spikelet, floret and grain, while discussing the identification and functions of genes which regulate their development. We also discuss those genes whose variation contributed to architectural changes during domestication and those with yield potential. Lastly, we describe environmental control of inflorescence development, with special attention to flowering time and the agronomic environment
Major chromosome 5H haplotype switch structures the European two-rowed spring barley germplasm of the past 190 years
Full text linkKey message: Selection over 70 years has led to almost complete fixation of a haplotype spanning ~ 250 Mbp of chomosome 5H in European two-rowed spring barleys, possibly originating from North Africa. Abstract: Plant breeding and selection have shaped the genetic composition of modern crops over the past decades and centuries and have led to great improvements in agronomic and quality traits. Knowledge of the genetic composition of breeding germplasm is essential to make informed decisions in breeding programs. In this study, we characterized the structure and composition of 209 barley cultivars representative of the European two-rowed spring barley germplasm of the past 190 years. Utilizing high-density SNP marker data, we identified a distinct centromeric haplotype spanning a ~ 250 Mbp large region on chromosome 5H which likely was first introduced into the European breeding germplasm in the early to mid-twentieth century and has been non-recombining and under strong positive selection over the past 70 years. Almost all cultivars in our panel that were released after 2000 carry this new haplotype, suggesting that this region carries one or several genes conferring highly beneficial traits. Using the global barley collection of the German Federal ex situ gene bank at IPK Gatersleben, we found the new haplotype at high frequencies in six-rowed spring-type landraces from Northern Africa, from which it may have been introduced into modern European barley germplasm via southern European landraces. The presence of a 250 Mbp genomic region characterized by lack of recombination and high levels of fixation in modern barley germplasm has substantial implications for the genetic diversity of the modern barley germplasm and for barley breeding.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
ELIGULUM-A regulates lateral branch and leaf development. Original figure files
No full textTIFF and JPEG files for the photographs used in constructing figures and supplemental figures in the manuscript, "ELIGULUM-A regulates lateral branch and leaf development," submitted to Plant Physiology. The images document a mutation that alters most of the structures of the plant and how the ELIGULUM-A gene interacts with different developmental pathways. The Figure Legend files describe the images individually.Shoot development is controlled by the actions of the shoot apical and axillary meristems resulting in the development of lateral branches and leaves. The barley (Hordeum vulgare L.) uniculm2 (cul2) mutation blocks axillary meristem development, and mutant plants lack lateral branches, tillers, that normally develop from the crown. A genetic screen for cul2 suppressors recovered two recessive alleles of ELIGULUM-A (ELI-A) that partially rescued the cul2 tillering phenotype. Mutations in ELI-A produce shorter plants with fewer tillers, disrupt the leaf blade – sheath boundary resulting in a liguleless leaf, and secondary cell wall formation is reduced. ELI-A encodes a previously un-annotated plant gene that is conserved in land plants. ELI-A transcript accumulates at the preligule boundary, the developing ligule, leaf margins, cells destined to develop secondary cell walls, and cells surrounding leaf vascular bundles. Recent studies have identified commonalities in the genetic control of boundaries during leaf and lateral organ development. Interestingly, we observed ELI-A transcript at the preligule boundary, indicating a role in establishing the boundary between the blade and sheath. However, we did not observe ELI-A transcript at the axillary meristem boundary in leaf axils, indicating that it does not play a role in establishing the boundary for axillary meristem development. Our results provide a new player in the model for leaf and lateral branch development in which ELI-A acts as a boundary gene for ligule development but not during lateral branch development.Department of Agriculture-CSREES-NRI Plant Growth and Development program grant # 2004-03440Triticeae Coordinated Agricultural Project, US Department of Agriculture/National Institute for Food and Agriculture grant number 2011-68002-30029Okagaki, Ron J; Muehlbauer, Gary J. (2018). ELIGULUM-A regulates lateral branch and leaf development. Original figure files. Retrieved from the University Digital Conservancy, https://doi.org/10.13020/D61H4D
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
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