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  • 1
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    Analysis of the bread wheat genome using whole-genome shotgun sequencing (2012)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2012-11-30
    Description: Bread wheat (Triticum aestivum) is a globally important crop, accounting for 20 per cent of the calories consumed by humans. Major efforts are underway worldwide to increase wheat production by extending genetic diversity and analysing key traits, and genomic resources can accelerate progress. But so far the very large size and polyploid complexity of the bread wheat genome have been substantial barriers to genome analysis. Here we report the sequencing of its large, 17-gigabase-pair, hexaploid genome using 454 pyrosequencing, and comparison of this with the sequences of diploid ancestral and progenitor genomes. We identified between 94,000 and 96,000 genes, and assigned two-thirds to the three component genomes (A, B and D) of hexaploid wheat. High-resolution synteny maps identified many small disruptions to conserved gene order. We show that the hexaploid genome is highly dynamic, with significant loss of gene family members on polyploidization and domestication, and an abundance of gene fragments. Several classes of genes involved in energy harvesting, metabolism and growth are among expanded gene families that could be associated with crop productivity. Our analyses, coupled with the identification of extensive genetic variation, provide a resource for accelerating gene discovery and improving this major crop.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510651/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510651/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Brenchley, Rachel -- Spannagl, Manuel -- Pfeifer, Matthias -- Barker, Gary L A -- D'Amore, Rosalinda -- Allen, Alexandra M -- McKenzie, Neil -- Kramer, Melissa -- Kerhornou, Arnaud -- Bolser, Dan -- Kay, Suzanne -- Waite, Darren -- Trick, Martin -- Bancroft, Ian -- Gu, Yong -- Huo, Naxin -- Luo, Ming-Cheng -- Sehgal, Sunish -- Gill, Bikram -- Kianian, Sharyar -- Anderson, Olin -- Kersey, Paul -- Dvorak, Jan -- McCombie, W Richard -- Hall, Anthony -- Mayer, Klaus F X -- Edwards, Keith J -- Bevan, Michael W -- Hall, Neil -- B/J004588/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/E004725/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G012865/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G013004/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G013985/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G024650/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/H022333/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- G0900753/Medical Research Council/United Kingdom -- G0900753(91100)/Medical Research Council/United Kingdom -- England -- Nature. 2012 Nov 29;491(7426):705-10. doi: 10.1038/nature11650.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Centre for Genome Research, University of Liverpool, Liverpool L69 7ZB, UK.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23192148" target="_blank"〉PubMed〈/a〉
    Keywords: Brachypodium/genetics ; *Bread ; Chromosomes, Plant/genetics ; Crops, Agricultural/genetics ; DNA, Complementary/genetics ; DNA, Plant/genetics ; Evolution, Molecular ; Genes, Plant/genetics ; Genome, Plant/*genetics ; Genomics ; Multigene Family/genetics ; Oryza/genetics ; Polymorphism, Single Nucleotide/genetics ; Polyploidy ; Pseudogenes/genetics ; Sequence Alignment ; Sequence Analysis, DNA ; Triticum/classification/*genetics ; Zea mays/genetics
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Epigenetic reprogramming that prevents transgenerational inheritance of the vernalized state (2014)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2014-09-16
    Description: The reprogramming of epigenetic states in gametes and embryos is essential for correct development in plants and mammals. In plants, the germ line arises from somatic tissues of the flower, necessitating the erasure of chromatin modifications that have accumulated at specific loci during development or in response to external stimuli. If this process occurs inefficiently, it can lead to epigenetic states being inherited from one generation to the next. However, in most cases, accumulated epigenetic modifications are efficiently erased before the next generation. An important example of epigenetic reprogramming in plants is the resetting of the expression of the floral repressor locus FLC in Arabidopsis thaliana. FLC is epigenetically silenced by prolonged cold in a process called vernalization. However, the locus is reactivated before the completion of seed development, ensuring the requirement for vernalization in every generation. In contrast to our detailed understanding of the polycomb-mediated epigenetic silencing induced by vernalization, little is known about the mechanism involved in the reactivation of FLC. Here we show that a hypomorphic mutation in the jumonji-domain-containing protein ELF6 impaired the reactivation of FLC in reproductive tissues, leading to the inheritance of a partially vernalized state. ELF6 has H3K27me3 demethylase activity, and the mutation reduced this enzymatic activity in planta. Consistent with this, in the next generation of mutant plants, H3K27me3 levels at the FLC locus stayed higher, and FLC expression remained lower, than in the wild type. Our data reveal an ancient role for H3K27 demethylation in the reprogramming of epigenetic states in plant and mammalian embryos.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247276/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4247276/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Crevillen, Pedro -- Yang, Hongchun -- Cui, Xia -- Greeff, Christiaan -- Trick, Martin -- Qiu, Qi -- Cao, Xiaofeng -- Dean, Caroline -- 233039/European Research Council/International -- BB/C517633/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- BB/G009562/1/Biotechnology and Biological Sciences Research Council/United Kingdom -- England -- Nature. 2014 Nov 27;515(7528):587-90. doi: 10.1038/nature13722. Epub 2014 Sep 14.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉1] Department of Cell &Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK [2]. ; Department of Cell &Developmental Biology, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, UK. ; State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences. Beijing 100101, China.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25219852" target="_blank"〉PubMed〈/a〉
    Keywords: Amino Acid Sequence ; Arabidopsis/enzymology/*genetics ; Arabidopsis Proteins/*genetics/metabolism ; Cellular Reprogramming/genetics ; Chromosome Mapping ; DNA Methylation ; *Epigenesis, Genetic ; *Gene Expression Regulation, Plant ; Gene Silencing ; MADS Domain Proteins/*genetics ; Molecular Sequence Data ; Mutation ; Sequence Alignment ; Transcription Factors/genetics/metabolism
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 3
    Electronic Resource
    Electronic Resource
    Involvement of SLR1 genes in pollen adhesion to the stigmatic surface in Brassicaceae (1997)
    Springer
    Sexual plant reproduction 10 (1997), S. 227-235 
    Details
    ISSN: 1432-2145
    Keywords: Key words Brassicaceae ; Pollen-stigma adhesion ; SLR glycoproteins ; Self-incompatibility ; Unilateral incompatibility
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The S-locus-related gene SLR1 is highly conserved and highly expressed in several species of the Brassicaceae family. Its function has not been determined, although several features would suggest a fundamental role in pollination. A second related gene (SLR2) is conserved and expressed in a subset of Brassica genotypes. We analysed the stigmatic expression of SLR1 and SLR2 genes among 11 different plants from various species or genera of the Brassicaceae and examined the extent of the pollen-stigma interaction during intraspecific, interspecific and intergeneric pollinations between them. Appropriate statistical tests on these variables (pollen adhesion, germination, penetration into the stigma, style and ovary, and SLR gene expression) showed that expression of SLR1 (but not SLR2) may be a factor in pollen-stigma adhesion. This hypothesis was supported by the observation of reduced pollen-stigma adhesion in transgenic B. napus plants modified for SLR1 expression.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004970050091
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  • 4
    Electronic Resource
    Electronic Resource
    SLR1 function is dispensable for both self-incompatible rejection and self-compatible pollination processes inBrassica (1996)
    Springer
    Sexual plant reproduction 9 (1996), S. 203-208 
    Details
    ISSN: 1432-2145
    Keywords: Brassica ; Self-incompatibility ; SLR1 Transformation ; Antisense
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract TheSLR1 gene inBrassica is related both in DNA sequence and in pattern of expression to theS-locus glycoprotein (SLG) gene involved in the self-incompatibility mechanism which recognises and arrests the germination of self pollen. However,SLR1 shows minimal allelic variation and is expressed in both self-incompatible and compatibleBrassica lines and in related, self-compatible cruciferous plants. The function of the SLR1 protein is unknown. TheSLR1 gene was specifically ablated in self-incompatible and self-compatibleBrassica plants byAgrobacterium-mediated transformation with an antisense construct. Primary transformants and homozygous T2 progeny of both self-incompatibleB. oleracea and self-compatibleB. napus recipients were found to exhibit normal pollination responses despite having no detectable SLR1 glycoprotein. This shows that the high, wild-type level of SLR1 protein is not required to sustain the self-incompatibility reaction, nor is it necessary for successful intra-specific cross-pollination between compatible lines.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF02173099
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  • 5
    Electronic Resource
    Electronic Resource
    SLR1 function is dispensable for both self-incompatible rejection and self-compatible pollination processes in Brassica (1996)
    Springer
    Sexual plant reproduction 9 (1996), S. 203-208 
    Details
    ISSN: 1432-2145
    Keywords: Key words Brassica ; Self-incompatibility ; SLR1 ; Transformation ; Antisense
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract  The SLR1 gene in Brassica is related both in DNA sequence and in pattern of expression to the S-locus glycoprotein (SLG) gene involved in the self-incompatibility mechanism which recognises and arrests the germination of self pollen. However, SLR1 shows minimal allelic variation and is expressed in both self-incompatible and compatible Brassica lines and in related, self-compatible cruciferous plants. The function of the SLR1 protein is unknown. The SLR1 gene was specifically ablated in self-incompatible and self-compatible Brassica plants by Agrobacterium-mediated transformation with an antisense construct. Primary transformants and homozygous T2 progeny of both self-incompatible B. oleracea and self-compatible B. napus recipients were found to exhibit normal pollination responses despite having no detectable SLR1 glycoprotein. This shows that the high, wild-type level of SLR1 protein is not required to sustain the self-incompatibility reaction, nor is it necessary for successful intra-specific cross-pollination between compatible lines.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/s004970050032
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  • 6
    Electronic Resource
    Electronic Resource
    An analysis of the relative activities of a number of promoter constructs from genes which are expressed during late pollen development as determined by particle bombardment (1995)
    Springer
    Plant cell reports 15 (1995), S. 154-158 
    Details
    ISSN: 1432-203X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The promoters of a tobacco actin gene, a tobacco pectate lyase, a tobacco and maize polygalacturonase and aBrassica S-locus related gene have been fused to theβ-glucuronidase reporter gene and their activities determined by biolistic transient assay in tobacco pollen. In stably transformed tobacco all the transgenes with the exception of Cauliflower Mosaic Virus-35S-β-glucuronidase appear to express efficiently in maturing pollen. Transient assay analysis showed that the tobacco pectate lyase and the polygalacturonase constructs were 8x more active than the tobacco actin construct, and that the tobacco polygalacturonase construct was some 33x more active than the maize polygalacturonase construct. Constructional manipulations that altered the lengths of the 5′-untranslated leaders including one which resulted in the removal of a 490 bp leader intron had little effect on the observed level of expression. However, the alteration of the context of the ATG from A/TnnATGG to CnnATGT resulting in a 70% reduction in the observed levels of activity, was obtained with the pectate lyase and polygalacturonase promoters. An identical reductional was also observed in transgenic plant populations transformed with the polygalacturonase transgenes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF01690275
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  • 7
    Electronic Resource
    Electronic Resource
    Genomic sequence of a Brassica S locus-related gene (1990)
    Springer
    Plant molecular biology 15 (1990), S. 203-205 
    Details
    ISSN: 1573-5028
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00017746
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  • 8
    Electronic Resource
    Electronic Resource
    PCR detection of transcripts homologous to the self-incompatibility gene in anthers ofBrassica (1991)
    Springer
    Theoretical and applied genetics 82 (1991), S. 466-472 
    Details
    ISSN: 1432-2242
    Keywords: Brassica oleracea ; Self-incompatibility ; S-locus ; Polymerase chain reaction ; Anther
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The polymerase chain reaction (PCR) is particularly well suited for the detection of rare sequences. Taking advantage of the recent isolation of sequences associated with stigma self-incompatibility inBrassica oleracea, we used PCR amplifications with primers synthesized to the S6 cDNA sequence, to demonstrate the presence of mRNA homologous to stigmaS-locus gene (SLG) in anthers during early microsporogenesis. In addition, otherS-locus-related (SLR) sequences were shown to be transcribed in sexual as well as in vegetative tissues (roots, leaves), suggesting that the SLG family might be involved not only in pollen-stigma recognition, but more generally in various forms of plant cell signalling processes. This information corroborates the recent discovery of a cDNA-deduced protein kinase from maize roots, whose extracellular receptor displays high homology withBrassica S-locus-specific glycoproteins.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00588600
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  • 9
    Electronic Resource
    Electronic Resource
    The computational difficulty of manipulating an election (1989)
    Springer
    Social choice and welfare 6 (1989), S. 227-241 
    Details
    ISSN: 1432-217X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Sociology , Economics
    Notes: Abstract We show how computational complexity might protect the integrity of social choice. We exhibit a voting rule that efficiently computes winners but is computationally resistant to strategic manipulation. It is NP-complete for a manipulative voter to determine how to exploit knowledge of the preferences of others. In contrast, many standard voting schemes can be manipulated with only polynomial computational effort.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00295861
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  • 10
    Electronic Resource
    Electronic Resource
    Voting schemes for which it can be difficult to tell who won the election (1989)
    Springer
    Social choice and welfare 6 (1989), S. 157-165 
    Details
    ISSN: 1432-217X
    Source: Springer Online Journal Archives 1860-2000
    Topics: Sociology , Economics
    Notes: Abstract We show that a voting scheme suggested by Lewis Carroll can be impractical in that it can be computationally prohibitive (specifically, NP-hard) to determine whether any particular candidate has won an election. We also suggest a class of “impracticality theorems” which say that any fair voting scheme must, in the worst-case, require excessive computation to determine a winner.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00303169
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