Literature DB >> 16739574

Genotyping and mapping with high-density oligonucleotide arrays.

Justin Borevitz1.   

Abstract

This chapter discusses the specific details of how oligonucleotide arrays originally designed for expression analysis can be used for high-density genotyping to reveal tens of thousands of single-feature polymorphisms (SFPs). Cluster of SFPs reveal potential natural deletion polymorphisms. SFPs can be readily used for mapping mutations using bulk segregant analysis. An example is given using the Columbia and Landsberg erecta strains of Arabidopsis thaliana.

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Year:  2006        PMID： 16739574     DOI： 10.1385/1-59745-003-0:137

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  14 in total

1.  Fluorescence-microscopy screening and next-generation sequencing: useful tools for the identification of genes involved in organelle integrity.

Authors:  Giovanni Stefano; Luciana Renna; Federica Brandizzi
Journal:  J Vis Exp       Date:  2012-04-13       Impact factor: 1.355

2.  Adaptation and extinction in experimentally fragmented landscapes.

Authors:  Sima Fakheran; Cloé Paul-Victor; Christian Heichinger; Bernhard Schmid; Ueli Grossniklaus; Lindsay A Turnbull
Journal:  Proc Natl Acad Sci U S A       Date:  2010-10-18       Impact factor: 11.205

3.  AXY8 encodes an α-fucosidase, underscoring the importance of apoplastic metabolism on the fine structure of Arabidopsis cell wall polysaccharides.

Authors:  Markus Günl; Lutz Neumetzler; Florian Kraemer; Amancio de Souza; Alex Schultink; Maria Pena; William S York; Markus Pauly
Journal:  Plant Cell       Date:  2011-11-11       Impact factor: 11.277

4.  Regulatory network construction in Arabidopsis by using genome-wide gene expression quantitative trait loci.

Authors:  Joost J B Keurentjes; Jingyuan Fu; Inez R Terpstra; Juan M Garcia; Guido van den Ackerveken; L Basten Snoek; Anton J M Peeters; Dick Vreugdenhil; Maarten Koornneef; Ritsert C Jansen
Journal:  Proc Natl Acad Sci U S A       Date:  2007-01-19       Impact factor: 11.205

5.  Chloroplastic phosphoadenosine phosphosulfate metabolism regulates basal levels of the prohormone jasmonic acid in Arabidopsis leaves.

Authors:  Víctor M Rodríguez; Aurore Chételat; Paul Majcherczyk; Edward E Farmer
Journal:  Plant Physiol       Date:  2010-01-06       Impact factor: 8.340

6.  A simple optimization can improve the performance of single feature polymorphism detection by Affymetrix expression arrays.

Authors:  Youko Horiuchi; Yoshiaki Harushima; Hironori Fujisawa; Takako Mochizuki; Masanori Kawakita; Takayuki Sakaguchi; Nori Kurata
Journal:  BMC Genomics       Date:  2010-05-20       Impact factor: 3.969

7.  Golgi traffic and integrity depend on N-myristoyl transferase-1 in Arabidopsis.

Authors:  Luciana Renna; Giovanni Stefano; Wojciech Majeran; Chiara Micalella; Thierry Meinnel; Carmela Giglione; Federica Brandizzi
Journal:  Plant Cell       Date:  2013-05-14       Impact factor: 11.277

8.  Genome-wide patterns of single-feature polymorphism in Arabidopsis thaliana.

Authors:  Justin O Borevitz; Samuel P Hazen; Todd P Michael; Geoffrey P Morris; Ivan R Baxter; Tina T Hu; Huaming Chen; Jonathan D Werner; Magnus Nordborg; David E Salt; Steve A Kay; Joanne Chory; Detlef Weigel; Jonathan D G Jones; Joseph R Ecker
Journal:  Proc Natl Acad Sci U S A       Date:  2007-07-12       Impact factor: 11.205

9.  Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes.

Authors:  Piotr A Ziolkowski; Grzegorz Koczyk; Lukasz Galganski; Jan Sadowski
Journal:  Nucleic Acids Res       Date:  2009-03-21       Impact factor: 16.971

10.  Comprehensive analysis of Arabidopsis expression level polymorphisms with simple inheritance.

Authors:  Stephanie Plantegenet; Johann Weber; Darlene R Goldstein; Georg Zeller; Cindy Nussbaumer; Jérôme Thomas; Detlef Weigel; Keith Harshman; Christian S Hardtke
Journal:  Mol Syst Biol       Date:  2009-02-17       Impact factor: 11.429
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