Literature DB >> 22649081

SNP-Ratio Mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing.

Heike Lindner1, Michael T Raissig, Christian Sailer, Hiroko Shimosato-Asano, Rémy Bruggmann, Ueli Grossniklaus.   

Abstract

We present a generally applicable method allowing rapid identification of causal alleles in mutagenized genomes by next-generation sequencing. Currently used approaches rely on recovering homozygotes or extensive backcrossing. In contrast, SNP-ratio mapping allows rapid cloning of lethal and/or poorly transmitted mutations and second-site modifiers, which are often in complex genetic/transgenic backgrounds.

Mesh：

Year:  2012        PMID： 22649081      PMCID： PMC3416015          DOI： 10.1534/genetics.112.141341

Source DB:  PubMed          Journal:  Genetics        ISSN： 0016-6731            Impact factor:   4.562


  14 in total

Review 1.  Positional cloning in Arabidopsis. Why it feels good to have a genome initiative working for you.

Authors:  W Lukowitz; C S Gillmor; W R Scheible
Journal:  Plant Physiol       Date:  2000-07       Impact factor: 8.340

2.  Next-generation mapping of Arabidopsis genes.

Authors:  Ryan S Austin; Danielle Vidaurre; George Stamatiou; Robert Breit; Nicholas J Provart; Dario Bonetta; Jianfeng Zhang; Pauline Fung; Yunchen Gong; Pauline W Wang; Peter McCourt; David S Guttman
Journal:  Plant J       Date:  2011-07-18       Impact factor: 6.417

Review 3.  Arabidopsis map-based cloning in the post-genome era.

Authors:  Georg Jander; Susan R Norris; Steven D Rounsley; David F Bush; Irena M Levin; Robert L Last
Journal:  Plant Physiol       Date:  2002-06       Impact factor: 8.340

4.  A strategy for direct mapping and identification of mutations by whole-genome sequencing.

Authors:  Steven Zuryn; Stéphanie Le Gras; Karine Jamet; Sophie Jarriault
Journal:  Genetics       Date:  2010-07-06       Impact factor: 4.562

5.  SHOREmap: simultaneous mapping and mutation identification by deep sequencing.

Authors:  Korbinian Schneeberger; Stephan Ossowski; Christa Lanz; Trine Juul; Annabeth Høgh Petersen; Kåre Lehmann Nielsen; Jan-Elo Jørgensen; Detlef Weigel; Stig Uggerhø Andersen
Journal:  Nat Methods       Date:  2009-08       Impact factor: 28.547

6.  Rapid whole-genome mutational profiling using next-generation sequencing technologies.

Authors:  Douglas R Smith; Aaron R Quinlan; Heather E Peckham; Kathryn Makowsky; Wei Tao; Betty Woolf; Lei Shen; William F Donahue; Nadeem Tusneem; Michael P Stromberg; Donald A Stewart; Lu Zhang; Swati S Ranade; Jason B Warner; Clarence C Lee; Brittney E Coleman; Zheng Zhang; Stephen F McLaughlin; Joel A Malek; Jon M Sorenson; Alan P Blanchard; Jarrod Chapman; David Hillman; Feng Chen; Daniel S Rokhsar; Kevin J McKernan; Thomas W Jeffries; Gabor T Marth; Paul M Richardson
Journal:  Genome Res       Date:  2008-09-04       Impact factor: 9.043

Review 7.  The art and design of genetic screens: Arabidopsis thaliana.

Authors:  Damian R Page; Ueli Grossniklaus
Journal:  Nat Rev Genet       Date:  2002-02       Impact factor: 53.242

8.  Caenorhabditis elegans mutant allele identification by whole-genome sequencing.

Authors:  Sumeet Sarin; Snehit Prabhu; M Maggie O'Meara; Itsik Pe'er; Oliver Hobert
Journal:  Nat Methods       Date:  2008-08-01       Impact factor: 28.547

9.  Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing.

Authors:  Danielle V Irvine; Derek B Goto; Matthew W Vaughn; Yukinobu Nakaseko; W Richard McCombie; Mitsuhiro Yanagida; Rob Martienssen
Journal:  Genome Res       Date:  2009-05-07       Impact factor: 9.043

10.  Identification of EMS-induced mutations in Drosophila melanogaster by whole-genome sequencing.

Authors:  Justin P Blumenstiel; Aaron C Noll; Jennifer A Griffiths; Anoja G Perera; Kendra N Walton; William D Gilliland; R Scott Hawley; Karen Staehling-Hampton
Journal:  Genetics       Date:  2009-03-23       Impact factor: 4.562
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  30 in total

1.  Receptor-like cytoplasmic kinase MARIS functions downstream of CrRLK1L-dependent signaling during tip growth.

Authors:  Aurélien Boisson-Dernier; Christina Maria Franck; Dmytro S Lituiev; Ueli Grossniklaus
Journal:  Proc Natl Acad Sci U S A       Date:  2015-09-16       Impact factor: 11.205

2.  Next-generation sequencing as a tool to quickly identify causative EMS-generated mutations.

Authors:  J M Thole; L C Strader
Journal:  Plant Signal Behav       Date:  2015

Review 3.  Next-Generation Sequencing-Based Approaches for Mutation Mapping and Identification in Caenorhabditis elegans.

Authors:  Maria Doitsidou; Sophie Jarriault; Richard J Poole
Journal:  Genetics       Date:  2016-10       Impact factor: 4.562

Review 4.  Using next-generation sequencing to isolate mutant genes from forward genetic screens.

Authors:  Korbinian Schneeberger
Journal:  Nat Rev Genet       Date:  2014-08-20       Impact factor: 53.242

5.  Growth Control: A Saga of Cell Walls, ROS, and Peptide Receptors.

Authors:  Sebastian Wolf; Herman Höfte
Journal:  Plant Cell       Date:  2014-05-07       Impact factor: 11.277

6.  User guide for mapping-by-sequencing in Arabidopsis.

Authors:  Geo Velikkakam James; Vipul Patel; Karl J V Nordström; Jonas R Klasen; Patrice A Salomé; Detlef Weigel; Korbinian Schneeberger
Journal:  Genome Biol       Date:  2013-06-17       Impact factor: 13.583

7.  Discovery of genomic regions and candidate genes for grain weight employing next generation sequencing based QTL-seq approach in rice (Oryza sativa L.).

Authors:  Reddyyamini Bommisetty; Navajeet Chakravartty; Reddaiah Bodanapu; Jeevula B Naik; Sanjib K Panda; Sivarama P Lekkala; Krishna Lalam; George Thomas; S J Mallikarjuna; G R Eswar; Gopalakrishna M Kadambari; Swarajyalakshmi N Bollineni; Keerthi Issa; Srividhya Akkareddy; C Srilakshmi; K Hariprasadreddy; P Rameshbabu; P Sudhakar; Saurabh Gupta; V B R Lachagari; Lakshminarayana R Vemireddy
Journal:  Mol Biol Rep       Date:  2020-10-24       Impact factor: 2.316

8.  The Protein Phosphatases ATUNIS1 and ATUNIS2 Regulate Cell Wall Integrity in Tip-Growing Cells.

Authors:  Christina Maria Franck; Jens Westermann; Simon Bürssner; Roswitha Lentz; Dmytro Sergiiovych Lituiev; Aurélien Boisson-Dernier
Journal:  Plant Cell       Date:  2018-07-10       Impact factor: 11.277

9.  A high-quality cucumber genome assembly enhances computational comparative genomics.

Authors:  Paweł Osipowski; Magdalena Pawełkowicz; Michał Wojcieszek; Agnieszka Skarzyńska; Zbigniew Przybecki; Wojciech Pląder
Journal:  Mol Genet Genomics       Date:  2019-10-16       Impact factor: 3.291

10.  The Cell Wall Arabinose-Deficient Arabidopsis thaliana Mutant murus5 Encodes a Defective Allele of REVERSIBLY GLYCOSYLATED POLYPEPTIDE2.

Authors:  Christopher K Dugard; Rachel A Mertz; Catherine Rayon; Davide Mercadante; Christopher Hart; Matheus R Benatti; Anna T Olek; Phillip J SanMiguel; Bruce R Cooper; Wolf-Dieter Reiter; Maureen C McCann; Nicholas C Carpita
Journal:  Plant Physiol       Date:  2016-05-23       Impact factor: 8.340
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