A User’s Guide to the Arabidopsis T-DNA Insertion Mutant Collections

  • Ronan C. O’Malley
  • Cesar C. Barragan
  • Joseph R. EckerEmail author
Part of the Methods in Molecular Biology book series (MIMB, volume 1284)


The T-DNA sequence-indexed mutant collections contain insertional mutants for most Arabidopsis thaliana genes and have played an important role in plant biology research for almost two decades. By providing a large source of mutant alleles for in vivo characterization of gene function, this resource has been leveraged thousands of times to study a wide range of problems in plant biology. Our primary goal in this chapter is to provide a general guide to strategies for the effective use of the data and materials in these collections. To do this, we provide a general introduction to the T-DNA insertional sequence-indexed mutant collections with a focus on how best to use the available data sources for good line selection. As isolation of a homozygous line is a common next step once a potential disruption line has been identified, the second half of the chapter provides a step-by-step guide for the design and implementation of a T-DNA genotyping pipeline. Finally, we describe interpretation of genotyping results and include a troubleshooting section for common types of segregation distortions that we have observed. In this chapter we introduce both basic concepts and specific applications to both new and more experienced users of the collections for the design and implementation of small- to large-scale genotyping pipelines.

Key words

T-DNA Insertional mutagenesis T-DNA express SiGNAL SALK homozygous Plant genotyping High-throughput genotyping 



We would like to thank the entire National Science Foundation for funding of projects related to development of the Arabidopsis T-DNA insertion line resources (NSF MCB-1122250).


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Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Ronan C. O’Malley
    • 1
    • 2
  • Cesar C. Barragan
    • 1
  • Joseph R. Ecker
    • 1
    • 2
    • 3
    Email author
  1. 1.Genomic Analysis LaboratorySalk Institute for Biological StudiesLa JollaUSA
  2. 2.Plant Biology LaboratorySalk Institute for Biological StudiesLa JollaUSA
  3. 3.Howard Hughes Medical InstituteNew YorkUSA

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