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Resources for Reverse Genetics Approaches in Arabidopsis thaliana

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Genetics and Genomics of the Brassicaceae

Part of the book series: Plant Genetics and Genomics: Crops and Models ((PGG,volume 9))

Abstract

Having many characteristics of an ideal experimental system, Arabidopsis thaliana became a very important model system for flowering plants. Its completed genome sequence data provided scientists the first fundamental tool towards understanding its genome structure and genes that it possess. There are more than 33,000 predicted genes in Arabidopsis and this number is increasing as novel methods develop and our understanding of genome organization and regulation expands. Reverse genetics that aim to reveal the functions of all Arabidopsis genes and the related resources were next most important tools that plant scientists needed. Numerous consortia were formed to supply scientists with such resources and tools necessary to determine the functions of Arabidopsis genes. Thanks to these international community efforts, now there are around 426,000 independent T-DNA/transposon insertion lines representing near saturation of all genes in Arabidopsis available for the research community. Besides insertion lines, several other sophisticated technologies and resources crucial for large-scale gene function studies in Arabidopsis were also developed. In this chapter, we discuss most of these important reverse genetics resources for gene function analysis.

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Abbreviations

Ac/Ds :

Activator/dissociation

AchrDNA:

Agrobacterium chromosomal DNA

AGI:

Arabidopsis genome initiative

AGRICOLA:

Arabidopsis genomic RNAi knock-out line analysis

AMAZE/ZIGIA:

Arabidopsis En-1 transposon insertion lines from Max-Planck-institute for plant breeding, Cologne

amiRNAs:

artificial microRNAs

CaMV:

Cauliflower mosaic virus

BLAST:

Basic local alignment search tool

DHPLC:

High-performance liquid chromatography

dsRNA:

double-stranded RNA

EMS:

Ethylmethanesulfonate

En/Spm :

Enhancer/supressor–mutator

FLAGdb:

Functional analysis of the Arabidopsis genome database, also known as INRA/Versailles lines

FST:

Flanking sequence tag

GABI-Kat:

Genomanalyse im biologischen System Pflanze Arabidopsis T-DNA lines

GFP:

Green fluorescent protein

GUS:

β-glucuronidase

LUC:

Luciferase protein

INDELS:

Insertions/deletions

MASC:

Multinational Arabidopsis steering committee

MIPS:

The Munich Institute for Protein Sequences

miRNAs:

microRNAs

NASC:

Nottingham Arabidopsis stock centre

PCR:

Polymerase chain reaction

SNPs:

Single nucleotide polymorphisms

SLAT:

Sainsbury laboratory Arabidopsis thaliana transposants

SAIL:

Syngenta Arabidopsis insertion library, formerly known as GARLIC (Gilroy Arabidopsis reverse lethal insertion collection)

SALK:

SALK institute T-DNA insertion lines

siRNA:

small interfering RNA

TAIR:

The Arabidopsis information resource

TAIL PCR:

Thermal asymmetric interlaced polymerase chain reaction

TAMARA:

Transposable element-mediated activation tagging mutagenesis in Arabidopsis

taRNAs:

Transacting RNAs

T-DNA:

Transferred DNA

TILLING:

Targeting-Induced Local Lesions In Genomes

tiling arrays:

Arrays that cover the whole genome

Ti plasmid:

Tumour inducing plasmid

TT1:

Arabidopsis transparent testa 1 protein

uidA :

Gene coding for β-glucuronidase

ZFN:

Zinc finger nuclease

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Authors and Affiliations

  1. Plant Molecular Engineering Group, IZMB (Institute of Cellular and Molecular Botany), University of Bonn, D-53115, Bonn, Germany

    Bekir Ülker

  2. Faculty of Biology, Bielefeld University, D-33594, Bielefeld, Germany

    Bernd Weisshaar

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  1. Bekir Ülker
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Correspondence to Bekir Ülker .

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  1. Kulturpflanzenforschung (IPK), Leibniz-Institut für Pflanzengenetik und, Corrensstr. 3, Gatersleben, 06466, Germany

    Renate Schmidt

  2. John Innes Institute, Norwich Research Park, Colney, Norwich, NR4 7UH, United Kingdom

    Ian Bancroft

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Ülker, B., Weisshaar, B. (2011). Resources for Reverse Genetics Approaches in Arabidopsis thaliana . In: Schmidt, R., Bancroft, I. (eds) Genetics and Genomics of the Brassicaceae. Plant Genetics and Genomics: Crops and Models, vol 9. Springer, New York, NY. https://doi.org/10.1007/978-1-4419-7118-0_19

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