Genotyping Arabidopsis T-DNA lines v1

This protocol is used for genotyping Arabidopsis seedlings to test for the presence of a transfer DNA (T-DNA) insertion. By using two primer sets it is possible to determine whether a seedling is homozygous, heterozygous or azygous for an insertion in the predicted genomic location. To identify lines with T-DNA insertions in a gene of interest, you need the Arabidopsis Genome Identifier (AGI) number corresponding to the genomic locus (e.g. RCS1A = AT1G67090), then visit the Salk Institute T-DNA Express site to find all the mapped insertions at your locus of interest. Genotyping primers have been pre-designed for each T-DNA line, these can be retrieved from the Salk Institute T-DNA primer site, and ordered at any supplier of DNA oligonucleotides before starting the protocol. In the US T-DNA lines can be purchased from the Arabidopsis Biological Resource Center (ABRC) and in the UK and EU from the European Arabidopsis Stock Center (NASC). Recommended reading http://signal.salk.edu/tdnaprimers.2.html Setting up the PCR reaction Genotyping is performed with the Phire Direct PCR Mix, this includes the polymerase, nucleotides and salts necessary for amplification. We use the “dilution protocol” which involves taking a small leaf disk and homogenizing it in dilution buffer using a gel tip (see manufacturer’s instructions for more details.)

Genotyping Arabidopsis T-DNA lines v3

This protocol is used for genotyping Arabidopsis seedlings to test for the presence of a transfer DNA (T-DNA) insertion. By using two primer sets it is possible to determine whether a seedling is homozygous, heterozygous or azygous for an insertion in the predicted genomic location. To identify lines with T-DNA insertions in a gene of interest, you need the Arabidopsis Genome Identifier (AGI) number corresponding to the genomic locus (e.g. RCS1A = AT1G67090), then visit the Salk Institute T-DNA Express site to find all the mapped insertions at your locus of interest. Genotyping primers have been pre-designed for each T-DNA line, these can be retrieved from the Salk Institute T-DNA primer site, and ordered at any supplier of DNA oligonucleotides before starting the protocol. In the US T-DNA lines can be purchased from the Arabidopsis Biological Resource Center (ABRC) and in the UK and EU from the European Arabidopsis Stock Center (NASC). Recommended reading http://signal.salk.edu/tdnaprimers.2.html Setting up the PCR reaction Genotyping is performed with the Phire Plant Direct PCR Mix, this includes the polymerase, nucleotides and salts necessary for amplification. We use the “dilution protocol” which involves taking a small leaf disk and homogenizing it in dilution buffer using a gel tip (see manufacturer’s instructions for more details.)

Genotyping Arabidopsis T-DNA lines v1

This protocol is used for genotyping Arabidopsis seedlings to test for the presence of a transfer DNA (T-DNA) insertion. By using two primer sets it is possible to determine whether a seedling is homozygous, heterozygous or azygous for an insertion in the predicted genomic location. To identify lines with T-DNA insertions in a gene of interest, you need the Arabidopsis Genome Identifier (AGI) number corresponding to the genomic locus (e.g. RCS1A = AT1G67090), then visit the Salk Institute T-DNA Express site to find all the mapped insertions at your locus of interest. Genotyping primers have been pre-designed for each T-DNA line, these can be retrieved from the Salk Institute T-DNA primer site, and ordered at any supplier of DNA oligonucleotides before starting the protocol. In the US T-DNA lines can be purchased from the Arabidopsis Biological Resource Center (ABRC) and in the UK and EU from the European Arabidopsis Stock Center (NASC). Recommended reading http://signal.salk.edu/tdnaprimers.2.html Setting up the PCR reaction Genotyping is performed with the Phire Direct PCR Mix, this includes the polymerase, nucleotides and salts necessary for amplification. We use the “dilution protocol” which involves taking a small leaf disk and homogenizing it in dilution buffer using a gel tip (see manufacturer’s instructions for more details.)

A seed resource for screening functionally redundant genes and isolation of new mutants impaired in CO2 and ABA responses

The identification of homologous genes with functional overlap in forward genetic screens is severely limited. Here we report the generation of over 14,000 amiRNA-expressing plants that enable screens of the functionally redundant gene space in Arabidopsis. A protocol is developed here for isolating robust and reproducible amiRNA-mutants. Examples of validation approaches and essential controls are presented for two new amiRNA mutants that exhibit genetically redundant phenotypes and circumvent double mutant lethality. In a forward genetic screen for abscisic acid (ABA)-mediated inhibition of seed germination, amiRNAs that target combinations of known redundant ABA receptor and SnRK2 kinase genes were rapidly isolated, providing a strong proof of principle for this approach. A new ABA insensitive amiRNA line is isolated, which targets three genes encoding avirulence-induced gene2-like (AIG2) genes. A thermal imaging screen for plants with impaired stomatal opening in response to low CO2 exposure led here to isolation of a new amiRNA targeting two essential proteasomal subunits, PAB1 and PAB2. The seed library of 14,000 T2 amiRNA lines generated here provides a new platform for forward genetic screens and is being made available to the Arabidopsis Biological Resource Center (ABRC) and optimized procedures for amiRNA screening and controls are described.HighlightThe generation of over 14,000 amiRNA-expressing plants is reported that are being made publicly available enabling screens of redundant genes in Arabidopsis. Identification of known and new genes is reported.

Following Phenotypes: An Exploration of Mendelian Genetics Using Arabidopsis Plants

Arabidopsis thaliana, a model system for plant research, serves as the ideal organism for teaching a variety of basic genetic concepts including inheritance, genetic variation, segregation, and dominant and recessive traits. Rapid advances in the field of genetics make understanding foundational concepts, such as Mendel's laws, ever more important to today's biology student. Coupling these concepts with hands-on learning experiences better engages students and deepens their understanding of the topic. In our article, we present a teaching module from the Arabidopsis Biological Resource Center as a tool to engage students in lab inquiry exploring Mendelian genetics. This includes a series of protocols and assignments that guide students through growing two generations of Arabidopsis, making detailed observations of mutant phenotypes, and determining the inheritance of specific traits, thus providing a hands-on component to help teach genetics at the middle and high school level.