SDN (Site-Directed Nucleases) : SDN are proteins comprised of a DNA binding domain linked to a DNA cleavage domain introducing a DNA double strand break. DNA binding domains can be custom-designed to bind to a specific site within a given locus, thereby providing a highly specific targeting tool.
Agrobacterium tumefaciens : A naturally occurring pathogenic bacterium of plants that can incorporate a part of its DNA into plant cells.

DNA (Deoxyribonucleic acid) : DNA is a polymer of deoxyribonucleotides which is the primary genetic material (Rieger et al., 1968).
Epigenetic : Refers to alterations of gene activity without altering the nucleotide sequence or genotype of an organism.

Gene : A segment of nucleic acid that codes for a protein or RNA with a defined function in the structure or metabolism of the organism, and containing the regulatory sequence elements for its expression. The unit of inheritance (Glick and Pasternak, 2003).

Genetically modified : Refers to an organism whose genotype has been altered in a way that does not naturally occur.

Genome : The entire complement of genetic material of an organism, virus, or organelle; in eukaryotes, the haploid set of chromosomes.

Homologous recombination : Recombination between similar DNA sequences (Lawrence, 1995).

Meiosis : The special cell division process by which the chromosome number of a reproductive cell becomes reduced to half (n) the diploid (2n) or somatic number.

Mutations : Any detectable and heritable change in the genetic material not caused by segregation or genetic recombination, which is transmitted to daughter cells and even to succeeding generations giving rise to mutant cells or mutant individuals provided it does not act as a dominant lethal factor (Rieger et al., 1968).

Phenotype/Phenotypic : The observable properties (structural and functional) of an organism, produced by the interaction between the organism’s genetic potential (genotype) and the environment in which it finds itself (Rieger et al., 1968).

Polyploid : Somatic cells and tissues, as well as individuals, having tree (triploid), four (tetraploid), five (pentaploid), or more complete chromosome sets instead of two as in diploids (Rieger et al., 1968).

Promoter : A segment of DNA to which RNA polymerase attaches, allowing the initiation of the transcription of a gene. It usually lies upstream of (5’ to) a gene (adjusted from Glick and Pasternak, 2003).

Protoplast : The protoplasm of a single cell, obtained by the enzymatic digestion of the cell wall (adapted from Mauseth, 1991).

Recombination : Any process which gives rise to cells or individuals associating in new ways two or more heritable determinants by which their parents differed (Rieger et al., 1968).

Segregation : The separation of allele pairs from one another and their distribution to different cells, usually at meiosis and sometimes at mitosis (Rieger et al., 1968).

Silencing : Shutdown of transcription of a gene.

Somaclonal variation : Genetic variation arising from mutations, or heritable epigenetic variation, in somatic plant cells undergoing regeneration in culture.

Somatic tissue : Tissues other than the germline.

T-DNA : DNA encoded on a plasmid of Agrobacterium that is transferred to the plant cell.

Trait : A phenotypic character of an organism.

Transgenesis : The use of recombinant DNA techniques for the introduction of genetic information into animal or plant cells that leads to the transmission of the input gene (transgene) to successive generations.

TALEN (Transcription Activator-Like Effector Nuclease) : TALEN are artificial restriction enzymes generated by fusing a TAL effector DNA binding domain to a DNA cleavage domain.

TAL (transcription activator-like) effectors : TAL are proteins secreted by Xanthomonas bacteria via their type III secretion system when they infect various plant species. These proteins can bind promoter sequences in the host plant and activate the expression of plant genes that aid bacterial infection. They recognize plant DNA sequences through a central repeat domain consisting of a variable number of ~34 amino acid repeats.

NHEJ, non-homologous end joining : NHEJ is a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" because the break ends are directly ligated without the need for a homologous template, in contrast to homologous recombination, which requires a homologous sequence to guide repair.

HR, homologous recombination : HR is a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks.