Diagram illustrating insertional mutagenesis by an enhancer detector element. (a) The origin recognition complex (ORC) gene is expressed in the embryo and endosperm of the seed. (d) This expression pattern is visualized using labelled probes for ORC mRNAs. (b) and (e) Insertional mutagenesis by enhancer detection can lead to reporter gene activity that mimics the pattern of gene expression since it is influenced by enhancer elements in the gene's regulatory sequences, which are often found upstream of the gene. (c) This pattern of expression can sometimes be seen even when the gene itself is disrupted by the enhancer detector element. The advantage of disrupting the gene is that a mutant phenotype can be observed. (f) Here seed abortion is observed in the 1/4 homozygous mutant seeds. Images d and f reprinted from Collinge MA, Spillane C, Köhler C, Gheyselinck J and Grossniklaus U (2004) Genetic interaction of an origin recognition complex subunit and the Polycomb group gene MEDEA during seed development. The Plant Cell16: 1035–1046. Copyright (2004) with permission from the American Society of Plant Biologists.

Genetic interactions. This picture shows the carpel of a kanadi1 (kan1) and kanadi2 (kan2) double mutant (right) as compared to the wild type (left). Reprinted from Eshed Y, Baum SF, Perea JV and Bowman JL (2001) Establishment of polarity in lateral organs of plants. Current Biology11: 1251–1260. Copyright (2001), with permission from Elsevier.

Activation tagging. (a) T‐DNA insertion sites at the jaw locus relative to annotated genes. (b) Overexpression of the JAW microRNA leads to alterations in leaf shape. Reprinted from Palatnik JF, Allen E, Wu X et al. (2003) Control of leaf morphogenesis by microRNAs. Nature425: 257–263. Copyright (2003), with permission from Macmillan Publishers Ltd.

When two characters segregate independently, four classes of gametes are produced by the F1 generation. The F2 generation will segregate in a 9:3:3:1 phenotypic ratio. See text for details.

Dominance relationships. (a) Illustrates an allelic series, where an intermediate phenotype is produced by a hypomorphic allele (pink) of the wild‐type allele (red). The amorphic allele is white (null mutant). (Images kindly provided with permission by Ronald Koes Professor of Developmental Genetics at the Vrije Universiteit, Amsterdam.) This should not be confused with incomplete (partial) dominance in which the heterozygous progeny of a cross between a homozygous red‐flowering plant and a homozygous white‐flowering plant produces a similar pink‐flowering intermediate, or blend, of the trait. (b) Illustrates two co‐dominant alleles, where both parental phenotypes (the two left panels) are expressed in the progeny (right panel). See text for details.

Positional cloning. A typical recessive mutation, in which only a homozygous mutant plant displays the phenotype, can be mapped by crossing the mutant with an individual that carries other genetic variants. In this example (a), the mutant phenotype is displayed by an A. thaliana Columbia accession and is crossed with the A. thaliana Landsberg erecta accession. These two plant accessions show a high degree of polymorphism at the level of the DNA sequence. (b) The F1 generation is heterozygous for the mutation and shows no phenotype. (c) The F1 plant is allowed to self fertilize and the mutant F2 progeny is collected. Crossover events in these plants allow fragments of DNA from one parent or the other to segregate independently, so that individual progeny have a unique pattern of assorted DNA segments derived from its parents. Owing to the selection regime, the only common region of DNA among this population is a homozygous region of Columbia DNA at the mutant locus. Chromosome‐specific markers are used to identify regions of homozygous Columbia DNA that segregate with the mutant phenotype at a high frequency. (Two to three markers can be used per chromosome with 20 mutant progeny to identify the chromosome arm (long or short) that contains the mutated gene.) Here the analysis identifies the mutation at the base of the long‐arm of chromosome 1. A second F2 population is generated with approximately 1000 mutant F2 progeny. (d) Markers in the region are used to identify recombination events that reduce the size of the interval that contains homozygous Columbia DNA. (e) The recombination frequency at each marker helps to position the mutation within an ever‐decreasing interval. (f) Individual bacterial artificial chromosome (BAC) clones that form a continuous tiling path between the markers that flank the mutation can be analysed for candidate genes. The gene responsible for the mutant phenotype should have a change in its DNA sequence (mutation) compared to the wild type. Complementation of the mutation by an introduced transgene (in this case a gene on BAC T27G7) unambiguously identifies the mutated gene responsible for the mutant phenotype.