Arabidopsis thaliana, a member of the Brassicaceae (cabbage) family of plants, is a relatively late arrival as a genetic model organism. Most work has been done in the past 20 years. It has no economic significance: it grows prolifically as a weed in many temperate parts of the world. However, because of its small size, short life cycle, and small genome, it has overtaken the more traditional genetic plant models such as corn and wheat and has become the dominant model for plant molecular genetics.

In comparison with other plants, Arabidopsis is small in regard to both its physical size and its genome size—features that are advantageous for a model organism. Arabidopsis grows to a height of less than 10 cm under appropriate conditions; hence, it can be grown in large numbers, permitting large-scale mutant screens and progeny analyses. Its total genome size of 125 Mb made the genome relatively easy to sequence compared with other plant model organism genomes, such as the maize genome (2500 Mb) and the wheat genome (16,000 Mb).

The analysis of Arabidopsis mutations through crossing relies on tried and true methods—essentially those used by Mendel. Plant stocks carrying useful mutations relevant to the experiment in hand are obtained from public stock centers. Lines can be manually crossed with each other or self-fertilized. Although the flowers are small, cross-pollination is easily accomplished by removing undehisced anthers (which are sometimes eaten by the experimenter as a convenient means of disposal). Each pollinated flower then produces a long pod containing a large number of seeds. This abundant production of offspring (thousands of seeds per plant) is a boon to geneticists searching for rare mutants or other rare events. If a plant carries a new recessive mutation in the germ line, selfing allows progeny homozygous for the recessive mutation to be recovered in the plant’s immediate descendants.

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Transgenesis. Agrobacterium T-DNA is a convenient vector for introducing transgenes (see Chapter 10). The vector–transgene construct inserts randomly throughout the genome. Transgenesis offers an effective way to study gene regulation. The transgene is spliced to a reporter gene such as GUS, which produces a blue dye at whatever positions in the plant the gene is active. Targeted knockouts. Because homologous recombination is rare in Arabidopsis, specific genes cannot be easily knocked out by homologous replacement with a transgene. Hence, in Arabi-dopsis, genes are knocked out by the random insertion of a T-DNA vector or transposon (maize transposons such as Ac-Ds are used), and then specific gene knockouts are selected by applying PCR analysis to DNA from large pools of plants. The PCR uses a sequence in the T-DNA or in the transposon as one primer and a sequence in the gene of interest as the other primer. Thus, PCR amplifies only copies of the gene of interest that carry an insertion. Subdividing the pool and repeating the process lead to the specific plant carrying the knockout. Alternatively, RNAi may be used to inactivate a specific gene.

Large collections of T-DNA insertion mutants are available; they have the flanking plant sequences listed in public databases; so, if you are interested in a specific gene, you can see if the collection contains a plant that has an insertion in that gene. A convenient feature of knockout populations in plants is that they can be easily and inexpensively maintained as collections of seeds for many years, perhaps even decades. This feature is not possible for most populations of animal models. The worm Caenorhabditis elegans can be preserved as a frozen animal, but fruit flies (Drosoph-ila melanogaster) cannot be frozen and revived. Thus, lines of fruit-fly mutants must be maintained as living organisms.

As the first plant genome to be sequenced, Arabidopsis has provided an important model for plant genome architecture and evolution. In addition, studies of Arabidopsis have made key contributions to our understanding of the genetic control of plant development. Geneticists have isolated homeotic mutations affecting flower development, for example. In such mutants, one type of floral part is replaced by another. Integration of the action of these mutants has led to an elegant model of flower-whorl determination based on overlapping patterns of regulatory-gene expression in the flower meristem. Arabidopsis has also contributed broadly to the genetic basis of plant physiology, gene regulation, and the interaction of plants and the environment (including the genetics of disease resistance). Because Arabidopsis is a natural plant of worldwide distribution, it has great potential for the study of evolutionary diversification and adaptation.

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