Plant Evolutionary Developmental Biology - Organisms, Databases and Tools

Organisms, Databases and Tools

The most important model systems in plant development have been arabidopsis and maize. Maize has traditionally been the favorite of plant geneticists, while extensive resources in almost every area of plant physiology and development are available for Arabidopsis thaliana. Apart from these, rice, Antirrhinum majus, Brassica, tomato are also being used in a variety of studies. The genomes of Arabidopsis thaliana and rice have been completely sequenced, while the others are in process. It must be emphasized here that the information from these "model" organisms form the basis of our developmental knowledge. While Brassica has been used primarily because of its convenient location in the phylogenetic tree in the mustard family, Antirrhinum majus is a convenient system for studying leaf architecture. Rice has been traditionally used for studying responses to hormones like abscissic acid and gibberelin as well as responses to stress. However, recently, not just the domesticated rice strain, but also the wild strains have been studied for their underlying genetic architectures.

Some people have objected against extending the results of model organisms to the plant world. One argument is that the effect of gene knockouts in lab conditions wouldn't truly reflect even the same plant's response in the natural world. Also, these supposedly crucial genes might not be responsible for the evolutionary origin of that character. For these reasons, a comparative study of plant traits has been proposed as the way to go now.

Since the past few years, researchers have indeed begun looking at non-model, "non-conventional" organisms using modern genetic tools. One example of this is the Floral Genome Project, which envisages to study the evolution of the current patterns in the genetic architecture of the flower through comparative genetic analyses, with a focus on EST sequences. Like the FGP, there are several such ongoing projects that aim to find out conserved and diverse patterns in evolution of the plant shape. Expressed sequence tag (EST) sequences of quite a few non-model plants like Sugarcane, Apple, Lotus, Barley, Cycas, Coffee, to name a few, are available freely online. The Cycad Genomics Project, for example, aims to understand the differences in structure and function of genes between gymnosperms and angiosperms through sampling in the order Cycadales. In the process, it intends to make available information for the study of evolution of structures like seeds, cones and evolution of life cycle patterns. Presently the most important sequenced genomes from an evo-devo point of view include those of A.thaliana (a flowering plant), Poplar (a woody plant), Physcomitrella patens (a bryophyte), Maize (extensive genetic information), and Chlamydomonas reinhardtii (a green alga). The impact of such a vast amount of information on understanding common underlying developmental mechanisms can easily be realised.

Apart from EST and genome sequences, several other tools like PCR, Yeast two hybrid system, microarrays, RNA Interference, SAGE, QTL mapping etc. permit the rapid study of plant developmental patterns. Recently, cross-species hybridization has begun to be employed on microarray chips, to study the conservation and divergence in mRNA expression patterns between closely related species. Techniques for analyzing this kind of data have also progressed over the past decade. We now have better models for molecular evolution, more refined analysis algorithms and better computing power as a result of advances in computer sciences.