The Arabidopsis genome: A foundation for plant research

Abstract

The sequence of the first plant genome was completed and published at the end of 2000. This spawned a series of large-scale projects aimed at discovering the functions of the 25,000+ genes identified in Arabidopsis thaliana (Arabidopsis). This review summarizes progress made in the past five years and speculates about future developments in Arabidopsis research and its implications for crop science. The provision of large populations of gene disruption lines to the research community has greatly accelerated the impact of genomics on many areas of plant science. The tools and community organization required for plant integrative and systems biology approaches are now ready to accomplish the next big step in plant biology—the integration of knowledge and modeling of biological processes. In the future, plant science will continue to be enriched by the alignment of high-quality basic research (generally conducted in Arabidopsis), with strategic objectives in crop plants. The sequence and analysis of an increasing number of crop plant genomes enhance this alignment and provide new insights into genome evolution and crop plant domestication.

Plant responses to plant growth-promoting rhizobacteria

“…As crop plants are estimated to possess even more genes than the model plant Arabidopsis (about 25,000) (Bevan and Walsh 2006), those percentages correspond to a total of a few 1,000 genes, substantially more than the numbers described in the other studies. However, the nature of the genes with altered expression levels was not investigated.…”

Sequencing Multiple and Diverse Rice Varieties. Connecting Whole-Genome Variation with Phenotypes

“…Considering the wide experimental options possible with plants using natural populations, historical breeding pedigrees, and specially designed segregating populations , we expect great utility of genomewide association analysis for gene discovery in rice. With the exception of Arabidopsis (Bevan and Walsh, 2005;Nordborg et al, 2005), as yet no other plant species has an extensive, genome-wide SNP dataset.…”

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

“…For example, this comparative approach has been used to leverage genomic information from the model species Arabidopsis thaliana to related crop species (Van Dodeweerd et al 1999;Grant et al 2000;Ku et al 2000;Bevan and Walsh 2005). However, the value of comparative genomic information is inversely proportional to the evolutionary distance of the species being compared.…”