Natural genetic variation in Arabidopsis: tools, traits and prospects for evolutionary ecology

Abstract

Background: The model plant Arabidopsis thaliana (Arabidopsis) shows a wide range of genetic and trait variation among wild accessions. Because of its unparalleled biological and genomic resources, the potential of Arabidopsis for molecular genetic analysis of this natural variation has increased dramatically in recent years.

Scope: Advanced genomics has accelerated molecular phylogenetic analysis and gene identification by quantitative trait loci (QTL) mapping and/or association mapping in Arabidopsis. In particular, QTL mapping utilizing natural accessions is now becoming a major strategy of gene isolation, offering an alternative to artificial mutant lines. Furthermore, the genomic information is used by researchers to uncover the signature of natural selection acting on the genes that contribute to phenotypic variation. The evolutionary significance of such genes has been evaluated in traits such as disease resistance and flowering time. However, although molecular hallmarks of selection have been found for the genes in question, a corresponding ecological scenario of adaptive evolution has been difficult to prove. Ecological strategies, including reciprocal transplant experiments and competition experiments, and utilizing near-isogenic lines of alleles of interest will be a powerful tool to measure the relative fitness of phenotypic and/or allelic variants.

Conclusions: As the plant model organism, Arabidopsis provides a wealth of molecular background information for evolutionary genetics. Because genetic diversity between and within Arabidopsis populations is much higher than anticipated, combining this background information with ecological approaches might well establish Arabidopsis as a model organism for plant evolutionary ecology.

Fig. 1.

Arabidopsis accessions are classified into summer-annual and winter-annual types. Accessions behaving as winter-annual types germinate during late summer or autumn, over-winter as rosettes and grow to initiate the reproductive phase in spring. Under greenhouse conditions, the flowering of winter-annual types is delayed, but can be accelerated by extended low temperature that is equivalent to over-wintering in nature. The summer-annual types are able to complete all steps of the life cycle during the same summer season, as long as the climatic conditions are appropriate for seed production. Accessions of this type, also referred to as rapid cyclers, over-winter as seeds and therefore display increased seed dormancy.

Fig. 2.

Schematic methodologies for analysing natural variation in Arabidopsis accessions. In addition to the conventional genetic analysis with laboratory standard lines, a series of genetic analyses utilizing natural accessions are expected to allow the evaluation of the evolutionary significance of a given gene. AFLP, amplified fragment length polymorphism; QTL, quantitative trait loci; RFLP, restriction fragment length polymorphism; SNP, single nucleotide polymorphism.