Genetic analyses of natural variation in the model plant Arabidopsis thaliana: neutral marker, quantitative genetic, and population genetic approaches

The model flowering plant Arabidopsis thaliana is a popular system for studies of development, molecular biology, physiology, and more recently, ecology and evolution. The work described here represents several approaches toward understanding natural variation within this species. A molecular marker approach was taken to evaluate the distribution of neutral genetic variation. This study examined variation at 20 microsatellite loci in 126 accessions of A. thaliana. Substantial variability in mutation pattern was found among loci, most of which is not explained by the assumptions of traditional mutation models. Instead, it was discovered that the degree of locus diversity is strongly correlated with the average number of contiguous repeats within a locus, supporting a strong role for repeat disruptions in stabilizing microsatellite loci by reducing the substrate for polymerase slippage and recombination. Cluster analyses generated from these same data demonstrate the potential of microsatellite loci for resolving relationships among accessions of A. thaliana. To explore the genetic bases of phenotypic variation observed within A. thaliana, a quantitative trait locus (QTL) mapping approach was employed focusing on a broadly distributed, selectively important trait, trichome density. While such experiments are typically conducted in a single mapping population, to better characterize the genetic architecture of this trait, QTL were mapped in four recombinant inbred line populations. The results of this work identify eight new QTL for trichome density and show that many lineage-specific alleles that either increase or decrease trichome density persist in natural populations. Several of the QTL identified in these studies mapped near a candidate gene. One of these loci, ATMYC1, was particularly intriguing because previously it had not been linked to the trichome initiation genetic pathway. To test the hypothesis that ATMYC1 is a QTL for trichome density, genetic complementation tests and a screen for molecular variation were employed. Combined, these data revealed that alleles of ATMYC1 from different accessions of A. thaliana vary in their abilities to recover the mutant atmyc1 trichome phenotype, indicating that ATMYC1 is a QTL for trichome density. Sequence analyses of alleles of ATMYC1 revealed high levels of molecular divergence, suggestive of strong intraspecific, divergent selection.