The genetic and molecular basis of natural variation for plant growth and related traits in Arabidopsis thaliana

Plant growth is a complex quantitative trait of which the (eco)physiological aspects have been researched in great detail. In contrast, little is known about the genetic basis and molecular basis of plant growth. Most of what is known today has been discovered by using reverse genetic approaches that target single genes. Forward genetics using naturally occurring variation provides the possibility to investigate genetic effects within the context of the genetic background. This thesis describes the results of a study that aimed at elucidating the genetic basis and the underlying molecular basis of natural genetic variation for plant growth and related traits in Arabidopsis thaliana. A set of over 30 growth related traits has been quantified in two Arabidopsis RIL populations, derived from crosses between the accessions Landsberg erecta (Ler) x Kashmir-2 and Landsberg erecta x Shakdara (Sha) respectively. The projected rosette area (PRA) and Feret diameter of each plant was measured repeatedly during its growth using digital image analysis and. A logistic model and a linear model were fitted to the PRA data for quantification of plant growth rate. The dimensions of the largest rosette leaves, plant hight and chlorophyll content index were measured. Furthermore, flowering time and leaf numbers were recorded. A selection of 15 traits was used to perform a multi-trait QTL analysis using mixed-model methodology. A total 19 QTL were detected of which some art similar locations in both populations. QTL important for flowering time were also found to explain nearly half of the genetic variance for plant growth rate. These QTL mainly mapped to similar locations in both populations indicating a common genetic basis for the affected traits in the studied accessions. However, population specific QTL with no effect on flowering time accounted for the remaining genetic variance explained for plant growth. These QTL were chosen for follow-up studies in order to elucidate the underlying molecular basis. The detected QTL effects were validated in a selected set of near isogenic lines (NILs). These NILs will provide the opportunity to fine-map the QTL in order to identify the genes, and in particular the DNA polymorphisms responsible for these effects. For a single QTL fine-mapping could be advanced efficiently, currently down to 151 genes, due to particularly penetrant effects on plant morphology. QTL that also affected flowering time were not the main interest of these studies because they mapped to positions of genes that were already described for their role in the regulation of this trait. However, although the relation between flowering time and plant growth of such QTL had been described in literature, no distinction between pleiotropy and closely linked QTL could be made so far. A QTL that effected flowering time and plant growth rate, among other traits, located on the bottom end of chromosome 5 has been fine-mapped and cloned using NILs with introgressions of Sha in the genetic background of Ler. Fine-mapping achieved a resolution at which it could be proven that the cluster of MAF2-MAF5 (MADS affecting flowering) genes was underlying the detected QTL effects on flowering time. The effects on plant growth were fine-mapped to a slightly larger region this included an additional 3 genes. Although it was known that these genes affect flowering time, their role in natural variation for this trait had not been directly shown before. Sequence analysis of the cluster showed that Sha carried a fusion consisting of the 5’ portion of MAF2 and the 3’ portion of MAF3. An intact MAF3 gene was not found in this accession. Recently it was shown that such MAF2/MAF3 fusions are relatively common among Arabidopsis accessions but the loss of MAF3 makes Sha unique. Genomic complementation indicated that neither MAF2, MAF3 nor MAF4 can explain the QTL effects by itself. The current hypothesis is therefore that both MAF2 and MAF3 are required in the regulation of flowering time to reconstitute the phenotypical value of Ler in a NIL.