Investigating the genetic basis of natural leaf shape variation in Arabidopsis thaliana

Leaf shape varies considerably between natural accessions of Arabidopsis thaliana. In this project we aimed to identify the genetic basis of this naturally occurring leaf shape variation. To score natural variation in leaf shape, we used a geometric morphometric approach, recording the shape of leaves with co-ordinates. We identified and scored the major shape variations in datasets of leaf shape models using Principal Component Analysis (PCA). To identify loci associated with differences in leaf shape, we used genetic mapping. We scored leaf shape in the Bay-0 x Shahdara Recombinant Inbred Line (RIL) population and carried out Quantitative Trait Loci (QTL) mapping. We also scored leaf shape in multiple growth experiments at different harvest points for a collection of over three hundred natural Arabidopsis accessions, and carried out Genome Wide Association (GWA) mapping. We identified loci associated with variation in our leaf shape traits in both approaches. Indicative of leaf shape as a polygenic quantitative trait, associated loci were typically of small to medium effect. However, we did identify, associated with variation in a leaf size and margin morphology trait, one single large locus, suggesting that naturally occurring loci can also have a dramatic effect on leaf morphology. We also found correlations between leaf shape and hypocotyl length and leaf number, suggesting natural leaf shape variation may coincide with other changes in plant morphology. Several of the loci associated with leaf shape traits in our GWA mapping contained Nucleotide Binding Leucine Rich Repeat (NBLRR) genes, and so we tested for leaf shape differences in T-DNA insertion lines annotated for these associated NBLRR genes. We found several of these T-DNA lines had differences in leaf shape and hypocotyl length, and that some of these differences in morphology were specific to temperature and light conditions.