Combining quantitative genetics and genomics to identify polymorphisms associated with drought physiology in Arabidopsis and Brassica napus

The following research was performed using a combination of quantitative genetic and molecular biological approaches in relation to drought physiology in two members of the Brassicaceae family, Arabidopsis thaliana and Brassica napus..;Arabidopsis is the model dicotyledonous species and stands alone as the most well characterized of all angiosperms. Brassica crops are ideally suited for applying the extensive genetic and genomic information gained in Arabidopsis due to a recent common ancestor (∼20 million years). DNA sequence comparisons between A. thaliana and several Brassica species has revealed a strong conservation of genic space (i.e. synteny) suggesting that the Brassicas are well-positioned for validating the potential of comparative genomics for crop improvement.;Near-isogenic lines (NILs) are inbred plant lines carrying one, or a few, small genomic introgressions from a "donor" line in a different and otherwise homogeneous genomic background (termed the recurrent parent). A new NIL population derived from two Arabidopsis lines which differ in many aspects of drought physiology was created. The study utilized a new genotyping-by-sequencing (GBS) method in which the recent advancements in DNA sequencing technology (i.e. "next-gen sequencing") are exploited to increase the number of genotyped loci. The result was a 3-fold increase in marker density compared to previously described NIL populations. The power of this new population is demonstrated as a locus underlying a drought physiology trait (night-time stomatal conductance) is validated using homozygous NILs. At the same time, a heterozygous NIL is used in combination with molecular markers to identify recombinants within the target interval to begin "fine-mapping" the locus with the end goal being the identification of the causal genetic variant.;Drought escape and dehydration avoidance represent the most prevalent drought coping strategies among annual crops. However, a tradeoff between them seems to exist as negative correlations in their underlying mechanisms has been reported in several studies. In order to understand if such a tradeoff exists in B. napus, and what the genetic basis of such a tradeoff might be, a quantitative trait locus (QTL) analysis was conducted for root mass and flowering time. Root mass represents a mechanism of dehydration avoidance (minimization of water loss and/or maximization of water uptake) and flowering time represents drought escape (completion of the life cycle prior to drought). Maximum segregating variation was achieved as the study population was derived from a cross between an annual (spring) and biennial (winter) variety, life-history traits which differentiate genetic and morphological classes.;Next-gen sequencing technology is revolutionizing our ability to analyze genomes. These technologies were used to sequence the annual and biennial parent lines of the mapping population in order to characterize molecular variation in the parental genomes at the scale of the genome, QTL and gene. Sequence data was used to construct a reference based assembly where recently released Brassica draft genomes were used as references. On average, the overall single nucleotide polymorphism (SNP) density was higher in the A genome whereas the rate of non-synonymous substitutions was elevated in the C genome. Non-synonymous substitutions were used to select gene ontology (GO) terms which distinguish the parent genomes and to select a list of candidate genes contained within each QTL. Marker assays developed for several of the discovered SNPs improved the density and overall quality of the genetic map. QTL analysis with the new map resulted in an improvement in model fit, suggesting the new markers were more tightly linked to the causal variants. Ultimately, this research provides a long list of molecular variants differentiating the parent lines that can be used in hypothesis development for research focused on the genetics of drought physiology in B. napus..