Fast genetic mapping of complex traits in C. elegans using millions of individuals in bulk.

Genetic studies of complex traits in animals have been hindered by the need to generate, maintain, and phenotype large panels of recombinant lines. We developed a new method, C. elegans eXtreme Quantitative Trait Locus (ceX-QTL) mapping, that overcomes this obstacle via bulk selection on millions of unique recombinant individuals. We use ceX-QTL to map a drug resistance locus with high resolution. We also map differences in gene expression in live worms and discovered that mutations in the co-chaperone sti-1 upregulate the transcription of HSP-90. Lastly, we use ceX-QTL to map loci that influence fitness genome-wide confirming previously reported causal variants and uncovering new fitness loci. ceX-QTL is fast, powerful and cost-effective, and will accelerate the study of complex traits in animals

Mechanisms of buffering of phenotypic variation in A. thaliana: Features of HSP90 and characterization of AGO1 as a new regulator of robustness

Thesis (Ph.D.)--University of Washington, 2015Biological systems have molecular mechanisms that allow them to maintain a constant phenotype despite environmental and genetic perturbations. These mechanisms can take the form of master regulator of robustness, gene products that are epistatic to environmental and genetic perturbations. When these regulators are perturbed, the phenotypic variation of the biological systems increases. The best example of a master regulator of robustness is HSP90. HSP90 interacts with proteins involved in different biological pathways, and thus is a central node of many genetic networks. HSP90 provides robustness to environmental and genetic perturbations, and it has been hypothesized that influences the evolution of its clients. Here, I provide evidence that HSP90 impacts the evolutionary trajectories of clients belonging to pairs of duplicate genes or gene families. MicroRNAs (miRNAs) have been shown to provide robustness to environmental and genetic perturbations of specific phenotypic traits. The central node of the miRNA pathway in A. thaliana is AGO1. In my thesis, I show that AGO1 is another master regulator of robustness, since AGO1 can buffer both environmental and genetic perturbations for a variety of traits. I also show that AGO1-dependent variation is background specific. Two of the AGO1-revealed phenotypes, lesions in cotyledons and lack of correlation between days to flowering and leaf number were analyzed to further detail

Island-specific evolution of a sex-primed autosome in a sexual planarian

The sexual strain of the planarian Schmidtea mediterranea, indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite1,2 . Here we isolate individual chromosomes and use sequencing, Hi-C3,4 and linkage mapping to assemble a chromosome-scale genome reference. The linkage map reveals an extremely low rate of recombination on chromosome 1. We confrm suppression of recombination on chromosome 1 by genotyping individual sperm cells and oocytes. We show that previously identifed genomic regions that maintain heterozygosity even after prolonged inbreeding make up essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicates that this phenomenon has evolved specifcally in populations from Sardinia and Corsica. We fnd that most known master regulators5-13 of the reproductive system are located on chromosome 1. We used RNA interference14,15 to knock down a gene with haplotype-biased expression, which led to the formation of a more pronounced female mating organ. On the basis of these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosom

Island-specific evolution of a sex-primed autosome in a sexual planarian.

The sexual strain of the planarian Schmidtea mediterranea, indigenous to Tunisia and several Mediterranean islands, is a hermaphrodite1,2. Here we isolate individual chromosomes and use sequencing, Hi-C3,4 and linkage mapping to assemble a chromosome-scale genome reference. The linkage map reveals an extremely low rate of recombination on chromosome 1. We confirm suppression of recombination on chromosome 1 by genotyping individual sperm cells and oocytes. We show that previously identified genomic regions that maintain heterozygosity even after prolonged inbreeding make up essentially all of chromosome 1. Genome sequencing of individuals isolated in the wild indicates that this phenomenon has evolved specifically in populations from Sardinia and Corsica. We find that most known master regulators5-13 of the reproductive system are located on chromosome 1. We used RNA interference14,15 to knock down a gene with haplotype-biased expression, which led to the formation of a more pronounced female mating organ. On the basis of these observations, we propose that chromosome 1 is a sex-primed autosome primed for evolution into a sex chromosome