Catherine E. Welsh

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Here we provide a genome-wide, high-resolution map of the phylogenetic origin of the genome of most extant laboratory mouse inbred strains. Our analysis is based on the genotypes of wild-caught mice from three subspecies of Mus musculus. We show that classical laboratory strains are derived from a few fancy mice with limited haplotype diversity. Their(More)
The JAX Diversity Outbred population is a new mouse resource derived from partially inbred Collaborative Cross strains and maintained by randomized outcrossing. As such, it segregates the same allelic variants as the Collaborative Cross but embeds these in a distinct population architecture in which each animal has a high degree of heterozygosity and(More)
The Collaborative Cross (CC) is a panel of recombinant inbred lines derived from eight genetically diverse laboratory inbred strains. Recently, the genetic architecture of the CC population was reported based on the genotype of a single male per line, and other publications reported incompletely inbred CC mice that have been used to map a variety of traits.(More)
Complex human traits are influenced by variation in regulatory DNA through mechanisms that are not fully understood. Because regulatory elements are conserved between humans and mice, a thorough annotation of cis regulatory variants in mice could aid in further characterizing these mechanisms. Here we provide a detailed portrait of mouse gene expression(More)
Inbred model organisms are powerful tools for genetic studies because they provide reproducible genomes for use in mapping and genetic manipulation. Generating inbred lines via sibling matings, however, is a costly undertaking that requires many successive generations of breeding, during which time many lines fail. We evaluated several approaches for(More)
Numerous methods exist for inferring the ancestry mosaic of an admixed individual based on its genotypes and those of its ancestors. These methods rely on bialleic SNPs obtained from genotype calling algorithms, which classify each marker as belonging to one of four states (reference allele, alternate allele, heterozygous, or no call) based on probe(More)
Genotyping microarrays are an important resource for genetic mapping, population genetics, and monitoring of the genetic integrity of laboratory stocks. We have developed the third generation of the Mouse Universal Genotyping Array (MUGA) series, GigaMUGA, a 143,259-probe Illumina Infinium II array for the house mouse (Mus musculus). The bulk of the content(More)
The Collaborative Cross (CC) and the complementary Diversity Outbred (DO) population were conceived as a platform for the next generation of studies of the genetic basis for complex traits in mouse (Churchill et al. 2004). The CC promised to combine the strengths of existing panels of recombinant inbred (RI) lines [e.g., BXD (Taylor et al. 1973), LXS(More)
In this paper, we contrast the resolution and accuracy of determining recombination boundaries using genotyping arrays compared to high-throughput sequencing. In addition, we consider the impacts of sequence coverage and genetic diversity on localizing recombination boundaries. We developed a hidden Markov model for estimating recombination breakpoints(More)
Soil fumigation, commonly used in vegetable production, may alter the rate of nitrification, affecting availability of N for crop use. The objective of this research was to examine effects of soil fumigation and N fertilizer source on tomato growth and soil NO3–N and NH4–N in field production. Experiments 1 and 2 included application of methyl bromide at(More)