A comprehensive SNP-based genetic analysis of inbred mouse strains

Abstract

Dense genetic maps of mammalian genomes facilitate a variety of biological studies including the mapping of polygenic traits, positional cloning of monogenic traits, mapping of quantitative or qualitative trait loci, marker association, allelic imbalance, speed congenic construction, and evolutionary or phylogenetic comparison. In particular, single nucleotide polymorphisms (SNPs) have proved useful because of their abundance and compatibility with multiple high-throughput technology platforms. SNP genotyping is especially suited for the genetic analysis of model organisms such as the mouse because biallelic markers remain fully informative when used to characterize crosses between inbred strains. Here we report the mapping and genotyping of 673 SNPs (including 519 novel SNPs) in 55 of the most commonly used mouse strains. These data have allowed us to construct a phylogenetic tree that correlates and expands known genealogical relationships and clarifies the origin of strains previously having an uncertain ancestry. All 55 inbred strains are distinguishable genetically using this SNP panel. Our data reveal an uneven SNP distribution consistent with a mosaic pattern of inheritance and provide some insight into the changing dynamics of the physical architecture of the genome. Furthermore, these data represent a valuable resource for the selection of markers and the design of experiments that require the genetic distinction of any pair of mouse inbred strains such as the generation of congenic mice, positional cloning, and the mapping of quantitative or qualitative trait loci.

Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis

“…1F). This strong correlation between frequencies of SNPs and small indels is similar to the mosaic pattern in mouse (Sakai et al 2005;Tsang et al 2005;Yang et al 2011), which is probably due to variation in divergence time among different genomic regions. Since Col and Ler were derived from the same natural population, some genomic regions might have inherited the same haplotype, whereas in other regions Col and Ler might have had different haplotypes with longer divergence time and more polymorphisms.…”

From Markers to Molecular Mechanisms: Type 1 Diabetes in the Post-GWAS Era

“…The availability of dense maps of polymorphic genetic markers (microsatellites and SNPs) revolutionized the localization of non-HLA-linked disease genes [48][49][50][51]. Linkage analyses rely on disproportionate transmission of alleles to affected and unaffected progeny.…”

Heligmosomoides bakeri: a model for exploring the biology and genetics of resistance to chronic gastrointestinal nematode infections

“…Both strains have been known for some time to be closely related (Rice and O'Brien, 1980), and this has been confirmed recently by SNP-based analyses. They form a tight clade with various other strains not yet assessed for resistance to H. bakeri (Tsang et al 2005 ;Sakai et al 2005). However, despite their close ancestry, SJL and SWR mice differ in one fundamental aspect of their response to intestinal nematodes : SWR produce the classic mastocystosis, but SJL mice do not and little, if any, parasite-specific IgE (Mitchell et al 1982 ;Watanabe et al 1993 ;Ben-Smith et al 2003).…”