Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse

Abstract

The nature and organization of polymorphisms, or differences, between genomes of individuals are of great interest, because these variations can be associated with or even underlie phenotypic traits, including disease susceptibility. To gain insight into the genetic and evolutionary factors influencing such biological variation, we have examined the arrangement (haplotype) of single-nucleotide polymorphisms across the genomes of eight inbred strains of mice. These analyses define blocks of high or low diversity, often extending across tens of megabases that are delineated by abrupt transitions. These observations provide a striking contrast to the haplotype structure of the human genome.

Figure 1

Distribution of SNPs and haplotypes in SNPview on chromosome 4. (A) Polymorphic nucleotides for each strain plotted by physical position and colored by nucleotide. G, blue; A, green; T, black; C, red; insertions/deletions, orange; multiple nucleotide insertion/deletion, gray. All SNP-containing loci (sequence-tagged sites) are indicated by black stripes (row 9). (B) Polymorphic nucleotides (six laboratory strains) shown colored as major (blue) and minor (yellow) alleles. (C) Haplotypes, defined as regions in which two or more strains share the same SNP alleles across multiple loci, are indicated by colored blocks. Colors are reused for visual simplicity. Colors should be interpreted only to indicate similarity among strains at a particular position in the vertical axis, and no relationship is implied by similarly colored blocks that are separated in the horizontal axis. No color indicates an absence of data. (D) Dendrogram of strain relatedness based on CLUSTALW analysis of SNP alleles among six inbred strains for chromosome 4.

Figure 2

SNP density varies greatly by strain combination, chromosome, and chromosomal region. (A) SNP density (SNPs per 500 kb) on chromosome 16 is plotted by physical position for specific strain pairs. Common haplotype blocks largely correspond to areas of low SNP density. In some cases, haplotype analysis missed small regions of high diversity due to undersampling, e.g., 71–74 Mb (Upper). In other cases a single data point may define a haplotype block in the six-way strain comparison, but that region may contain few SNPs, e.g., 93–98 Mb (Lower). (B) Percentages of 500-kb windows containing <100 SNPs are plotted by chromosome for all combinations of 129/Sv, A/J, DBA/2J, and C57BL/6J sequence data. Generally, low-density blocks span 30–60% of each chromosome for any strain comparison. (C) Consistent with B, analysis of chromosome 10 indicates very limited haplotype diversity, with >90% of the chromosome having no more than two haplotypes.

Figure 3

Comparative analysis of SSLP and SNP distribution. A/J and BALB/cByJ SSLPs and SNPs are plotted by physical position for chromosomes 12 and 5. For each panel, the top row indicates the position of all loci containing polymorphic CA repeats. SSLPs polymorphic between A/J and DBA/2J (rows 2 and 3), SNPs colored by allele (rows 4 and 5), haplotypes defined by sample sequencing (rows 6 and 7), and sequenced loci (row 8) are shown. SNPs and SSLPs display a degree of codistribution even on chromosome 5, where many short, shared, and disparate haplotypes are defined.

Figure 4

Validation and utility of SNP discovery by mapping and genotyping. (A) Experimentally determined allele frequencies within pooled DNA samples were compared with known combined individual genotypes (_Pred). Pools of DNA were constructed from 15 or 30 samples from the M. spretus backcross panel. Individual DNAs were assigned to a specific pool based on their known genotype at marker D38418 (located at 33.9 Mb). B pools (B15 and B30) had an allele frequency of 100% for the C57BL/6J allele of D38418. S pools (S15 and S30) contain both the M. spretus and C57BL/6J allele at a 1:1 ratio. Thus, the expected C57BL/6J allele frequencies (100% and 50%) were detected at loci tightly linked to D38418, and the expected shift in frequency (to ≈75%), due to recombination, is seen in distal markers. (B and C) SNP assays can be used by reaction multiplexing. The histogram indicates mutant mice having abnormally low plasma high-density lipoprotein levels (nine, 17%). A genome scan of nine mutant mice (M1–9) and six normal littermates (WT1–6) identified a 15-Mb region on MMU8 that cosegregated with the phenotype. Names of individual markers (the first two digits indicate chromosome, and the next six digits indicate megabase and kilobase position) are listed in the first column. Genotypes are indicated by either a B (homozygous C57BL/6J) at that locus or H (heterozygote). (D) Dendrogram of genetic relationship among 29 mouse strains.