Mapping the mouse genome
In a new study published online this week in the open access journal PLoS Biology, Sagiv Shifman, Jonathan Flint, and colleagues present a high resolution genetic map for the mouse genome--one of the most detailed genetic maps now available aside from that for humans.
To create this map, they used two groups of mice: one consisting of outbred, heterogeneous stock (HS) and the other of recombinant inbred lines (RI). Using the single nucleotide polymorphism (SNP) data that resulted from physical mapping of the mouse genome, the authors were able to track the patterns of inheritance of >10,000 SNPs in both groups of mice. Next, they were able to calculate their relative genetic locations based on how frequently they co-occur. They used this information to create a genetic map that can distinguish between two points 0.37 cM apart in HS and 0.45 cM in RI.
Using their maps, Shifman and colleagues then investigate recombination rates of various genes by comparing physical and genetic distances for each strain. On average, the recombination rate was 0.63 cM per megabase (cM/Mb) for HS, and 0.62 cM/Mb for RI. They also saw a lot of variation in recombination rate across the genome, between the two study groups, and between the sexes. In fact, when calculating rates separately for male and female HS mice, they confirmed results seen previously for humans, that the average autosomal (non-sex) chromosomes had a higher recombination rate for females than males.
Observing where there was a particularly high, or low, rate of recombination, the authors identified "jungles" and "deserts." They looked for sequence motifs that might be representative of jungles and deserts. Sequences previously found in human recombination hot spots were also common in mouse genome jungles. They found one motif, CCTCCCT, corresponding to mouse jungles and deserts was conserved among rats, dogs, and chimpanzees, as well as humans.
This new, improved mouse genetic map has already yielded valuable information on how factors such as chromosome, chromosomal location, sex, and sequence composition are related to recombination rates--information that can improve our understanding of inheritance and inform future efforts to pinpoint the precise location of genes on individual chromosomes.
Citation: Shifman S, Bell JT, Copley RR, Taylor MS, Williams RW, et al. (2006) A high-resolution single nucleotide polymorphism genetic map of the mouse genome. PLoS Biol 4(12): e395. DOI: 10.1371/journal.pbio.0040395.
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