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Do you know any primers that can be used to genotype mice and check if they are still C57B6? I'm concerned about genetic drift in my colony. I bought a breeding pair 3 years ago and expanded. I wanna make sure my animals still retain genetic markers of c57b6. Thanks

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    $\begingroup$ Why not buy more mice? Breeders have schedules to make them as homogeneous as possible. Spontaneous mutations that are maintained in your colony won't show an association with any sort of markers. $\endgroup$ – Bryan Krause Dec 4 '19 at 16:07
  • $\begingroup$ Welcome to Biology.SE! The only way to check for genetic drift would be to sequence the entire genome of your mice — in all likelihood any pair of primers would give you the same result even if you had a significant accumulation of point mutations. As @BryanKrause says, buying more mice is much more practical. ——— You may also benefit from taking the tour and then going through the help pages starting with How to Ask questions effectively on this site. Thanks! 😊 $\endgroup$ – tyersome Dec 4 '19 at 21:23
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Jackson Labs offers a service for this for what looks like a reasonable price. I have no experience with the service other than general good feelings about Jackson.

We have a unique selection of mouse single nucleotide polymorphism (SNPs) panels useful for a diverse set of mouse research applications.

Applications of SNP scanning services

  • Development of congenic mouse lines
  • Confirmation of C57BL/6 substrain background

[...]

Available custom designed SNP panels specifically tailored for your needs

The right panel for your needs - $179/sample

[...]

C57BL/6 substrain characterization panel distinguishes between C57BL/6J (B6J) and C57BL/6N (B6N) or C57BL/6NTac (B6NTac) genetic backgrounds

--GENOME SCANNING SERVICE

Edit to include some points raised in comments:

  • "These panels [i.e. the ones Jackson labs offers, noted above] seem to be intended for comparing between known strains, like when you make a transgenic strain and are in the process of backcrossing. It would not be as useful for monitoring drift, or for comparing an unknown C57BL-derived line to a standard one." – Bryan Krause
  • Any mouse colony will diverge from other colonies, especially if there are relatively few founders.

The identification of two CNVs in the small portion of the genome screened demonstrates that individual mice of highly inbred strains are not isogenic and suggests other CNVs may be segregating within C57BL/6J as well as other carefully maintained inbred strains.

--Genomic copy number and expression variation within the C57BL/6J inbred mouse strain

  • At the very least, intermittent back-crossing to a mouse from a different source is recommended.

With time, isolation and a little spontaneous genetic drift, a founder pair can produce a new substrain in as little as three generations (something to bear in mind if you're breeding mice in-house without “refreshing” the gene pool with an intermittent backcross to a bona fide C57BL/6J ... Clearly, substrains of C57BL/6 (and other inbred strains) are not all the same.

--All (C57BL/6) Mice are not Created Equal

  • Simply buying new mice as needed, from the same (reliable and standard) source each time, gives you a better chance of consistency, since a large breeder is less likely to see on-going founder effects.

  • If you have a solid reason for keeping your own colony, talking to the experts at Jackson Labs would be a good starting point; presumably monitoring strain consistency is something they think about as an ongoing issue, and they can give better advice than we can.

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