on Mouse Genome Informatics."/>
Figure 3.2 Finding the gene and allele symbol on Mouse Genome Informatics. One of the chapter authors inquired about how to find the correct allele symbol to use relative to a specific reference
(Source: Tamai Y, Nakajima R, Ishikawa T, Takaku K, Seldin MF, Taketo MM. Colonic hamartoma development by anomalous duplication in Cdx2 knockout mice. Cancer Res. 1999 Jun 15;59(12):2965‐70).
Go to the Mouse Genome Informatics home page (http://www.informatics.jax.org/) and select “Gene.” The link goes to “Genes, Genome Features & Maps.” Then select “Genes and Marker Query.” In the Gene/Marker query box, enter the gene symbol or mutant mouse name, in this case Cdx2 was entered. Note, while gene symbols should be in italics no italics are given on this website or many other websites. This will give you all the genes for which this is part of the symbol or where Cdx2 was used as a synonym at some point in time. Selecting Cdx2 will yield the “Gene Detail” page. In the lower right area is the link to find all 14 of the currently reported allelic mutations (as of 1 May 2020) or the number of specific types of mutations. By selecting “All Mutations and Alleles” a summary field will appear. But which one is correct? By looking at the last author on the reference it is obvious from the summary. This is confirmed by selecting “Cdx2tm1Mmt” to reveal the data sheet on this specific allelic mutation. At the bottom of the field is the reference that is the original reference provided.
Source: The Jackson Laboratory.
Figure 3.3 Current symbols assigned to a variety of unrelated genes originally published as p38. If one searches for the gene symbol p38 the results indicate numerous genes on different chromosomes that at one time were all called p38. The new names not only separate out the different genes but also reflect to a degree what is currently known about the gene function. By following the links you can obtain much more detail on each gene, the number and details on allelic mutations, and links to the original and many subsequent publications on the topic (MGI accessed 22 April 2020).
Table 3.3 Inbred strains of mice.
| AdvantagesGenetic and phenotypic uniformity (smaller numbers needed)Well characterized (pathology and physiology)For most standard inbred strains >200 generationsIdeal controls (both biological and sequencing)Permits clear genetic mappingEnables identification of modifier genes |
| DisadvantagesNot as robust (smaller, lower reproductive performance [fecundity], shorter lifespan)Strain‐specific characteristics (deleterious mutations causing strain specific diseases)Expensive (when difficult to maintain) |
| UsesWidely used in all types of researchModels for human diseaseBackground for mice with spontaneous and induced mutations |
Table 3.4 Inbred strain nomenclature.
| C57BL/6J or C57BL/10J |
| C57BL is the parental strain name (since C57BL/6J is the actual strain name) |
| 6 or 10 indicate the substrain line number (C57BL/10J are prone to serious heart disease not seen in C57BL/6J) [8] |
| J indicates the breeder (The Jackson Laboratory) of these substrains |
| C3H/HeJ or C3H/HeN |
| C3H is the strain generated by Strong from a cross of Bagg albino with DBA |
| He is the substrain from the W.E. Heston laboratory at the National Cancer Institute |
| J indicates the subline received from Heston then bred by The Jackson Laboratory |
| N indicates the substrain bred at the National Institutes of Health |
An inbred strain is designated in capital letters.
A substrain is identified using a forward slash (/) after the strain name followed by a lab code of the strain breeder.
Further substrains derived from the founder add to the end of the lab code of subsequent breeders without another forward slash.
Note that C3H/HeJ has a mutation in the Tlr4 gene making it highly susceptible to gram negative bacterial infection while the C3H/HeN substrain is wildtype for Tlr4.
Figure 3.4 Nomenclature for hybrid stocks.
Table 3.5 Examples of inbred strain abbreviations.
| 129P3/J = 129P3 |
| 129S1/SvImJ = 129S1 |
| A/HeJ = AHe |
| A/J = A |
| AKR/J = AK |
| BALB/cByJ = CByJ |
| BALB/cJ = C |
| C57BL = B |
| C57BL/6J = B6 |
| C57BL/6JEi = B6Ei |
| C57BL/6NJ = B6NJ |
| C57BL/10J = B10 |
| C57BR/cdJ = BR |
| C57L = L |
| CBA/CaJ = CBACa |
| CBA/J = CBA |
| C3H/HeJ = C3 |
| C3HeB/FeJ = C3Fe |
| DBA/1J = D1 |
| DBA/2J = D2 |
| NZB/BINJ = NZB |
| NZW/LacJ = NZW |
| RIIIS/J = R3 |
| SJL/J = SJL or J |
| SWR/J = SW |
Table 3.6 F1 and F2 hybrid mice.
| F1 hybrids | F2 hybrids |
|---|---|
|
AdvantagesGenetic and phenotypic uniformityContains a 50 : 50 mix of both parental strainsHybrid vigorAccepts transplants of tissue from
|
