Background: Speed congenics is an important tool for creating congenic mice to investigate gene functions, but current SNP genotyping methods for speed congenics are expensive. These methods usually rely on chip or array technologies, and a different assay must be developed for each backcross strain combination. "Next generation" high throughput DNA sequencing technologies have the potential to decrease cost and increase flexibility and power of speed congenics, but thus far have not been utilized for this purpose.
Results: We took advantage of the power of high throughput sequencing technologies to develop a cost-effective, high-density SNP genotyping assay that can be used across many combinations of backcross strains. The assay surveys 1640 genome-wide SNPs known to be polymorphic across > 100 mouse strains, with an expected average of 549 ± 136 SD diagnostic SNPs between each pair of strains. We demonstrated that the assay has a high density of diagnostic SNPs for backcrossing the BALB/c strain into the C57BL/6J strain (807-819 SNPs), and a sufficient density of diagnostic SNPs for backcrossing the closely related substrains C57BL/6N and C57BL/6J (123-139 SNPs). Furthermore, the assay can easily be modified to include additional diagnostic SNPs for backcrossing other closely related substrains. We also developed a bioinformatic pipeline for SNP genotyping and calculating the percentage of alleles that match the backcross recipient strain for each sample; this information can be used to guide the selection of individuals for the next backcross, and to assess whether individuals have become congenic. We demonstrated the effectiveness of the assay and bioinformatic pipeline with a backcross experiment of BALB/c-IL4/IL13 into C57BL/6J; after six generations of backcrosses, offspring were up to 99.8% congenic.
Conclusions: The SNP genotyping assay and bioinformatic pipeline developed here present a valuable tool for increasing the power and decreasing the cost of many studies that depend on speed congenics. The assay is highly flexible and can be used for combinations of strains that are commonly used for speed congenics. The assay could also be used for other techniques including QTL mapping, standard F2 crosses, ancestry analysis, and forensics.
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http://dx.doi.org/10.1186/s12864-021-07698-9 | DOI Listing |
Zoolog Sci
October 2024
Amphibian Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan,
Biochem Biophys Res Commun
November 2024
Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Nagoya, 464-8601, Japan; Laboratory of Animal Integrative Physiology, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, 464-8601, Japan; Center for One Medicine Innovative Translational Research (COMIT), Nagoya University, Nagoya, 464-8601, Japan. Electronic address:
Seasonal affective disorder (SAD), also known as winter depression, is a subtype of depression typically manifesting in winter. Typical symptoms of SAD, such as an increased need for sleep and carbohydrate cravings associated with increased appetite and weight, are distinct from those of major depression, and the underlying mechanisms of SAD remain unclear. Although laboratory mice are generally considered non-seasonal animals, we observed depression-like behaviors in melatonin-proficient female CBA/N mice maintained under winter-mimicking conditions.
View Article and Find Full Text PDFVascul Pharmacol
June 2024
Neuromuscular Immunopathology Research Laboratory, Division of Neuromuscular Disease, Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA. Electronic address:
Mouse models are invaluable to understanding fundamental mechanisms in vascular biology during development, in health and different disease states. Several constitutive or inducible models that selectively knockout or knock in genes in vascular endothelial cells exist; however, functional and phenotypic differences exist between microvascular and macrovascular endothelial cells in different organs. In order to study microvascular endothelial cell-specific biological processes, we developed a Tamoxifen-inducible von Willebrand Factor (vWF) Cre recombinase mouse in the SJL background.
View Article and Find Full Text PDFTransgenic Res
October 2023
Department of Pathology, FARAH, Faculty of Veterinary Medicine, University of Liege, Liège, Belgium.
Mice are the most widely used mammalian animal model worldwide. Their use presents many advantages, including our ability to manipulate their genome. Unfortunately, transgenic mice often need to be introgressed to transfer the transgene of interest in a specific mouse line.
View Article and Find Full Text PDFGenes Genet Syst
November 2023
Laboratory of Bioresources, National Institute for Basic Biology.
The congenic strain, an inbred strain containing a small genomic region from another strain, is a powerful tool to assess the phenotypic effect of polymorphisms and/or mutations in the substituted genomic region. Recent substantial progress in the genetic studies of complex traits increases the necessity of congenic strains and, therefore, a quick breeding system for congenic strains has become increasingly important in model organisms such as mouse and medaka. Traditionally, more than ten generations are necessary to produce a congenic strain.
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