Utilization of a whole genome SNP panel for efficient genetic mapping in the mouse

Abstract

Phenotype-driven genetics can be used to create mouse models of human disease and birth defects. However, the utility of these mutant models is limited without identification of the causal gene. To facilitate genetic mapping, we developed a fixed single nucleotide polymorphism (SNP) panel of 394 SNPs as an alternative to analyses using simple sequence length polymorphism (SSLP) marker mapping. With the SNP panel, chromosomal locations for 22 monogenic mutants were identified. The average number of affected progeny genotyped for mapped monogenic mutations is nine. Map locations for several mutants have been obtained with as few as four affected progeny. The average size of genetic intervals obtained for these mutants is 43 Mb, with a range of 17-83 Mb. Thus, our SNP panel allows for identification of moderate resolution map position with small numbers of mice in a high-throughput manner. Importantly, the panel is suitable for mapping crosses from many inbred and wild-derived inbred strain combinations. The chromosomal localizations obtained with the SNP panel allow one to quickly distinguish between potentially novel loci or remutations in known genes, and facilitates fine mapping and positional cloning. By using this approach, we identified DNA sequence changes in two ethylnitrosourea-induced mutants.

Figure 1.

Genetic mapping of two recessive mutations with the SNP panel. Only data from informative SNPs for each mapping cross are shown. SNP names are displayed on the right. The mutated strain (M) for each mutant is red; background strain (B), blue; heterozygotes, yellow; and No Calls, white. A plot of LOD scores is shown. The vertical line indicates a LOD score of zero, with the boundaries, –52 (left) and 7.2 (right). (A) Retention of mutated alleles (C57BL/6J; LOD 5.38) in baldy affecteds (denoted as A) on distal Chr. 14 demonstrates linkage of SNP C14.065.150 (62.3 Mb) to the baldy locus. (B) Retention of mutated alleles (A/J) demonstrates linkage of hydrops fetalis to Chr. 7. Because of limited informativeness on Chr. 7 between A/J and FVB/NJ, the strain contribution of A/J or FVB/NJ is potentially ambiguous. However, allele origin can be inferred across haplotypes by the retention of A/J alleles for two A/J and FVB/NJ polymorphic SNPs (07.023.307 and 07.039.006).

Figure 2.

Genetic interval size is inversely correlated with the number of affecteds analyzed.

Figure 3.

hr is mutated in the ENU-induced mutant baldy. (A) An 18-d-old baldy affected displaying patchy alopecia and wrinkled skin. (B) Chromatograms of wild-type C57BL/6J (top) and baldy affected (bottom) sequence showinga C to T mutation in baldy affecteds at nucleotide 385 of 5′ noncoding exon 2.

Figure 4.

Igf1r is mutated in the ENU-induced mutant hydrops fetalis (hyft). (A) Normal littermate (left) and hyft mutant (right) at E16.5, showing reduced fetal crown-to-rump length. Arrow points to subcutaneous edema present in the affected. (B) Western blot analysis of Igf1r on protein extracts of hyft mutants and normal littermates shows an absence of Igf1r protein in affected mice. (C) Chromatograms of Igf1r sequence in wild-type FVB (top) and hyft affected (bottom) mice showing a T to A mutation, which encodes a premature stop codon in hyft mutants.