The PCR-LDR Genotyping System For The Population Construction Of Chromosome 1 Substitution Strains From Wild Mice

The population of chromosome 1 substitution strains (PCSSs) derived from wild mice, show great potential in genetic dissection of complex traits. The PCSS as a brand-new strategy, can be used for fine mapping quantitative trait locus(QTL) and fast identification of genes.More than 400 QTLs have been mapped in mice on chromosome one. These QTLs regulate many kinds of complex diseases, such as hypertension, diabetes, cancer, etc. But so far, only small fraction of these genes have been identified. The linkage disequilibrium(LD) attenuation is slow and the haplotype block is large in the population of inbred strains. The lack of genetic diversity brings a hard inconvenience in fine mapping with inbred strains.In the PCSSs constructing process, each individual of every generation need to be genotyped and the individuals without recombination on Chromosome 1 should be selected out, which provide the Chromosome 1 from the wild mice completely inducing into the new generation. In general, short tandem repeat markers (STRs) were used to detect the recombination events. Because the wild mouse population harbors varied STR alleles, it is more difficult to genotype the STR in it. Hence, single nuclear polymorphisms (SNPs) with two alleles could provide reliable information are rather choice than STR.In the present study, a total of 29 SNPs with the average density of 6.25 centimorgan (cM) were genotyped based on Polymerase chain reaction and ligase detection reaction (PCR-LDR). All SNPs were genotyped in three panels, and each panel contains at least 9 SNPs.In conclusion, the genotyping results of the sample of F1 crossed between wild mouse and inbred C57BL/6J, indicate that PCR-LDR could be used to detect the recombination events, with convenience and high throughout.