Deletion detection and functional annotation of chromosome 1 substitution strains from Chinese wild mice / 中国实验动物学报

Objective Deletion detection and annotation of 18 lines from the population of specific chromosome 1 substitution strains ( PCSSs) derived from Chinese wild mice based on whole genome re-sequencing data. Methods Whole genome re?sequencing of the 18 lines were performed on the Illumina Hiseq platform. SpeedSeq software was used to detect the deletion after read alignment. Further annotation was obtained using SnpEff software. Results 13803 dele?tions were identified among the 18 lines, the length of deletion was ranged from 51bp to 70 kb, among them nearly 50%were less than 500 bp. Through functional annotation,we found most of the variants were located in intronic (50. 361%) and intergenic (28. 745%) regions. However, we also identified 31 protein coding genes harboring loss?of?function dele?tions. Among them, 3 genes were associated with human diseases, 7 genes were participated in 11 KEGG pathways. Conclusion The chromosome 1 of PCSSs harbors abundant deletion mutations which can be used as genetic markers in genetic studies.

Establishment of a SNP genetic identification method for frozen embryos and sperm of inbred mice / 中国实验动物学报

Objective To establish a rapid SNP( single-nucleotide polymorphism) genetic identification method for the frozen samples, such as frozen embryos and sperm of inbred mice.Methods In this study, the frozen embryos and sperm of inbred mice were provided by Shanghai Lab.Animal Research Center.Whole genome amplification and PCR-LDR genotyping system were used to get the rich DNA sample.Forty-five SNP were genotyped by multiple polymerase chain re-action and ligase detection reaction( PCR-LDR) .Results The electrophoresis results showed that the whole genome am-plification technique could highly increase the total DNA of frozen embryos.PCR-LDR typing method was suitable for the mouse genome typing of 45 SNPs.Ten strains of inbred frozen embryos and sperms of C57BL/6, BALB/c, FVB/NJ mice were genotyping identified, and their SNP loci data obtained by PCR-LDR were as the same as those of database.The num-ber of frozen mouse embryos was proportional to the number of SNPs detected, and when the embryo number reached more than 12, the detection rate of SNP was 100%.Conclusions This method can be used to the genetic quality identification, and rapidly identify the inbreed frozen mouse embryos and sperms.

Establishment of a universal fluorescent multiplex cPCR method for detection of copy number variations in mice / 中国实验动物学报

Objective To establish a high throughput general multiple competitive polymerase chain reaction ( cPCR) detecting method of copy number variations ( CNVs) for the population of chromosome 1 substitution strains from wild mice.Method The selected 14 loci, including 11 CNVs on chromosome 1 and internal control loci on other three chromosmes (Chr 7, Chr 19 and Chr X), were detected based on the universal fluorescent primer multiple competitive pol-ymerase chain reaction.All specific cloned plasmids were constructed as competitors.Results Altogether 11 CNVs were designed in one panel, and the copy of Chr X accurately reflects the gender.Conclusions A rapid and high-throughput fluorescent multiplex cPCR assay is established which can be used for detection of copy number variations on chromosome 1 in mice.