ABSTRACT
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.
ABSTRACT
Objective To analyze the growth phenotype and blood biochemical parameters of chromosome 1 substi-tution mouse strain(CSS1), and investigate their potential of QTL mapping .Methods Body weight, body length, tail length, organ weight of the CCS1 mice were measured at different days to create a growth curve while blood biochemical in -dexes were measured at about the 80th day.Results The CCS1 mice were different from C57BL/6 mice in several inde-xes.Compared with the C57BL/6 mice during different developmental stages , six strains including B6-Chr1KM mice were significantly different in body weight .There were five strains including B6-Chr1CM mice significantly different with C57BL/6 mice in body length, and all of the CSS1 mice were significantly different from C57BL/6 mice in tail length.Part of CCS1 mice were significantly different from C57BL/6 mice in the weight of liver, spleen, kidney and brain.The ALT of female B6-Chr1CM mice was significantly higher than that in the C 57BL/6 mice.The ALP of female B6-Chr1HZ mice was signifi-cantly higher than that in the male C57BL/6 and B6-Chr1KM mice, and was significantly lower than that in the C57BL/6 mice.The TB of male B6-Chr1CM, B6-Chr1SMX and B6-Chr1HZ mice was significantly higher than that of the C 57BL/6 mice.The TG of male B6-Chr1SMX mice and male B6-Chr1TW mice was significantly higher than that in the C 57BL/6 mice. Conclusions The phenotype of Chr1 CSS mice is quite different from commonly used inbred strain C 57BL/6 mice.CCS1 mice show great potential in QTL mapping for their characteristic growth phenotype and blood biochemical indexes .
ABSTRACT
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.