Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animal Samples
2.2. DNA Extraction
2.3. Sequencing and Quality Control
2.4. SNP Locus Selection
2.5. Primer Design and Sequencing
2.6. Population Genetic Analysis
2.7. Compilation of Principal Component Analyses and Population Structure
3. Results
3.1. Establishment and Optimization of the SNP Detection System
3.2. Genetic Analysis of the Outbred Mongolian Gerbil Populations
3.3. Structure Analysis of the Three Mongolian Gerbil Populations
3.4. Principal Component Analysis in the Three Mongolian Gerbil Populations
3.5. Genetic Analysis of the Outbred Mongolian Gerbil Populations
3.6. Genetic Analysis of the Inbred Mongolian Gerbil Lines
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Mongolian Gerbils | Na | ne | I | Obs Hom | Obs Het | Exp Hom | Exp Het | Ave Het | Percentage of Polymorphic Loci |
---|---|---|---|---|---|---|---|---|---|
CMU | 1.9903 | 1.6953 | 0.5753 | 0.6019 | 0.3981 | 0.6002 | 0.3998 | 0.3934 | 99.03% |
Zhejiang | 2.0000 | 1.6550 | 0.5594 | 0.6229 | 0.3771 | 0.6167 | 0.3833 | 0.3782 | 100% |
Dalian | 1.5146 | 1.3408 | 0.2882 | 0.7770 | 0.2230 | 0.8014 | 0.1986 | 0.1955 | 51.46% |
Number | Genotyping | Zhejiang | Dalian | CMU | p Value |
---|---|---|---|---|---|
MG15 | AA | 0.08 | 0.09 | 0.00 | <0.001 |
AG | 0.35 | 0.47 | 0.00 | ||
GG | 0.57 | 0.44 | 1.00 | ||
MG89 | CC | 0.00 | 0.00 | 0.68 | <0.001 |
CT | 0.05 | 0.00 | 0.32 | ||
TT | 0.95 | 1.00 | 0.00 | ||
MG126 | CC | 0.03 | 1.00 | 0.00 | <0.001 |
CT | 0.09 | 0.00 | 0.00 | ||
TT | 0.89 | 0.00 | 1.00 | ||
MG159 | CC | 0.97 | 0.59 | 0.97 | <0.001 |
TT | 0.03 | 0.41 | 0.03 | ||
MG164 | AA | 0.32 | 0.97 | 0.74 | <0.001 |
AC | 0.35 | 0.03 | 0.26 | ||
CC | 0.32 | 0.00 | 0.00 | ||
MG206 | AA | 0.22 | 0.97 | 0.39 | <0.001 |
AG | 0.62 | 0.03 | 0.42 | ||
GG | 0.16 | 0.00 | 0.19 | ||
MG215 | CC | 0.03 | 0.00 | 0.90 | <0.001 |
CT | 0.54 | 0.00 | 0.10 | ||
TT | 0.43 | 1.00 | 0.00 |
Number | CHROM | POS | Variant_Classification | REF | ALT | Inbred Cerebral Ischemia Line | Inbred Diabetes Line |
---|---|---|---|---|---|---|---|
MG37 | NW_018657859.1 | 1,081,095 | 5′Flank | C | G | G/G | C/C |
MG46 | NW_018657888.1 | 735,326 | Missense_Mutation | A | G | A/A | G/G |
MG47 | NW_018657888.1 | 1,469,235 | Nonstop_Mutation | A | T | T/T | A/A |
MG49 | NW_018657893.1 | 1,416,535 | Missense_Mutation | C | T | C/C | T/T |
MG54 | NW_018657915.1 | 154,939 | Intron | T | C | T/T | C/C |
MG73 | NW_018658000.1 | 110,223 | Missense_Mutation | T | C | T/T | C/C |
MG82 | NW_018658044.1 | 1,083,386 | Missense_Mutation | G | T | T/T | G/G |
MG94 | NW_018658087.1 | 982,880 | Missense_Mutation | T | C | C/C | T/T |
MG107 | NW_018658151.1 | 621,718 | 3′Flank | G | T | T/T | G/G |
MG114 | NW_018658168.1 | 333,441 | 5′Flank | C | T | T/T | C/C |
MG124 | NW_018658203.1 | 697,270 | Missense_Mutation | C | T | T/T | C/C |
MG132 | NW_018658278.1 | 540,596 | Nonsense_Mutation | C | A | A/A | C/C |
MG142 | NW_018658707.1 | 206,847 | Missense_Mutation | C | A | A/A | C/C |
MG190 | NW_018661696.1 | 2303 | Missense_Mutation | A | G | G/G | A/A |
MG219 | NW_018692212.1 | 1211 | 5′Flank | G | A | G/G | A/A |
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Guo, Y.; Cui, Y.; Sun, M.; Zhu, X.; Zhang, Y.; Lu, J.; Li, C.; Lv, J.; Guo, M.; Liu, X.; et al. Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils. Genes 2024, 15, 817. https://doi.org/10.3390/genes15060817
Guo Y, Cui Y, Sun M, Zhu X, Zhang Y, Lu J, Li C, Lv J, Guo M, Liu X, et al. Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils. Genes. 2024; 15(6):817. https://doi.org/10.3390/genes15060817
Chicago/Turabian StyleGuo, Yafang, Yutong Cui, Minghe Sun, Xiao Zhu, Yilang Zhang, Jing Lu, Changlong Li, Jianyi Lv, Meng Guo, Xin Liu, and et al. 2024. "Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils" Genes 15, no. 6: 817. https://doi.org/10.3390/genes15060817
APA StyleGuo, Y., Cui, Y., Sun, M., Zhu, X., Zhang, Y., Lu, J., Li, C., Lv, J., Guo, M., Liu, X., Chen, Z., Du, X., & Huo, X. (2024). Establishment and Application of a Novel Genetic Detection Panel for SNPs in Mongolian Gerbils. Genes, 15(6), 817. https://doi.org/10.3390/genes15060817