Identification of Nonsynonymous SNPs in Immune-Related Genes Associated with Pneumonia Severity in Pigs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Pig Populations and Measurement of Trait Data
2.2. Targeted Resequencing
2.3. Genotyping
2.4. Data Analysis
3. Results
3.1. Characteristics of Pig Populations and Traits
3.2. Extraction and Narrowing Down of Target Genes and Polymorphisms
3.3. Association between Polymorphisms in Immune-Related Genes and Traits
4. Discussion
5. Conclusions
6. Patents
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Year | Farm | Sex | Sampling Season | Total | |||
---|---|---|---|---|---|---|---|
Summer | Fall | Winter | Spring | ||||
2016 | A | Female | 48 | 27 | 15 | 24 | 114 |
Male | 61 | 30 | 48 | 26 | 165 | ||
Unknown | 0 | 0 | 1 | 0 | 1 | ||
B | Female | 57 | 25 | 25 | 21 | 128 | |
Male | 56 | 30 | 36 | 29 | 151 | ||
Unknown | 0 | 0 | 0 | 0 | 0 | ||
2019 | A | Female | 0 | 0 | 66 | 12 | 78 |
Male | 0 | 0 | 76 | 23 | 99 | ||
Unknown | 0 | 0 | 1 | 0 | 1 | ||
C | Female | 45 | 23 | 0 | 0 | 68 | |
Male | 41 | 16 | 0 | 0 | 57 | ||
Unknown | 0 | 0 | 0 | 0 | 0 |
Gene | Chromosome: Position | dbSNPID | Resistance | Susceptibility | He | Ne | Function | |||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
Allele | Amino Acid | Frequency | Allele | Amino Acid | Frequency | |||||||
CGAS | 1:92483865 | rs329876422 | A | Met | 0.156 | G | Val | 0.844 | 0.263 | 1.357 | PRR for cytosolic DNA | |
FCGR2B | 4:88887587 | rs320243268 | T | His | 0.260 | C | Arg | 0.740 | 0.385 | 1.625 | Receptor for antibody heavy chain | |
4:88892821 | rs331355666 | A | Ser | 0.054 | C | Ala | 0.946 | 0.102 | 1.114 | |||
IFI16 | 4:91393489 | rs80915627 | T | Asp | 0.180 | G | Ala | 0.820 | 0.295 | 1.419 | PRR for cytosolic DNA | |
LRRFIP1 | 15:137424903 | rs319566914 | G | Ala | 0.885 | T | Ser | 0.115 | 0.204 | 1.256 | PRR for cytosolic DNA | |
MX1 | 13:204856712 | rs81214124 | T | Glu | 0.816 | G | Ala | 0.184 | 0.300 | 1.429 | Involvement in antiviral activity | |
13:204856656 | rs55618275 | G | Asp | 0.816 | C | Glu | 0.184 | 0.300 | 1.429 | |||
PRKDC | 4:79757139 | rs80900450 | T | Met | 0.420 | C | Thr | 0.580 | 0.487 | 1.950 | PRR for cytosolic DNA; involvement in V(D)J recombination in T and B cells | |
RIGI | 10:33900015 | rs334436029 | G | Cys | 0.335 | C | Ser | 0.665 | 0.446 | 1.804 | PRR for viral RNA | |
STING1 | 2:141360482 | rs81218215 | A | Asp | 0.170 | T | Val | 0.830 | 0.282 | 1.393 | PRR for cytosolic DNA | |
TRIM40 | 7:22713980 | rs327309867 | G | Ser | 0.548 | A | Leu | 0.452 | 0.495 | 1.982 | Involvement in intracellular protein degradation | |
7:22713916 | rs339299789 | T | Ser | 0.994 | G | Arg | 0.006 | 0.012 | 1.012 |
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Shinkai, H.; Suzuki, K.; Itoh, T.; Yoshioka, G.; Takenouchi, T.; Kitazawa, H.; Uenishi, H. Identification of Nonsynonymous SNPs in Immune-Related Genes Associated with Pneumonia Severity in Pigs. Genes 2024, 15, 1103. https://doi.org/10.3390/genes15081103
Shinkai H, Suzuki K, Itoh T, Yoshioka G, Takenouchi T, Kitazawa H, Uenishi H. Identification of Nonsynonymous SNPs in Immune-Related Genes Associated with Pneumonia Severity in Pigs. Genes. 2024; 15(8):1103. https://doi.org/10.3390/genes15081103
Chicago/Turabian StyleShinkai, Hiroki, Kasumi Suzuki, Tomohito Itoh, Gou Yoshioka, Takato Takenouchi, Haruki Kitazawa, and Hirohide Uenishi. 2024. "Identification of Nonsynonymous SNPs in Immune-Related Genes Associated with Pneumonia Severity in Pigs" Genes 15, no. 8: 1103. https://doi.org/10.3390/genes15081103