Effect of Genetic Diversity in Swine Leukocyte Antigen-DRA Gene on Piglet Diarrhea
Abstract
:1. Introduction
2. Materials and Methods
2.1. Samples Collection and DNA Extraction
2.2. PCR Amplification and Single-Stranded Conformational Polymorphism (SSCP) Analysis
2.3. Cloning and Sequencing
2.4. Sequence and Statistical Analysis
3. Results
3.1. SSCP Analysis of SLA-DRA Gene Exons
3.2. Gene Variations and Population Genetic Parameters of SLA-DRA Gene
3.3. Amino Acid Alignments of the DRA Gene
3.4. Effects of SLA-DRA Gene Genotypes on Piglet Diarrhea
4. Discussion
5. Conclusions
Supplementary Materials
Acknowledgments
Author Contributions
Conflicts of Interest
References
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Region | Location a | Primer F/R(5′→3′) | Amplification Fragment | Annealing Temperature (°C) | SSCP Condition |
---|---|---|---|---|---|
Exon 1 | 151–226 | F: CTTTGCTTGTATTGC R: ACCTAACTACCCCTC | 186 bp | 56.8 | 4 °C, 12%, 39:1, 190 V 20 h |
Exon 3 | 4595–4876 | F: TGCTAAACAGGGAAGGCT R: ACAAAGGAGACTGAGGGATG | 352 bp | 56.8 | 4 °C, 10%, 39:1, 200 V 20 h |
Exon 4 | 4155–4309 | F: TCCCGTAATACATCGTTC R: TTCCTTTCCTTGGCTCAT | 357 bp | 55.6 | 18 °C, 10%, 29:1, 200 V 18 h |
Locus | Allele | F (%) A | GenBank Accession Number | AE B | oHet/eHet C | PIC D | χ2 E | GenBank Ident 100% |
---|---|---|---|---|---|---|---|---|
Accession Number/Breed | ||||||||
Exon 1 | A1 | 0.55 | KR023998 | 1.979 | 0.260/0.495 | 0.372 | 65.77 * | JX135565/Landrace |
B1 | 0.45 | KR023999 | LC002669/Hebao pig FJ905824/Gansu white pig | |||||
Exon 4 | A4 | 0.41 | KM485553 | 3.087 | 0.439/0.677 | 0.612 | 511.97 * | KP324812/Juema pig FJ905836/Hezuo pig |
B4 | 0.34 | KM485554 | Not found | |||||
C4 | 0.20 | KM487705 | KP324810/Juema pig AY247781/Hebao pig | |||||
D4 | 0.01 | KM487706 | KP324814/Juema pig AY191779/Banna minipig | |||||
E4 | 0.04 | KM487707 | EU432071/Meishan pig EU722916/CMS minipig DQ883222/Korean native pig |
Exon 1 | Exon 4 | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Genotype | SN A | Case | Control | OR B | LSM ± SE C | p | Genotype | SN | Case | Control | OR | LSM ± SE | p |
A1A1 | 123 | 60 | 63 | 1.140 | 1.00 ± 0.11 | 0.679 | A4A4 | 66 | 26 | 40 | 0.674 | 0.81 ± 0.14 | 0.302 |
B1B1 | 92 | 44 | 48 | 0.957 | 1.08 ± 0.12 | 0.424 | B4B4 | 80 | 40 | 40 | 0.623 | 0.98 ± 0.13 | 0.462 |
A1B1 | 75 | 32 | 43 | 0.794 | 0.89 ± 0.14 | 0.348 | A4B4 | 12 | 4 | 8 | 0.553 | 0.80 ± 0.33 | 0.114 |
C4C4 | 12 | 8 | 4 | 2.344 | 1.80 ± 0.33 | 0.001 | |||||||
A4C4 | 72 | 32 | 40 | 0.877 | 0.85 ± 0.14 | 0.933 | |||||||
B4C4 | 22 | 8 | 14 | 0.625 | 0.77 ± 0.25 | 0.715 | |||||||
A4E4 | 22 | 14 | 8 | 2.094 | 1.66 ± 0.25 | 0.002 |
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Huang, X.; Yang, Q.; Yuan, J.; Liu, L.; Sun, W.; Jiang, Y.; Zhao, S.; Zhang, S.; Huang, W.; Gun, S. Effect of Genetic Diversity in Swine Leukocyte Antigen-DRA Gene on Piglet Diarrhea. Genes 2016, 7, 36. https://doi.org/10.3390/genes7070036
Huang X, Yang Q, Yuan J, Liu L, Sun W, Jiang Y, Zhao S, Zhang S, Huang W, Gun S. Effect of Genetic Diversity in Swine Leukocyte Antigen-DRA Gene on Piglet Diarrhea. Genes. 2016; 7(7):36. https://doi.org/10.3390/genes7070036
Chicago/Turabian StyleHuang, Xiaoyu, Qiaoli Yang, Junhu Yuan, Lixia Liu, Wenyang Sun, Yingdi Jiang, Shengguo Zhao, Shengwei Zhang, Wangzhou Huang, and Shuangbao Gun. 2016. "Effect of Genetic Diversity in Swine Leukocyte Antigen-DRA Gene on Piglet Diarrhea" Genes 7, no. 7: 36. https://doi.org/10.3390/genes7070036