Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds
Abstract
1. Introduction
2. Materials and Methods
2.1. Sample Collection and Quality Control
2.2. Population Structure
2.3. Whole-Genome Analysis of Genomic Introgression
2.4. Selection Scan
3. Results
3.1. Inference of Population Structure and Degree of Breed Admixture
3.2. Introgression from European Pigs to Chinese Indigenous Breeds
3.3. Investigation of Introgressed Regions Affected by Artificial Selection
4. Discussion
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Breed | Code | Origin | Number * |
---|---|---|---|
Dongbei boar | DBW | Northeast China | 3 |
Zhejiang boar | ZJW | Zhejiang province, China | 15 |
South China boar | HNW | South of China | 15 |
Jiangxi boar | JXW | Jiangxi province, China | 5 |
Tibetan pig | TIB | Tibet A.R., China | 35 |
Erhualian pig | EHL | Jiangsu province, China | 36 |
Jinhua pig | JH | Zhejiang province, China | 44 |
Min pig | MIN | Northeast China | 22 |
Rongchang pig | RC | Sichuan province, China | 32 |
Wuzhishan pig | WZS | Hainan province, China | 27 |
Polish boar | PLW | Poland | 6 |
Swedish boar | SWE | Sweden | 6 |
British Saddleback # | BRS | United Kingdom | 20 |
Tamworth # | TAM | United Kingdom | 20 |
Landrace # | LAD | Europe | 20 |
Large White # | LW | United Kingdom | 20 |
Pietrain # | PIT | Belgium | 20 |
Other European boar # | EUW | Europe | 88 |
Duroc # | DUR | United States | 52 |
Warthogs + | OUT | Africa | 39 |
Total | 525 |
COM | p-Value | ED | p-Value | DUR | p-Value | EW | p-Value | |
---|---|---|---|---|---|---|---|---|
EHL | 0.03 | 2.2 × 10−03 | 0.03 | 1.1 × 10−03 | 0.03 | 9.0 × 10−04 | 0.03 | 0.02 |
TIB | 0.12 | 2.2 × 10−16 | 0.13 | 6.1 × 10−15 | 0.11 | 2.2 × 10−16 | 0.61 | 1.0 × 10−26 |
WZS | 0.03 | 4.9 × 10−04 | 0.02 | 0.01 | 0.03 | 5.9 × 10−04 | 0.04 | 5.4 × 10−04 |
RC | 1.9 × 10−03 | 0.43 | 5.3 × 10−03 | 0.30 | 1.4 × 10−05 | 0.49 | 3.8 × 10−03 | 0.07 |
JH | 0.24 | 1.0 × 10−26 | 0.26 | 1.0 × 10−26 | 0.29 | 1.0 × 10−26 | 0.40 | 1.0 × 10−26 |
MIN | 0.45 | 1.0 × 10−26 | 0.43 | 1.0 × 10−26 | 0.42 | 1.0 × 10−26 | 0.61 | 1.0 × 10−26 |
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Wang, J.; Liu, C.; Chen, J.; Bai, Y.; Wang, K.; Wang, Y.; Fang, M. Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds. Genes 2020, 11, 275. https://doi.org/10.3390/genes11030275
Wang J, Liu C, Chen J, Bai Y, Wang K, Wang Y, Fang M. Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds. Genes. 2020; 11(3):275. https://doi.org/10.3390/genes11030275
Chicago/Turabian StyleWang, Jue, Chengkun Liu, Jie Chen, Ying Bai, Kejun Wang, Yubei Wang, and Meiying Fang. 2020. "Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds" Genes 11, no. 3: 275. https://doi.org/10.3390/genes11030275
APA StyleWang, J., Liu, C., Chen, J., Bai, Y., Wang, K., Wang, Y., & Fang, M. (2020). Genome-Wide Analysis Reveals Human-Mediated Introgression from Western Pigs to Indigenous Chinese Breeds. Genes, 11(3), 275. https://doi.org/10.3390/genes11030275