Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals and Phenotype Data
2.2. Genotype Data and Quality Control
2.3. Statistical Analyses
2.4. SNP–SNP Network and Linkage Disequilibrium (LD) Analysis
2.5. Identification of Candidate Genes
3. Results
3.1. Additive Effects
3.2. Dominance Effects
3.3. Epistatic Analysis
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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Trait | Mean ± SD | Max. | Min. | C.V. (%) | Number of Records |
---|---|---|---|---|---|
ADG (g/day) | 661.66 ± 57.52 | 824.94 | 512.03 | 9.10 | 1854 |
AGE (day) | 152.33 ± 13.86 | 195.30 | 121.22 | 17.67 | 1854 |
BF (mm) | 9.58 ± 1.69 | 15.54 | 5.70 | 8.69 | 1847 |
LMD (mm) | 54.87 ± 6.52 | 74.01 | 27.35 | 11.89 | 1651 |
Trait | SNP | Chr | Location (bp) | Allele | MAF | p-Value | % DEBV | Nearest Gene | Distance (bp) |
---|---|---|---|---|---|---|---|---|---|
ADG | CNCB10006667 | 9 | 41,538,619 | C/T | 0.086 | 8.95 × 10−6 | 0.83 | HTR3B | Within |
CNCB10006791 | 9 | 67,900,715 | C/T | 0.086 | 9.09 × 10−6 | 0.83 | CD55 | +32,354 | |
CNCB10006792 | 9 | 67,967,237 | A/G | 0.086 | 9.09 × 10−6 | 0.83 | CD55 | −6855 | |
AGE | CNCB10001620 | 2 | 20,310,474 | A/G | 0.216 | 1.59 × 10−5 | 0.78 | / | / |
CNCB10006667 | 9 | 41,538,619 | C/T | 0.086 | 2.07 × 10−5 | 0.76 | HTR3B | Within | |
CNCB10006791 | 9 | 67,900,715 | C/T | 0.086 | 2.68 × 10−5 | 0.74 | CD55 | +32,354 | |
CNCB10006792 | 9 | 67,967,237 | A/G | 0.086 | 2.68 × 10−5 | 0.74 | CD55 | −6855 | |
BF | CNCB10010792 | 15 | 89,052,971 | G/A | 0.051 | 7.89 × 10−6 | 0.84 | / | / |
CNCB10005591 | 7 | 113,533,476 | T/G | 0.074 | 9.44 × 10−6 | 0.82 | TRIP11 | Within | |
rs81433919 | 12 | 33,673,968 | G/A | 0.116 | 1.74 × 10−5 | 0.77 | MSI2 | Within | |
CNCB10008592 | 13 | 45,621,675 | G/A | 0.072 | 2.45 × 10−5 | 0.75 | PRICKLE2 | Within | |
LMD | rs709317845 | 7 | 97,614,602 | T/G | 0.469 | 1.33 × 10−6 | 0.98 | VRTN | +105 |
CNC11071978 | 7 | 97,615,897 | A/G | 0.469 | 1.33 × 10−6 | 0.98 | VRTN | Within |
Trait | SNP | Chr | Location (bp) | Allele | MAF | p-Value | % DEBV | Nearest Gene | Distance (bp) |
---|---|---|---|---|---|---|---|---|---|
AGE | CNC10133718 | 13 | 179,900,741 | C/T | 0.285 | 1.60 × 10−5 | 0.78 | NRIP1 | Within |
rs81441574 | 13 | 180,051,342 | T/C | 0.364 | 2.90 × 10−5 | 0.73 | NRIP1 | −135,116 | |
rs80867343 | 13 | 180,004,272 | G/A | 0.362 | 2.98 × 10−5 | 0.73 | NRIP1 | −88,046 | |
BF | rs81373550 | 3 | 93,497,234 | A/G | 0.061 | 1.85 × 10−6 | 0.95 | TTC7A | Within |
CNCB10002800 | 3 | 97,223,093 | T/C | 0.149 | 2.03 × 10−6 | 0.95 | ZFP36L2 | +19,999 | |
rs81373610 | 3 | 93,655,118 | A/C | 0.060 | 2.80 × 10−6 | 0.92 | MCFD2 | +22,100 | |
rs80966590 | 3 | 93,722,940 | C/T | 0.060 | 2.80 × 10−6 | 0.92 | SOCS5 | −54,462 | |
rs81475091 | 3 | 93,732,314 | G/A | 0.060 | 2.80 × 10−6 | 0.92 | SOCS5 | −45,088 | |
rs81299554 | 3 | 93,771,724 | A/G | 0.060 | 2.80 × 10−6 | 0.92 | SOCS5 | −5678 | |
rs81373642 | 3 | 93,828,846 | C/T | 0.060 | 2.80 × 10−6 | 0.92 | SOCS5 | Within | |
rs81373648 | 3 | 93,902,023 | G/T | 0.060 | 2.80 × 10−6 | 0.92 | SOCS5 | Within | |
rs81373727 | 3 | 94,084,767 | A/G | 0.060 | 3.36 × 10−6 | 0.91 | TMEM247 | +17,743 | |
rs81373716 | 3 | 94,110,331 | G/A | 0.060 | 3.36 × 10−6 | 0.91 | TMEM247 | +43,307 | |
rs81373744 | 3 | 94,163,788 | G/A | 0.060 | 3.36 × 10−6 | 0.91 | EPAS1 | −3971 | |
rs81213041 | 3 | 93,394,317 | G/A | 0.059 | 4.80 × 10−6 | 0.88 | STPG4 | Within | |
rs81373880 | 3 | 94,599,697 | C/T | 0.075 | 2.09 × 10−5 | 0.76 | PRKCE | Within | |
CNC10070016 | 7 | 834,427 | A/C | 0.430 | 2.57 × 10−5 | 0.74 | GMDS | Within | |
CNC10120338 | 12 | 16,082,351 | T/C | 0.488 | 3.13 × 10−5 | 0.73 | MRC2 | Within | |
LMD | rs80785395 | 14 | 133,966,414 | A/G | 0.087 | 6.14 × 10−7 | 1.04 | LHPP | Within |
CNCB10007305 | 10 | 4,667,593 | A/G | 0.094 | 1.19 × 10−5 | 0.80 | / | / | |
rs81304718 | 15 | 7,424,079 | C/T | 0.091 | 2.21 × 10−5 | 0.76 | ZEB2 | −74,800 | |
CNCB10010367 | 15 | 8,203,810 | A/G | 0.060 | 2.34 × 10−5 | 0.75 | ARHGAP15 | Within |
Traits | N | A × A | A × D | D × D |
---|---|---|---|---|
ADG | 287 | 124 | 97 | 66 |
AGE | 355 | 159 | 135 | 61 |
LMD | 163 | 80 | 53 | 30 |
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Xue, Y.; Liu, S.; Li, W.; Mao, R.; Zhuo, Y.; Xing, W.; Liu, J.; Wang, C.; Zhou, L.; Lei, M.; et al. Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs. Genes 2022, 13, 1454. https://doi.org/10.3390/genes13081454
Xue Y, Liu S, Li W, Mao R, Zhuo Y, Xing W, Liu J, Wang C, Zhou L, Lei M, et al. Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs. Genes. 2022; 13(8):1454. https://doi.org/10.3390/genes13081454
Chicago/Turabian StyleXue, Yahui, Shen Liu, Weining Li, Ruihan Mao, Yue Zhuo, Wenkai Xing, Jian Liu, Chuang Wang, Lei Zhou, Minggang Lei, and et al. 2022. "Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs" Genes 13, no. 8: 1454. https://doi.org/10.3390/genes13081454
APA StyleXue, Y., Liu, S., Li, W., Mao, R., Zhuo, Y., Xing, W., Liu, J., Wang, C., Zhou, L., Lei, M., & Liu, J. (2022). Genome-Wide Association Study Reveals Additive and Non-Additive Effects on Growth Traits in Duroc Pigs. Genes, 13(8), 1454. https://doi.org/10.3390/genes13081454