Identification of Candidate Genes for Min Pig Villi Hair Traits by Genome-Wide Association of Copy Number Variation
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Animals and Phenotype Recording
2.3. Genotyping and Quality Control
2.4. Genome-Wide Association Study
2.5. Gene Enrichment Analysis and QTL Co-Location
2.6. Validation of CNVs by Real-Time Quantitative PCR (qRT-PCR)
3. Results
3.1. Phenotype Description
3.2. Copy Number Variation Genotyping
3.3. GWAS of Pig Villi Hair
3.4. Identification and Validation of the Selected CNVRs
3.5. Functional Enrichment and Annotation 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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Gene | Forward Primer | Reverse Primer |
---|---|---|
CNV13 | CCTGGCTTCCCTTCTCTCTT | GGAAGAATCGGGTGGGTATT |
CNV667 | AGCTTCCTGCTGGACACAGT | GCTGCTTTGGGCTTATTCTG |
CNV540 | CTTCAAAGCCAGCAATGTGA | GGATTATCCGAGTTGGCTCA |
CNV64 | TCTGAAAGGGATGGATCTGG | GAACCTTTGCTGCCTGTCTC |
GCG | GCAATATGGCTTTAGAATACACCTCTTA | GTCACTAATCAAGATCGTGTTCACAAC |
CNVR ID | Location | Nearest Genes | CHISQ | Type | p-Value |
---|---|---|---|---|---|
CNV13 | 1:67141601-67155200 | ASCC3/MCHR2/SIM1 | 18.9 | Del | 1.38 × 10−5 |
CNV667 | 7:97857601-97860000 | VSX2/ABCD4/VRTN/SYNDIG1L/ISCA2/LTBP2/NPC2/AREL1/FCF1/YLPM1/PROX2 | 17.97 | Dup | 2.24 × 10−5 |
CNV540 | 5:16751601-16754400 | DIP2B/ATF1/TMPRSS12/SLC4A8/SCN8A | 17.66 | Dup | 2.64 × 10−5 |
CNV64 | 7:75399601-75402400 | REC8/IRF9/FITM1/PSME1/RNF31/PSME2/EMC9/DCAF11/CARMIL3/CPNE6/PCK2/NRL/DHRS4/ZFHX2/JPH4/AP1G2/THTPA/MYH7/ENSSSCG00000002020 | 17.6 | Del | 2.73 × 10−5 |
CNV734 | 9:51430801-51434000 | OR8D1/OR8D2/ENSSSCG00000015179/ENSSSCG00000061653/ENSSSCG00000053222/ENSSSCG00000015193/ENSSSCG00000053475/OR8B8/ENSSSCG00000056190/ENSSSCG00000055348/ENSSSCG00000061394/ENSSSCG00000015154/ENSSSCG00000052681 | 15.12 | Del | 0.000101 |
CNV267 | 15:1259201-1261200 | ENSSSCG00000060497/NMI/TNFAIP6 | 14.56 | Del | 0.000135 |
CNV234 | 14:6050401-6053200 | ENSSSCG00000055110/GFRA2/XPO7/DOK2/DMTN/FGF17 | 14.26 | Dup | 0.000159 |
CNV321 | 16:61828001-61833200 | GABRG2/GABRA1/GABRA6/GABRB2 | 12.49 | Dup | 0.00041 |
CNV330 | 6:135400401-135405200 | FUBP1/DNAJB4/NEXN/MIGA1/USP33/GIPC2/ENSSSCG00000035986/ENSSSCG00000050806 | 11.61 | Del | 0.000657 |
CNV720 | 9:4729201-4731600 | ENSSSCG00000060217/ENSSSCG00000062640/ENSSSCG00000050624/ssc-mir-10390 | 11.13 | Dup | 0.000849 |
CNV510 | 4:47520801-47538800 | ENSSSCG00000042115 | 10.35 | Dup | 0.001295 |
CNV107 | 11:19803201-19810400 | ENSSSCG00000042466/SUCLA2/NUDT15/MED4/ENSSSCG00000053915 | 9.936 | Dup | 0.001621 |
CNV552 | 5:45503601-45508000 | CCDC91/ENSSSCG00000045661/PTHLH | 9.868 | Dup | 0.001682 |
CNV390 | 2:47668801-47674000 | NSSSCG00000031143/USP47/DKK3/U6/GALNT18 | 9.819 | Dup | 0.001727 |
CNV22 | 1:93250401-93252800 | ENSSSCG00000005790/ENSSSCG00000053538 | 9.671 | Dup | 0.001872 |
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He, X.; Tian, M.; Wang, W.; Feng, Y.; Li, Z.; Wang, J.; Song, Y.; Zhang, J.; Liu, D. Identification of Candidate Genes for Min Pig Villi Hair Traits by Genome-Wide Association of Copy Number Variation. Vet. Sci. 2023, 10, 307. https://doi.org/10.3390/vetsci10050307
He X, Tian M, Wang W, Feng Y, Li Z, Wang J, Song Y, Zhang J, Liu D. Identification of Candidate Genes for Min Pig Villi Hair Traits by Genome-Wide Association of Copy Number Variation. Veterinary Sciences. 2023; 10(5):307. https://doi.org/10.3390/vetsci10050307
Chicago/Turabian StyleHe, Xinmiao, Ming Tian, Wentao Wang, Yanzhong Feng, Zhongqiu Li, Jiahui Wang, Yan Song, Jinfeng Zhang, and Di Liu. 2023. "Identification of Candidate Genes for Min Pig Villi Hair Traits by Genome-Wide Association of Copy Number Variation" Veterinary Sciences 10, no. 5: 307. https://doi.org/10.3390/vetsci10050307