Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Animals and Phenotypes
2.3. Genotyping and Genotype Imputation
2.4. Estimation of Genetic Parameters and Genetic Correlation
2.5. Genome-Wide Association Study (GWAS)
2.6. Candidate Gene Search
3. Results
3.1. Genetic Parameters and Genetic Correlations of Reproductive Traits
3.2. Identification of Significant SNPs Associated with Reproductive Traits before Imputation
3.3. Identification of Significant SNPs Associated with Reproductive Traits after Imputation with PHARP
3.4. Identification of Significant SNPs Associated with Reproductive Traits after Imputation with SWIM
3.5. Bioinformatics Annotation Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Traits 1 | N-obs 2 | Mean | S.D. | CV 3 (%) | Min Value | Max Value |
---|---|---|---|---|---|---|
TNB | 10,088 | 9.93 | 2.54 | 25.6 | 3 | 18 |
NBA | 9862 | 9.25 | 2.53 | 27.2 | 3 | 17 |
LBW | 9897 | 12.47 | 3.72 | 29.8 | 2.4 | 30 |
GL | 10,193 | 114.65 | 1.49 | 1.3 | 105 | 127 |
NW | 5857 | 8.75 | 2.46 | 28.1 | 2 | 17 |
Traits 1 | 2 | 3 | 4 | h2 | SE |
---|---|---|---|---|---|
TNB | 0.2687 | 0.5289 | 5.2803 | 0.0442 | 0.0011 |
NBA | 0.2700 | 0.5531 | 5.2856 | 0.0442 | 0.0012 |
LBW | 0.6008 | 1.1104 | 10.9099 | 0.0476 | 0.0025 |
GL | 0.3313 | 0.1765 | 1.6008 | 0.1571 | 0.0009 |
NW | 0.4052 | 0.1744 | 4.9922 | 0.0727 | 0.0021 |
Traits 1 | TNB | NBA | LBW | GL | NW |
---|---|---|---|---|---|
TNB | 0.985 (0.001) | 0.886 (0.003) | −0.235 (0.010) | 0.751 (0.005) | |
NBA | 0.945 (0.001) | −0.188 (0.010) | 0.850 (0.003) | ||
LBW | −0.120 (0.015) | 0.934 (0.002) | |||
GL | −0.176 (0.011) | ||||
NW |
Traits 1 | SNP 2 | Chr 3 | Position | p -Value | Candidate Gene |
---|---|---|---|---|---|
GL | 13:150210534 | 13 | 150210534 | 2.13 × 10−7 | DPPA4 , DPPA2 |
13:156135228 | 13 | 156135228 | 2.24 × 10−7 | ||
13:156180521 | 13 | 156180521 | 6.75 × 10−7 |
Traits 1 | SNP 2 | Chr 3 | Position | p-Value | Candidate Genes |
---|---|---|---|---|---|
TNB | 6:77501624 | 6 | 77501624 | 6.07 × 10−36 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 |
6:77296986 | 6 | 77296986 | 1.36 × 10−27 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
12:10032955 | 12 | 10032955 | 1.16 × 10−12 | KCNJ2 | |
13:51852849 | 13 | 51852849 | 7.91 × 10−7 | MITF | |
6:77325166 | 6 | 77325166 | 1.30 × 10−11 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77330464 | 6 | 77330464 | 1.30 × 10−11 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77458051 | 6 | 77458051 | 1.30 × 10−11 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77462853 | 6 | 77462853 | 1.30 × 10−11 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77480978 | 6 | 77480978 | 1.30 × 10−11 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
9:105582098 | 9 | 105582098 | 2.14 × 10−11 | - | |
6:77352307 | 6 | 77352307 | 8.67 × 10−11 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77354514 | 6 | 77354514 | 8.67 × 10−11 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77364237 | 6 | 77364237 | 8.67 × 10−11 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77473320 | 6 | 77473320 | 8.67 × 10−11 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77335250 | 6 | 77335250 | 4.47 × 10−10 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77342385 | 6 | 77342385 | 9.30 × 10−10 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77500110 | 6 | 77500110 | 9.30 × 10−10 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77506794 | 6 | 77506794 | 9.30 × 10−10 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77551399 | 6 | 77551399 | 9.30 × 10−10 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
6:77401218 | 6 | 77401218 | 9.30 × 10−10 | MRTO4, TAS1R2, PAX7, CAPZB, UBR4 | |
2:41234740 | 2 | 41234740 | 1.89 × 10−8 | LDHA, LDHC, ABCC8 | |
10:67101509 | 10 | 67101509 | 3.72 × 10−8 | PFKP | |
GL | 13:139111128 | 13 | 139111128 | 1.25 × 10−8 | ARGFX |
13:141726529 | 13 | 141726529 | 1.96 × 10−8 | IGSF11 | |
13:141659895 | 13 | 141659895 | 3.47 × 10−8 | IGSF11 |
Traits 1 | SNP 2 | Chr 3 | Position | p-Value | Candidate Gene |
---|---|---|---|---|---|
TNB | 12:56839134 | 12 | 56839134 | 3.94 × 10−20 | MYOCD |
12:56840928 | 12 | 56840928 | 3.09 × 10−19 | MYOCD | |
13:202985373 | 13 | 202985373 | 2..91 × 10−12 | HMGN1 | |
11:43367981 | 11 | 43367981 | 2.78 × 10−10 | DACH1 | |
11:60300851 | 11 | 60300851 | 3.06 × 10−9 | GPC5 | |
10:3913625 | 10 | 3913625 | 3.82 × 10−9 | - | |
1:2245988 | 1 | 2245988 | 1.61 × 10−8 | RPS6KA2 | |
11:60226963 | 11 | 60226963 | 2.43 × 10−8 | - | |
NBA | 8:27377546 | 8 | 27377546 | 3.44 × 10−8 | ARAP2 |
2:151525142 | 2 | 151525142 | 4.56 × 10−8 | RPS14, NDST1, CAMK2A | |
2:151616302 | 2 | 151616302 | 4.56 × 10−8 | CAMK2A, SYNPO, NDST1 | |
LBW | 2:151525142 | 2 | 151525142 | 9.82 × 10−17 | RPS14, NDST1, CAMK2A |
2:151635734 | 2 | 151635734 | 1.01 × 10−14 | RPS14, NDST1, CAMK2A | |
3:14559878 | 3 | 14559878 | 4.05 × 10−10 | AUTS2 | |
3:2296285 | 3 | 2296285 | 3.29 × 10−9 | CARD11 | |
6:30206625 | 6 | 30206625 | 4.60 × 10−9 | IRX6 | |
8:27377546 | 8 | 27377546 | 2.24 × 10−8 | ARAP2 | |
17:13034535 | 17 | 13034535 | 2.64 × 10−8 | PSD3 | |
GL | 10:1796697 | 10 | 1796697 | 1.12 × 10−8 | RGS18 |
10:1805679 | 10 | 1805679 | 1.12 × 10−8 | RGS18 | |
10:1809838 | 10 | 1809838 | 1.12 × 10−8 | RGS18 | |
10:1820524 | 10 | 1820524 | 1.12 × 10−8 | RGS18 | |
10:1838406 | 10 | 1838406 | 1.12 × 10−8 | RGS18 | |
10:1847106 | 10 | 1847106 | 1.12 × 10−8 | RGS18 | |
10:1855846 | 10 | 1855846 | 1.12 × 10−8 | RGS18 | |
10:1784012 | 10 | 1784012 | 1.12 × 10−8 | RGS18 | |
10: 1801316 | 10 | 1801316 | 1.12 × 10−8 | RGS18 | |
10:1816938 | 10 | 1816938 | 1.12 × 10−8 | RGS18 | |
10:1824028 | 10 | 1824028 | 1.12 × 10−8 | RGS18 | |
10:1853098 | 10 | 1853098 | 1.12 × 10−8 | RGS18 | |
10:1898784 | 10 | 1898784 | 1.12 × 10−8 | RGS18 | |
10:1977819 | 10 | 1977819 | 1.12 × 10−8 | RGS18 | |
10:1990160 | 10 | 1990160 | 1.12 × 10−8 | RGS18 | |
10:2000211 | 10 | 2000211 | 1.12 × 10−8 | RGS18 | |
10:1711812 | 10 | 1711812 | 1.68 × 10−8 | RGS18 | |
10:1699892 | 10 | 1699892 | 1.96 × 10−8 | RGS18 | |
10:1516875 | 10 | 1516875 | 2.38 × 10−8 | RGS18 | |
10:1719667 | 10 | 1719667 | 2.63 × 10−8 | RGS18 | |
10:1722698 | 10 | 1722698 | 2.63 × 10−8 | RGS18 | |
10:1549545 | 10 | 1549545 | 3.75 × 10−8 | RGS18 | |
10:1768905 | 10 | 1768905 | 4.79 × 10−8 | RGS18 | |
10:1772064 | 10 | 1772064 | 4.79 × 10−8 | RGS18 |
Traits 1 | Term | Database 2 | ID | Gene Names |
---|---|---|---|---|
TNB | Glycolysis/gluconeogenesis | KEGG PATHWAY | ssc00010 | LDHC|LDHA|PFKP |
TGF-β signaling pathway | KEGG PATHWAY | ssc04350 | SMAD4|NBL1 | |
Oxytocin signaling pathway | KEGG PATHWAY | ssc04921 | KCNJ2|RYR2 | |
uterus development | Gene Ontology | GO:0060065 | SMAD4 | |
oocyte maturation | Gene Ontology | GO:0001556 | RPS6KA2 | |
NBA | Calcium signaling pathway | KEGG PATHWAY | ssc04020 | PDGFRB|ADRA1B|CAMK2A |
GnRH signaling pathway | KEGG PATHWAY | ssc04912 | MMP2|CAMK2A | |
Embryonic organ development | Gene Ontology | GO:0048568 | PDGFRB | |
LBW | MAPK signaling pathway | KEGG PATHWAY | ssc04010 | PDGFRB|GNA12|CSF1R |
PPAR signaling pathway | KEGG PATHWAY | ssc03320 | FABP4|FABP5 | |
Regulation of actin cytoskeleton | KEGG PATHWAY | ssc04810 | PDGFRB|GNA12 | |
In utero embryonic development | Gene Ontology | GO:0001701 | PDGFRB|GNA12 | |
Hormone receptor binding | Gene Ontology | GO:0051427 | FABP4 | |
cell development | Gene Ontology | GO:0048468 | IRX5|IRX6 | |
GL | mTOR signaling pathway | KEGG PATHWAY | ssc04150 | ATP6V1C2|ATP6V1A|GSK3B |
Ovarian steroidogenesis | KEGG PATHWAY | ssc04913 | ADCY5 | |
Prolactin signaling pathway | KEGG PATHWAY | ssc04917 | GSK3B | |
Embryo development | Gene Ontology | GO:0009790 | DLX4|DLX3 | |
Regulation of G protein-coupled receptor signaling pathway | Gene Ontology | GO:0008277 | RGS18 |
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Sun, J.; Xiao, J.; Jiang, Y.; Wang, Y.; Cao, M.; Wei, J.; Yu, T.; Ding, X.; Yang, G. Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs. Genes 2023, 14, 861. https://doi.org/10.3390/genes14040861
Sun J, Xiao J, Jiang Y, Wang Y, Cao M, Wei J, Yu T, Ding X, Yang G. Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs. Genes. 2023; 14(4):861. https://doi.org/10.3390/genes14040861
Chicago/Turabian StyleSun, Jingchun, Jinhong Xiao, Yifan Jiang, Yaxin Wang, Minghao Cao, Jialin Wei, Taiyong Yu, Xiangdong Ding, and Gongshe Yang. 2023. "Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs" Genes 14, no. 4: 861. https://doi.org/10.3390/genes14040861
APA StyleSun, J., Xiao, J., Jiang, Y., Wang, Y., Cao, M., Wei, J., Yu, T., Ding, X., & Yang, G. (2023). Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs. Genes, 14(4), 861. https://doi.org/10.3390/genes14040861