Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals and Phenotypes
2.2. Genotyping
2.3. Quality Control (QC) and Imputation
2.4. GWAS
2.4.1. Single Marker Regression (SMR)
2.4.2. Bayesian C (BayesC) Approach
2.5. Functional Annotations
3. Results
3.1. General Statistics
3.2. GWAS Based on the SMR
3.3. GWAS Based on the BayesC
3.4. Fine Mapping and Candidate Genes
3.5. PPI and KEGG Pathway Analysis
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Conflicts of Interest
References
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PHENOTYPE (DEBV) a | BTA (Mb) b | GV (%) c | Informative SNP | Rs Number | Position d | SNP Effect | Model Frequency | Region Annotation | Gene Annotation |
---|---|---|---|---|---|---|---|---|---|
MY | 14 (1) | 2.60 | AX-371638654 | rs211016627 | 1,807,655 | 23.9100 | 0.1845 | Intron | HSF1 |
AX-311625833 | rs384957047 | 1,793,616 | −22.1900 | 0.1717 | Upstream gene | DGAT1 (dist = 1735) | |||
AX-311625843 | rs211223469 | 1,799,476 | −20.4900 | 0.1617 | Intron | DGAT1 | |||
AX-419656711 | rs211282745 | 1,805,963 | −17.5500 | 0.1415 | Downstream gene | HSF1 (dist = 118) | |||
AX-311625845 | rs209876151 | 1,800,439 | −15.9000 | 0.1300 | Intron | DGAT1 | |||
AX-371657011 | rs208640292 | 1,806,875 | 12.8000 | 0.1095 | Synonymous | HSF1 | |||
AX-419792758 | rs207655744 | 1,806,340 | 12.3300 | 0.1057 | 3 prime UTR | HSF1 | |||
6 (88) | 1.03 | AX-185121607 | rs110775601 | 88,952,089 | 78.4400 | 0.6617 | Intergenic | NPFFR2 (dist = 100,121) | |
AX-106735408 | rs110527224 | 88,592,295 | 17.9900 | 0.1741 | Intergenic | SLC4A4 (dist = 54,249) | |||
8 (0) | 0.78 | AX-419764649 | rs721532493 | 887,406 | −1.0640 | 0.0183 | Intron | PALLD | |
23 (24) | 0.77 | AX-419655926 | rs380223715 | 24,021,950 | −1.3030 | 0.0180 | Intron | PKHD1 | |
23 (23) | 0.63 | AX-419634159 | rs517703887 | 23,999,941 | −1.0560 | 0.0169 | Intron | PKHD1 | |
7 (73) | 0.51 | AX-169404932 | rs135477609 | 73,561,312 | 4.0460 | 0.0477 | Intergenic | ADRA1B (dist = 49,805) | |
8 (69) | 0.50 | AX-419751453 | rs524049037 | 69,514,127 | −1.7210 | 0.0251 | Intron | GFRA2 | |
FY | 14 (1) | 5.92 | AX-429953677 | rs110812136 | 1,991,225 | 1.9290 | 0.3670 | Intron | SPATC1 |
AX-115099034 | rs109421300 | 1,801,116 | 1.5190 | 0.2793 | Intron | DGAT1 | |||
AX-371657011 | rs208640292 | 1,806,875 | −1.1010 | 0.2097 | Synonymous | HSF1 | |||
AX-419793247 | rs208317364 | 1,800,399 | −0.9766 | 0.1922 | Intron | DGAT1 | |||
AX-419656711 | rs211282745 | 1,805,963 | 0.8508 | 0.1682 | Downstream gene | HSF1 (dist = 118) | |||
AX-212342341 | rs135258919 | 1,808,145 | 0.8499 | 0.1693 | Missense | HSF1 | |||
AX-419792758 | rs207655744 | 1,806,340 | −0.8430 | 0.1675 | 3 prime UTR | HSF1 | |||
AX-117081655 | rs109234250 | 1,802,265 | −0.7752 | 0.1565 | Missense | DGAT1 | |||
AX-124353826 | rs109326954 | 1,802,266 | −0.6848 | 0.1395 | Missense | DGAT1 | |||
AX-311625843 | rs211223469 | 1,799,476 | 0.6695 | 0.1367 | Intron | DGAT1 | |||
AX-311625845 | rs209876151 | 1,800,439 | 0.6313 | 0.1319 | Intron | DGAT1 | |||
AX-311625833 | rs384957047 | 1,793,616 | 0.5941 | 0.1243 | Upstream gene | DGAT1 (dist = 1735) | |||
AX-371638654 | rs211016627 | 1,807,655 | −0.4948 | 0.1052 | Intron | HSF1 | |||
5 (104) | 1.66 | AX-419663582 | rs43454033 | 104,831,727 | −0.1767 | 0.0560 | Intron | ANO2 | |
8 (0) | 0.74 | AX-419764649 | rs721532493 | 887,406 | −0.0319 | 0.0143 | Intron | PALLD | |
23 (24) | 0.62 | AX-419669189 | rs435871639 | 24,210,330 | −0.0168 | 0.0086 | Intron | PKHD1 | |
3 (79) | 0.60 | AX-106724308 | rs42314807 | 79,480,234 | −1.8050 | 0.4151 | Intron | PDE4B | |
AX-169413290 | rs41596885 | 79,508,402 | 0.7012 | 0.1766 | Intron | PDE4B | |||
PY | 23 (24) | 0.73 | AX-419655926 | rs380223715 | 24,021,950 | −0.0118 | 0.0086 | Intron | PKHD1 |
8 (69) | 0.70 | AX-419606850 | rs211419403 | 69,542,993 | −0.0259 | 0.0144 | Intron | GFRA2 | |
8 (0) | 0.67 | AX-419764649 | rs721532493 | 887,406 | −0.0214 | 0.0137 | Intron | PALLD | |
1 (69) | 0.53 | AX-419771850 | rs799074643 | 69,736,662 | 0.0607 | 0.0294 | Intron | UMPS | |
SCS | 8 (0) | 1.60 | AX-419631051 | rs109008410 | 668,048 | 0.0012 | 0.0253 | Intron | PALLD |
23 (23) | 1.20 | AX-312701115 | rs467721520 | 23,807,184 | −0.0006 | 0.0150 | Intron | PKHD1 | |
23 (24) | 1.10 | AX-106721976 | rs109825181 | 24,117,682 | −0.0012 | 0.0246 | Intron | PKHD1 | |
5 (104) | 0.54 | AX-124344695 | rs110571898 | 104,682,238 | 0.0005 | 0.0127 | Missense | VWF |
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Kim, S.; Lim, B.; Cho, J.; Lee, S.; Dang, C.-G.; Jeon, J.-H.; Kim, J.-M.; Lee, J. Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle. Animals 2021, 11, 1392. https://doi.org/10.3390/ani11051392
Kim S, Lim B, Cho J, Lee S, Dang C-G, Jeon J-H, Kim J-M, Lee J. Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle. Animals. 2021; 11(5):1392. https://doi.org/10.3390/ani11051392
Chicago/Turabian StyleKim, Sangwook, Byeonghwi Lim, Joohyeon Cho, Seokhyun Lee, Chang-Gwon Dang, Jung-Hwan Jeon, Jun-Mo Kim, and Jungjae Lee. 2021. "Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle" Animals 11, no. 5: 1392. https://doi.org/10.3390/ani11051392
APA StyleKim, S., Lim, B., Cho, J., Lee, S., Dang, C.-G., Jeon, J.-H., Kim, J.-M., & Lee, J. (2021). Genome-Wide Identification of Candidate Genes for Milk Production Traits in Korean Holstein Cattle. Animals, 11(5), 1392. https://doi.org/10.3390/ani11051392