Genome-Wide Association Study of Age at First Calving in U.S. Holstein Cows
Abstract
:1. Introduction
2. Results and Discussion
2.1. Additive Effects
2.2. Dominance Effects
2.3. Elimination of Rare Negative Recessive Genotypes for Heifer Culling
2.4. Comparison with Previous Studies
2.5. Gene Ontology of Candidate Genes
3. Materials and Methods
3.1. Holstein Population and SNP Data
3.2. GWAS Analysis
4. 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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SNP | Chr | Position (bp) | Candidate Gene | Effect (α, −Days) | al+ | ae+ (−Days) | f_al+ | al− | ae− (−Days) | f_al− | log10(1/p) |
---|---|---|---|---|---|---|---|---|---|---|---|
rs110401500 | 19 | 31,252,963 | ARHGAP44 | −1.02 | 2 | 0.730 | 0.287 | 1 | −0.294 | 0.713 | 37.30 |
rs41257332 | 19 | 33,443,229 | TTC19 | −0.97 | 2 | 0.616 | 0.366 | 1 | −0.355 | 0.634 | 36.45 |
rs111004845 | 19 | 27,355,811 | SHBG (9664 bp u) a | −0.97 | 2 | 0.648 | 0.332 | 1 | −0.323 | 0.668 | 36.06 |
rs135712994 | 19 | 33,421,057 | NCOR1 | −0.89 | 2 | 0.359 | 0.597 | 1 | −0.531 | 0.403 | 33.14 |
rs110761858 | 19 | 33,358,794 | NCOR1 | −0.87 | 2 | 0.354 | 0.592 | 1 | −0.514 | 0.408 | 31.87 |
rs41621822 | 19 | 31,902,307 | LOC112442639 | −0.90 | 2 | 0.594 | 0.339 | 1 | −0.304 | 0.661 | 31.39 |
rs133729181 | 19 | 32,106,657 | COX10 | 0.86 | 1 | 0.519 | 0.394 | 2 | −0.337 | 0.606 | 30.40 |
rs134054295 | 23 | 32,599,962 | LOC537017 | −1.02 | 2 | 0.808 | 0.211 | 1 | −0.217 | 0.789 | 30.30 |
rs136368496 | 23 | 28,526,405 | LOC101905956 | −0.87 | 2 | 0.555 | 0.364 | 1 | −0.318 | 0.636 | 30.04 |
rs110845473 | 19 | 27,484,633 | DNAH2 | −0.98 | 2 | 0.753 | 0.234 | 1 | −0.230 | 0.766 | 29.89 |
rs41904669 | 19 | 27,073,319 | TNK1 | 0.97 | 1 | 0.738 | 0.239 | 2 | −0.232 | 0.761 | 29.43 |
rs109836072 | 15 | 7,475,196 | TRPC6 (3151 bp d) a | −1.04 | 2 | 0.818 | 0.212 | 1 | −0.220 | 0.788 | 29.38 |
rs137457305 | 23 | 26,926,436 | C23H6orf10 | 0.98 | 1 | 0.746 | 0.236 | 2 | −0.231 | 0.764 | 29.28 |
rs41904556 | 19 | 27,316,118 | MPDU1 | 0.96 | 1 | 0.732 | 0.240 | 2 | −0.231 | 0.760 | 29.03 |
rs42688274 | 19 | 29,273,714 | GAST (22,315 bp d) | −0.97 | 2 | 0.740 | 0.235 | 1 | −0.227 | 0.765 | 29.03 |
rs29010491 | 23 | 30,176,828 | ENSBTAG00000051232 (21,566 bp u) a | 0.81 | 1 | 0.442 | 0.453 | 2 | −0.366 | 0.547 | 28.03 |
rs137317833 | 23 | 29,958,908 | blank | −0.81 | 2 | 0.455 | 0.441 | 1 | −0.358 | 0.559 | 27.93 |
rs136764006 | 15 | 7,861,416 | PGR | 0.89 | 1 | 0.620 | 0.303 | 2 | −0.270 | 0.697 | 27.63 |
rs110654893 | 23 | 30,013,004 | ZNF311 (5017 bp u) a | −0.80 | 2 | 0.438 | 0.453 | 1 | −0.363 | 0.547 | 27.53 |
rs109681200 | 23 | 30,377,501 | ZSCAN31 | −0.83 | 2 | 0.538 | 0.354 | 1 | −0.294 | 0.646 | 27.39 |
SNP | Chr | Position | Candidate Gene | Effect (δ, −Days) | DR | d_DR (−Days) | f_DR | DD | d_DD (−Days) | f_DD | RR | d_RR (−Days) | f_RR | f_R | log10(1/p) |
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
rs109438971 | 5 | 26,964,045 | EIF4B (14,636 bp d) | 5.53 | 12 | 0.62 | 0.152 | 22 | −0.06 | 0.843 | 11 | −9.76 | 0.005 | 0.081 | 45.08 |
rs110558219 | 5 | 26,715,326 | AAAS | 5.51 | 12 | 0.62 | 0.152 | 11 | −0.06 | 0.843 | 22 | −9.72 | 0.005 | 0.081 | 44.89 |
rs43768813 | 6 | 101,887,271 | AFF1 | 4.87 | 12 | 0.61 | 0.131 | 22 | −0.05 | 0.864 | 11 | −8.48 | 0.005 | 0.07 | 33.36 |
rs42739334 | 6 | 102,065,812 | KLHL8 | 4.68 | 12 | 0.60 | 0.136 | 11 | −0.05 | 0.859 | 22 | −8.11 | 0.005 | 0.073 | 33.04 |
rs109675908 | 5 | 26,499,453 | ATF7 | 3.88 | 12 | 0.54 | 0.170 | 22 | −0.05 | 0.823 | 11 | −6.63 | 0.007 | 0.092 | 30.77 |
rs43480825 | 6 | 101,994,654 | AFF1 | 4.57 | 12 | 0.57 | 0.135 | 11 | −0.04 | 0.860 | 22 | −7.95 | 0.005 | 0.072 | 30.56 |
rs109933750 | 6 | 102,164,971 | U6 (16,972 bp d) | 4.50 | 12 | 0.56 | 0.134 | 22 | −0.04 | 0.861 | 11 | −7.83 | 0.005 | 0.072 | 29.18 |
rs135494774 | 5 | 25,556,149 | NCKAP1L | 3.46 | 12 | 0.53 | 0.180 | 11 | −0.06 | 0.811 | 22 | −5.80 | 0.008 | 0.099 | 27.34 |
rs134764130 | 5 | 26,385,947 | ATP5MC2 (7720 bp d) | 3.14 | 12 | 0.51 | 0.192 | 22 | −0.06 | 0.798 | 11 | −5.18 | 0.010 | 0.106 | 26.13 |
rs41603412 | 5 | 33,076,713 | PCED1B | 3.17 | 12 | 0.50 | 0.185 | 22 | −0.06 | 0.806 | 11 | −5.28 | 0.009 | 0.101 | 25.56 |
SNP | Formula of Negative Impact a | AFC (Days) | Milk Yield (kg) | Fat Yield (kg) | Protein Yield (kg) |
---|---|---|---|---|---|
rs109675908 | b | 7.69 | −470.06 | −20.14 | −14.22 |
rs110558219 | 10.75 | −646.33 | −26.03 | −19.27 | |
rs109438971 | 10.88 | −640.94 | −26.03 | −19.11 | |
rs43768813 | 12.50 | −169.35 | −9.05 | −5.73 | |
rs43480825 | 12.00 | −189.78 | −9.88 | −6.40 | |
rs42739334 | 12.83 | −240.84 | −10.50 | −7.41 | |
rs109933750 | 11.76 | −201.23 | −10.22 | −6.74 |
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Prakapenka, D.; Liang, Z.; Da, Y. Genome-Wide Association Study of Age at First Calving in U.S. Holstein Cows. Int. J. Mol. Sci. 2023, 24, 7109. https://doi.org/10.3390/ijms24087109
Prakapenka D, Liang Z, Da Y. Genome-Wide Association Study of Age at First Calving in U.S. Holstein Cows. International Journal of Molecular Sciences. 2023; 24(8):7109. https://doi.org/10.3390/ijms24087109
Chicago/Turabian StylePrakapenka, Dzianis, Zuoxiang Liang, and Yang Da. 2023. "Genome-Wide Association Study of Age at First Calving in U.S. Holstein Cows" International Journal of Molecular Sciences 24, no. 8: 7109. https://doi.org/10.3390/ijms24087109