Table 3.
Irish commercial beef-suckler and dairy calves GWAS results for passive immunity and disease traits.
| Population | Variable | Associated SNP | Chromosome | RS number | P value | Closest gene | Distance of SNP to gene |
|---|---|---|---|---|---|---|---|
| Combined dairy and beef | Immunoglobulin G | ARS-BFGL-NGS-114208 | 1 | rs110082431 | 3.76E−05* | ENSBTAG00000045984 | 25,324 |
| Albumin | ARS-BFGL-NGS-11531 | 12 | rs109028090 | 7.87E−06 | DHRS12 | 0 | |
| ARS-BFGL-NGS-100170 | 12 | rs109708871 | 2.68E−05 | SLC10A2 | − 462,315 | ||
| Total protein | BTB-01120104 | 4 | rs42277262 | 1.75E−05 | GNAI1 | −36,497 | |
| UA-IFASA-8558 | 24 | rs41646027 | 3.92E−05 | LPIN2 | 0 | ||
| BTB-00174357 | 4 | rs43383611 | 4.22E−05 | KIAA1324L | 22,817 | ||
| Globulin | UA-IFASA-8558 | 24 | rs41646027 | 3.17E−05 | LPIN2 | 0 | |
| BTB-01120104 | 4 | rs42277262 | 3.34E−05 | GNAI1 | − 36,497 | ||
| BOVINEHD2400010261 | 24 | rs109172808 | 4.44E−05 | LPIN2 | 0 | ||
| Specific gravity | BTB-01120104 | 4 | rs42277262 | 3.03E−06 | GNAI1 | − 36,497 | |
| Total solids Brix % | ARS-BFGL-NGS-69831 | 7 | rs42619441 | 2.71E−05 | ENSBTAG00000038284 | 0 | |
| BTB-01120104 | 4 | rs42277262 | 3.89E−05 | GNAI1 | −36,497 | ||
| ARS-BFGL-NGS-15820 | 11 | rs110788172 | 3.93E−05 | CDKL4 | 0 | ||
| UA-IFASA-8558 | 24 | rs41646027 | 4.05E−05 | LPIN2 | 0 | ||
| BOVINEHD2400010261 | 24 | rs109172808 | 4.80E−05 | LPIN2 | 0 | ||
| Pneumonia | ARS-BFGL-NGS-57317 | 25 | rs110476838 | 8.60E−06 | ENSBTAG00000014417 | 334,478 | |
| ARS-BFGL-NGS-50482 | 2 | rs110785912 | 2.73E−05 | CXCR4 | 447,880 | ||
| BOVINEHD2900007001 | 29 | rs42465360 | 3.60E−05 | SLC6A5 | 338,375 | ||
| HAPMAP52014-BTA-90653 | 5 | rs41593661 | 3.75E−05 | ENSBTAG00000046268 | 30,344 | ||
| Diarrhoea | ARS-BFGL-NGS-114897 | 11 | rs110764285 | 4.40E−05 | NFU1 | 1970 | |
| Crude illness | ARS-BFGL-NGS-110312 | 12 | rs110793235 | 3.77E−05 | KL | − 74,444 | |
| HAPMAP40647-BTA-110965 | 4 | rs41575187 | 3.91E−05 | DYNC1I1 | 0 | ||
| Beef calves | Immunoglobulin G | ARS-BFGL-BAC-27914 | 20 | rs110897405 | 2.20E−07 | PARP8 | 0 |
| HAPMAP51687-BTA-114691 | 20 | rs41616927 | 1.57E−05 | ISL1 | 85,644 | ||
| ARS-BFGL-NGS-67929 | 2 | rs110780508 | 3.56E−05 | MREG | 0 | ||
| Total protein | ARS-BFGL-BAC-27914 | 20 | rs110897405 | 2.91E−05 | PARP8 | 0 | |
| Globulin | HAPMAP47694-BTA-67030 | 3 | rs43710738 | 1.60E−05 | PTGFRN | 11,015 | |
| ARS-BFGL-BAC-27914 | 20 | rs110897405 | 2.99E−05 | PARP8 | 0 | ||
| BTB-00212876 | 4 | rs43420430 | 4.07E−05 | DPP6 | 0 | ||
| BTA-03263-RS29011028 | 21 | rs29011028 | 4.29E−05 | PPP2R5C | 20,692 | ||
| Zinc sulphate turbidity | BTA-47238-NO-RS | 1 | rs110704582 | 1.00E−05 | PLCH1 | − 144,011 | |
| BTB-00212876 | 4 | rs43420430 | 2.72E−05 | DPP6 | 0 | ||
| HAPMAP47742-BTA-80071 | 7 | rs41656596 | 4.51E−05 | RASA1 | 0 | ||
| ARS-BFGL-NGS-55396 | 10 | rs110351463 | 4.79E−05 | SYNE2 | 0 | ||
| Specific gravity | ARS-BFGL-NGS-4066 | 26 | rs109923400 | 4.53E−05 | ENSBTAG00000003529 | − 5054 | |
| Crude illness | ARS-BFGL-NGS-114450 | 24 | rs109440690 | 1.82E−05 | ATP8B1 | − 131,562 | |
| BOVINEHD0900029149 | 9 | rs109299906 | 2.62E−05 | QKI | − 73,861 | ||
| ARS-BFGL-NGS-43453 | 8 | rs110620477 | 4.58E−05 | SMARCA2 | 0 | ||
| Dairy calves | Immunoglobulin G | HAPMAP54718-RS29022960 | 9 | rs29022960 | 1.56E−05 | ZNF292 | 0 |
| UA-IFASA-8558 | 24 | rs41646027 | 3.78E−05 | LPIN2 | 0 | ||
| BOVINEHD2400010261 | 24 | rs109172808 | 4.15E−05 | LPIN2 | 0 | ||
| Albumin | ARS-BFGL-NGS-11531 | 12 | rs109028090 | 1.48E−05 | DHRS12 | 0 | |
| ARS-BFGL-NGS-6195 | 18 | rs109046420 | 2.27E−05 | BANP | 0 | ||
| HAPMAP39432-BTA-76145 | 6 | rs41596019 | 2.74E−05 | STIM2 | − 184,275 | ||
| Total protein | UA-IFASA-8558 | 24 | rs41646027 | 7.47E−06 | LPIN2 | 0 | |
| ARS-BFGL-NGS-83128 | 11 | rs110743782 | 8.54E−06 | OTOF | 0 | ||
| BOVINEHD2400010261 | 24 | rs109172808 | 9.62E−06 | LPIN2 | 0 | ||
| ARS-BFGL-NGS-11057 | 11 | rs109425927 | 2.17E−05 | OTOF | 0 | ||
| Globulin | UA-IFASA-8558 | 24 | rs41646027 | 5.68E−06 | LPIN2 | 0 | |
| BOVINEHD2400010261 | 24 | rs109172808 | 6.88E−06 | LPIN2 | 0 | ||
| ARS-BFGL-NGS-83128 | 11 | rs110743782 | 4.08E−05 | OTOF | 0 | ||
| Specific gravity | UA-IFASA-8558 | 24 | rs41646027 | 2.62E−05 | LPIN2 | 0 | |
| BOVINEHD2400010261 | 24 | rs109172808 | 2.81E−05 | LPIN2 | 0 | ||
| Total solids Brix % | ARS-BFGL-NGS-83128 | 11 | rs110743782 | 2.91E−06 | OTOF | 0 | |
| ARS-BFGL-NGS-11057 | 11 | rs109425927 | 7.78E−06 | OTOF | 0 | ||
| BOVINEHD2400010261 | 24 | rs109172808 | 1.65E−05 | LPIN2 | 0 | ||
| UA-IFASA-8558 | 24 | rs41646027 | 1.70E−05 | LPIN2 | 0 | ||
| BTB-02047078 | 6 | rs43152213 | 3.30E−05 | ENSBTAG00000040324 | − 406,779 | ||
| Pneumonia | ARS-BFGL-NGS-48754 | 8 | rs108973453 | 7.67E−06 | CAAP1 | 0 | |
| BOVINEHD0600010238 | 6 | rs135767642 | 1.70E−05 | GPRIN3 | 241,903 | ||
| HAPMAP31810-BTA-155140 | 2 | rs42738873 | 4.46E−05 | ARHGAP15 | 0 | ||
| Diarrhoea | BTA-41494-NO-RS | 1 | rs41641198 | 2.27E−05 | TBL1XR1 | 320,947 | |
| BTB-00647119 | 16 | rs41812941 | 2.81E−05 | PRDM2 | 320,495 |
P value = values are significant at the suggestive P value (P < 5 × 10−5), * = additionally significant at the Bonferroni genome wide significance P value threshold (i.e. Bonferroni P value threshold = 0.05/total no. of variants in analysis).
Sample sizes: Combined beef-suckler and dairy calves (Immunoglobulin G n = 1824, Pneumonia n = 1415 (77 case, 1338 control), Diarrhoea n = 1415 (237 case, 1178 control), Crude illness n = 1415 (357 case, 1058 control), Albumin n = 1838, Total protein n = 1838, Globulin n = 1833, Specific gravity n = 1839, Total solids Brix % n = 1836). Beef-suckler calves (Immunoglobulin G n = 679, Crude illness n = 686 (135 case, 551 control), Total protein n = 685, Globulin n = 681, Zinc sulphate turbidity n = 683, Specific gravity n = 686). Dairy calves (Immunoglobulin G n = 1143, Pneumonia n = 727 (33 case, 694 control), Diarrhoea n = 727 (176 case, 551 control), Albumin n = 1153, Total protein n = 1151, Globulin n = 1150, Specific gravity n = 1151, Total solids Brix % n = 1150).