Statistics of phenotypes
In this study, we measured the concentrations of immunoglobulins in both colostrum and serum for 620 Chinese Holstein cows. As a result, a total of 10 traits were acquired, including concentrations of total IgG, IgG1, IgG2, IgA and IgM. Means and the corresponding standard deviations for the original and corrected phenotypic values were shown in Table 1.
Table 1
Means and standard deviations for the original and corrected concentrations of immunoglobulins in colostrum and serum.
Traits | N | Mean | SD | Min | Max | Transformation | Mean | SD | Min | Max |
col_IgG | 540 | 33.70 | 43.17 | 1.16 | 342.05 | col_IgG_sqrt | 5.19 | 2.61 | 1.08 | 18.49 |
col_IgG1 | 542 | 15.09 | 7.78 | 0.24 | 44.83 | col_IgG1_sqrt | 3.74 | 1.05 | 0.49 | 6.70 |
col_IgG2 | 606 | 3.2 | 1.94 | 0.07 | 11.04 | col_IgG2_sqrt | 1.7 | 0.54 | 0.26 | 3.32 |
ser_IgG | 607 | 8.34 | 3.37 | 0.68 | 22.9 | ser_IgG_sqrt | 2.83 | 0.58 | 0.82 | 4.79 |
ser_IgG1 | 612 | 1.04 | 0.74 | 0.01 | 7.65 | ser_IgG1_sqrt | 1.04 | 0.31 | 0.09 | 2.77 |
ser_IgG2 | 614 | 13.79 | 6.51 | 0.69 | 42.36 | ser_IgG2_sqrt | 3.61 | 0.86 | 0.83 | 6.51 |
col_IgA | 613 | 3.11 | 3.59 | 0.01 | 51.18 | col_IgA_log | 0.28 | 0.49 | -1.91 | 1.71 |
col_IgM | 613 | 5.47 | 3.7 | 0.09 | 36.41 | col_IgM_log | 0.63 | 0.35 | -1.06 | 1.56 |
ser_IgA | 613 | 0.23 | 0.17 | 0.01 | 1.21 | ser_IgA_log | -0.73 | 0.39 | -5.4 | 0.08 |
ser_IgM | 613 | 2.25 | 1.68 | 0.01 | 14.93 | ser_IgM_log | 0.24 | 0.34 | -2.34 | 1.17 |
N, sample number; Mean, arithmetic mean; SD, standard deviation; Min, minimum; Max, maximum; col_IgG, col_IgG1, col_IgG2, col_IgA and col_IgM represented the concentration of total IgG, IgG1, IgG2, IgA and IgM in colostrum, respectively; ser_IgG, ser_IgG1, ser_IgG2, ser_IgA and ser_IgM represented the concentration of total IgG, IgG1, IgG2, IgA and IgM in serum, respectively; _sqrt, corrected phenotypes by square root transformation; _log, corrected phenotypes by log transformation.
Genotype imputation
After genotype imputation with BEAGLE 3.0.4, a total of 109,009 SNPs with R2 > 0.3 in the 32 imputed cows was retained, in which the average allelic R2 of imputed genotypes was 74.8% [33]. Out of these, 88,934 SNPs were included in the further association analysis after quality control.
Genome-wide association study
After LD analysis, a total of 15,820 effectively independent tests number were suggested. Thus, the threshold P-value for genome-wide significant association was set for 3.16E–6 (0.05/15,820) and that for suggestive significant association was 6.32E–5 (1/15,820) [27]. Based on the QQ plots (Figs. 1 and 2) and the estimated inflation factor (λ) of 0.98–1.02 for all traits, no population stratification was observed.
With GCTA 1.90.2, we performed the genome-wide association studies for the 10 traits. For the concentrations of immunoglobulins in colostrum (Fig. 1 and Table 2), 3 genome-wide significant SNPs for IgG2 were detected (P < 3.16E-6), including 1 SNP on BTA20 and 2 SNPs in BTA21; at suggestive level, a total of 11, 7 and 17 SNPs (P < 6.32E-5) were detected for total IgG, IgG1 and IgG2, respectively, locating on BTA1 (3 SNPs), 3 (2 SNPs), 5 (1 SNP), 6 (1 SNP), 20 (2 SNPs), 21 (15 SNPs), 23 (2 SNPs), 24 (7 SNPs) and 27 (2 SNPs). In addition, 2 SNPs in BTA10 and 2 SNPs in BTA17 associated with concentration of IgM were detected at genome-wide significant level (P < 3.16E-6); 3 and 6 significant SNPs (P < 6.32E-5) were detected for IgA and IgM at suggestive level, respectively, that distributed in BTA1 (1 SNP), 4 (1 SNP), 5 (1 SNP), 8 (1 SNP), 10 (2 SNPs), 15 (1 SNP) and 17 (2 SNPs).
For the concentrations of immunoglobulins in serum (Fig. 2 and Table 3), at genome-wide significant level, 16 SNPs in BTA21 and 1 SNP in BTA20 were identified associated with IgG2 (P < 3.16E-6); at suggestive significant level, 4 SNPs and 18 SNPs were detected for IgG1 and IgG2 (P < 6.32E-5), locating on BTA7 (1 SNP), 12 (2 SNPs), 19 (2 SNPs), 20 (1 SNP) 21 (15 SNPs) and 28 (1 SNP); at both level, total IgG did not show any significant associations. Simultaneously, for IgA and IgM in serum, 1 SNP in BTA17 was significantly associated with IgA at genome-wide level (P < 3.16E-6); 8 and 4 SNPs were identified for IgA and IgM at suggestive significant level (P < 6.32E-5), that spread in BTA2 (1 SNP), 15 (3 SNPs), 18 (1 SNP), 25 (2 SNP), 29 (1 SNP), 4 (1 SNP), 6 (1 SNP) and 7 (2 SNPs).
Through LD analysis, we observed that the 7 significant SNPs for total IgG concentration in colostrum in BTA24 (45.89 ~ 46.24 Mb) generated a haplotype block (D’=86 ~ 100, Fig. 3A); for IgG2 in colostrum, 18 significant SNPs in BTA21 (66.58 ~ 71.39 Mb) formed 3 haplotype blocks: block 1 (14 kb, 2 SNPs), block 2 (17 kb, 3 SNPs) and block 3 (14 kb, 2 SNPs) (D’=97 ~ 100, Fig. 3B); for IgG2 in serum, 3 haplotype blocks were found form 32 significant SNPs on BAT 21 (64.93 ~ 72.48 Mb) that were covered by blocks of IgG2 in colostrum, including block 1 (18 kb, 2 SNPs), block 2 (62 kb, 4 SNPs) and block 3 (14 kb, 2 SNPs) (D’=96 ~ 100, Fig. 3C).
Table 2
The significant SNPs for concentrations of total IgG, IgG1, IgG2, IgA and IgM in colostrum.
Traitsa | Chrb | SNP name | Position (bp) | Major/ minor allele | MAFc | SNP effect | SEd | P-value |
col_IgG | 1 | BovineHD0100036412 | 128805177 | A/G | 0.281 | 11.960 | 2.964 | 4.20E-06 |
col_IgG | 1 | BTB-02067404 | 129170050 | A/G | 0.253 | 12.451 | 3.067 | 6.02E-05 |
col_IgG | 23 | BovineHD2300015105 | 52008189 | A/G | 0.431 | 11.301 | 2.818 | 4.38E-06 |
col_IgG | 23 | BovineHD2300015111 | 52023784 | A/G | 0.430 | 11.358 | 2.813 | 2.15E-05 |
col_IgG | 24 | BovineHD2400012624 | 45892763 | C/A | 0.467 | 11.042 | 2.752 | 2.70E-05 |
col_IgG | 24 | ARS-BFGL-NGS-18561 | 45933554 | G/A | 0.452 | 11.211 | 2.728 | 5.45E-05 |
col_IgG | 24 | BovineHD2400012657 | 45972409 | A/G | 0.366 | 13.095 | 2.851 | 3.97E-05 |
col_IgG | 24 | ARS-BFGL-NGS-20011 | 45973112 | G/A | 0.364 | 13.160 | 2.860 | 5.40E-05 |
col_IgG | 24 | ARS-BFGL-NGS-106793 | 45998467 | A/C | 0.378 | 11.689 | 2.785 | 4.92E-05 |
col_IgG | 24 | ARS-BFGL-NGS-44158 | 46027109 | G/A | 0.377 | 11.869 | 2.794 | 6.06E-05 |
col_IgG | 24 | BovineHD2400012729 | 46241172 | A/G | 0.351 | 11.496 | 2.845 | 5.32E-05 |
col_IgG1 | 1 | BovineHD0100020052 | 70005456 | G/A | 0.363 | 2.027 | 0.457 | 9.23E-06 |
col_IgG1 | 3 | ARS-BFGL-NGS-105483 | 52329712 | A/G | 0.457 | -1.770 | 0.437 | 5.07E-05 |
col_IgG1 | 5 | BovineHD0500008574 | 29136394 | A/G | 0.195 | -2.652 | 0.571 | 3.43E-06 |
col_IgG1 | 6 | BovineHD0600010748 | 38816105 | G/A | 0.312 | 1.900 | 0.472 | 5.72E-05 |
col_IgG1 | 20 | BovineHD2000008079 | 27230044 | A/G | 0.386 | -1.946 | 0.483 | 5.59E-05 |
col_IgG1 | 22 | BovineHD2200013311 | 46250930 | G/A | 0.407 | -2.011 | 0.493 | 4.50E-05 |
col_IgG1 | 27 | ARS-BFGL-NGS-24322 | 19137853 | G/C | 0.398 | -1.936 | 0.462 | 2.75E-05 |
col_IgG2 | 3 | BTB-00163972 | 118145216 | A/G | 0.324 | 0.147 | 0.035 | 2.88E-05 |
col_IgG2 | 20 | BovineHD2000021006 | 71896856 | G/A | 0.273 | 0.223 | 0.037 | 1.13E-09 |
col_IgG2 | 21 | BovineHD2100019547 | 66578213 | A/G | 0.403 | -0.139 | 0.032 | 1.75E-05 |
col_IgG2 | 21 | BovineHD2100020165 | 69062573 | G/A | 0.399 | -0.135 | 0.032 | 2.72E-05 |
col_IgG2 | 21 | BovineHD2100020225 | 69289258 | A/G | 0.331 | 0.145 | 0.033 | 1.08E-05 |
col_IgG2 | 21 | BovineHD2100020241 | 69357379 | A/C | 0.427 | 0.139 | 0.033 | 2.87E-05 |
col_IgG2 | 21 | ARS-BFGL-NGS-115062 | 69395154 | G/A | 0.450 | 0.133 | 0.033 | 5.98E-05 |
col_IgG2 | 21 | BovineHD2100020341 | 69673486 | A/G | 0.361 | 0.148 | 0.032 | 5.34E-06 |
col_IgG2 | 21 | BovineHD2100020413 | 69920970 | G/A | 0.387 | 0.132 | 0.033 | 5.57E-05 |
col_IgG2 | 21 | ARS-BFGL-NGS-2644 | 70608408 | A/G | 0.350 | 0.155 | 0.034 | 5.00E-06 |
col_IgG2 | 21 | BovineHD2100020676 | 70621565 | G/A | 0.350 | 0.159 | 0.034 | 3.22E-06 |
col_IgG2 | 21 | BovineHD2100020685 | 70655075 | A/G | 0.327 | 0.174 | 0.035 | 5.78E-07 |
col_IgG2 | 21 | BovineHD2100020687 | 70665452 | G/A | 0.281 | -0.150 | 0.037 | 4.31E-05 |
col_IgG2 | 21 | BovineHD2100020689 | 70672433 | A/G | 0.379 | 0.142 | 0.034 | 3.35E-05 |
col_IgG2 | 21 | BovineHD2100020696 | 70687439 | G/A | 0.368 | 0.138 | 0.033 | 2.44E-05 |
col_IgG2 | 21 | ARS-BFGL-NGS-73522 | 70702245 | G/A | 0.347 | 0.152 | 0.034 | 7.68E-06 |
col_IgG2 | 21 | BovineHD4100015389 | 70726088 | C/A | 0.367 | -0.142 | 0.034 | 2.84E-05 |
col_IgG2 | 21 | BovineHD2100020833 | 71318798 | A/G | 0.286 | 0.169 | 0.035 | 1.11E-06 |
col_IgG2 | 21 | BovineHD2100020837 | 71338809 | G/A | 0.148 | 0.176 | 0.044 | 6.25E-05 |
col_IgG2 | 21 | BovineHD2100020853 | 71389313 | G/A | 0.248 | -0.167 | 0.039 | 1.55E-05 |
col_IgA | 1 | BovineHD0100012276 | 43138880 | A/C | 0.425 | 0.129 | 0.031 | 3.61E-05 |
col_IgA | 4 | BTB-00172973 | 31573521 | G/A | 0.267 | -0.140 | 0.033 | 2.87E-05 |
col_IgA | 5 | BovineHD0500021305 | 74998613 | G/A | 0.334 | -0.138 | 0.031 | 9.66E-06 |
col_IgM | 8 | BovineHD0800026113 | 88021995 | G/A | 0.484 | 0.189 | 0.047 | 6.22E-05 |
col_IgM | 10 | BovineHD1000019825 | 69080826 | A/C | 0.162 | -0.305 | 0.060 | 4.14E-07 |
col_IgM | 10 | BovineHD1000019983 | 69718494 | C/A | 0.323 | -0.242 | 0.049 | 9.53E-07 |
col_IgM | 10 | BovineHD1000020063 | 70071886 | A/G | 0.429 | -0.212 | 0.048 | 1.01E-05 |
col_IgM | 10 | Hapmap29285-BTA-162580 | 69721690 | T/A | 0.356 | -0.201 | 0.049 | 3.68E-05 |
col_IgM | 15 | ARS-BFGL-NGS-109495 | 1492400 | A/T | 0.379 | -0.187 | 0.047 | 6.16E-05 |
col_IgM | 17 | BTB-01973064 | 73349750 | A/G | 0.391 | 0.234 | 0.048 | 1.33E-06 |
col_IgM | 17 | BovineHD1700021434 | 73349278 | A/G | 0.457 | 0.227 | 0.047 | 1.35E-06 |
col_IgM | 17 | BovineHD1700021122 | 72466328 | G/A | 0.439 | -0.215 | 0.047 | 4.18E-06 |
col_IgM | 17 | ARS-BFGL-NGS-5369 | 71841734 | A/C | 0.298 | -0.216 | 0.051 | 2.51E-05 |
acol_IgG, col_IgG1, col_IgG2, col_IgA and col_IgM represented concentration of total IgG, IgG1 IgG2, IgA and IgM in colostrum, respectively. |
bCow chromosome number. |
cMinor allele frequency. |
dstandard error |
Table 3
The significant SNPs for concentrations of total IgG, IgG1, IgG2, IgA and IgM in serum.
Traitsa | Chrb | SNP name | Position (bp) | Major/ minor allele | MAFc | SNP effect | SEd | P-value |
ser_IgG1 | 28 | BovineHD2800011781 | 41894086 | A/G | 0.362 | 0.083 | 0.018 | 6.88E-06 |
ser_IgG1 | 19 | Hapmap57648-rs29022376 | 22709090 | G/A | 0.347 | -0.084 | 0.019 | 1.28E-05 |
ser_IgG1 | 7 | BovineHD0700032048 | 109730181 | A/G | 0.445 | -0.075 | 0.018 | 2.89E-05 |
ser_IgG1 | 19 | ARS-BFGL-NGS-20165 | 23561900 | C/A | 0.410 | -0.075 | 0.018 | 4.19E-05 |
ser_IgG2 | 12 | BovineHD1200008568 | 28980452 | C/A | 0.323 | 0.251 | 0.055 | 5.84E-06 |
ser_IgG2 | 12 | BovineHD1200008569 | 28987016 | A/G | 0.478 | -0.204 | 0.050 | 5.16E-05 |
ser_IgG2 | 20 | BovineHD2000021006 | 71896856 | G/A | 0.274 | 0.413 | 0.057 | 5.04E-13 |
ser_IgG2 | 21 | BovineHD2100018787 | 63926754 | A/G | 0.464 | -0.229 | 0.051 | 7.19E-06 |
ser_IgG2 | 21 | BTA-24891-no-rs | 63955841 | G/A | 0.357 | 0.214 | 0.052 | 4.18E-05 |
ser_IgG2 | 21 | BovineHD2100019656 | 66910728 | G/A | 0.416 | 0.215 | 0.051 | 2.36E-05 |
ser_IgG2 | 21 | ARS-BFGL-NGS-20339 | 67088847 | G/A | 0.333 | 0.240 | 0.052 | 4.71E-06 |
ser_IgG2 | 21 | BovineHD2100019814 | 67542721 | A/C | 0.363 | 0.240 | 0.053 | 5.03E-06 |
ser_IgG2 | 21 | BovineHD2100019834 | 67604077 | A/C | 0.147 | 0.289 | 0.071 | 5.19E-05 |
ser_IgG2 | 21 | BovineHD4100015366 | 67786313 | A/G | 0.421 | 0.267 | 0.052 | 2.94E-07 |
ser_IgG2 | 21 | BovineHD2100019888 | 67885290 | A/G | 0.217 | 0.246 | 0.060 | 4.21E-05 |
ser_IgG2 | 21 | BovineHD2100019906 | 67946189 | A/G | 0.319 | 0.241 | 0.054 | 6.86E-06 |
ser_IgG2 | 21 | ARS-BFGL-NGS-86477 | 68399787 | A/C | 0.482 | -0.213 | 0.052 | 4.06E-05 |
ser_IgG2 | 21 | BovineHD2100020157 | 69009950 | A/C | 0.442 | 0.229 | 0.052 | 1.07E-05 |
ser_IgG2 | 21 | BovineHD2100021033 | 69033145 | G/A | 0.201 | 0.331 | 0.062 | 7.14E-08 |
ser_IgG2 | 21 | BovineHD2100020225 | 69289258 | A/G | 0.331 | 0.272 | 0.052 | 1.37E-07 |
ser_IgG2 | 21 | BovineHD2100020232 | 69327116 | G/A | 0.349 | 0.271 | 0.051 | 1.32E-07 |
ser_IgG2 | 21 | BovineHD2100020241 | 69357379 | A/C | 0.424 | 0.224 | 0.053 | 2.14E-05 |
ser_IgG2 | 21 | ARS-BFGL-NGS-115062 | 69395154 | G/A | 0.450 | 0.231 | 0.053 | 1.17E-05 |
ser_IgG2 | 21 | BovineHD2100020317 | 69613677 | G/A | 0.243 | 0.254 | 0.060 | 2.29E-05 |
ser_IgG2 | 21 | BovineHD2100020341 | 69673486 | A/G | 0.366 | 0.299 | 0.051 | 4.21E-09 |
ser_IgG2 | 21 | BovineHD2100020413 | 69920970 | G/A | 0.386 | 0.263 | 0.052 | 3.92E-07 |
ser_IgG2 | 21 | ARS-BFGL-NGS-1345 | 69939350 | C/A | 0.420 | 0.232 | 0.052 | 7.32E-06 |
ser_IgG2 | 21 | BovineHD2100020439 | 70000656 | A/G | 0.446 | 0.239 | 0.053 | 6.19E-06 |
ser_IgG2 | 21 | ARS-USDA-AGIL-chr21-70182028-000470 | 70182028 | C/G | 0.376 | 0.212 | 0.052 | 5.34E-05 |
ser_IgG2 | 21 | BovineHD2100020653 | 70537404 | A/G | 0.182 | 0.380 | 0.063 | 2.17E-09 |
ser_IgG2 | 21 | BovineHD2100020670 | 70592463 | A/C | 0.415 | 0.251 | 0.052 | 1.52E-06 |
ser_IgG2 | 21 | ARS-BFGL-NGS-2644 | 70608408 | A/G | 0.353 | 0.330 | 0.053 | 6.66E-10 |
ser_IgG2 | 21 | BovineHD2100020676 | 70621565 | G/A | 0.353 | 0.343 | 0.054 | 1.74E-10 |
ser_IgG2 | 21 | BovineHD2100020685 | 70655075 | A/G | 0.329 | 0.342 | 0.055 | 4.05E-10 |
ser_IgG2 | 21 | BovineHD2100020689 | 70672433 | A/G | 0.381 | 0.256 | 0.054 | 1.73E-06 |
ser_IgG2 | 21 | BovineHD2100020696 | 70687439 | G/A | 0.370 | 0.296 | 0.051 | 8.63E-09 |
ser_IgG2 | 21 | ARS-BFGL-NGS-73522 | 70702245 | G/A | 0.349 | 0.287 | 0.053 | 6.29E-08 |
ser_IgG2 | 21 | BovineHD2100020833 | 71318798 | A/G | 0.286 | 0.322 | 0.055 | 6.15E-09 |
ser_IgG2 | 21 | BovineHD2100020883 | 71479429 | A/G | 0.165 | 0.400 | 0.068 | 3.18E-09 |
ser_IgA | 2 | ARS-BFGL-NGS-100214 | 132821698 | A/G | 0.139 | -0.142 | 0.033 | 1.76E-05 |
ser_IgA | 15 | BTA-91367-no-rs | 60316301 | G/A | 0.464 | -0.099 | 0.024 | 2.52E-05 |
ser_IgA | 15 | BovineHD1500016066 | 55611146 | G/A | 0.477 | -0.101 | 0.025 | 4.69E-05 |
ser_IgA | 15 | BovineHD1500016061 | 55590128 | G/A | 0.476 | -0.100 | 0.025 | 5.43E-05 |
ser_IgA | 18 | BovineHD1800015730 | 53613268 | G/A | 0.133 | -0.150 | 0.037 | 5.23E-05 |
ser_IgA | 25 | BovineHD2500007939 | 28524826 | A/G | 0.387 | -0.106 | 0.025 | 1.88E-05 |
ser_IgA | 25 | BovineHD2500007948 | 28580391 | A/G | 0.388 | -0.107 | 0.025 | 1.96E-05 |
ser_IgA | 29 | BovineHD2900006144 | 21381114 | A/G | 0.201 | -0.115 | 0.028 | 5.55E-05 |
ser_IgM | 4 | BovineHD0400027460 | 98194248 | A/G | 0.115 | 0.125 | 0.031 | 6.29E-05 |
ser_IgM | 6 | BovineHD0600009523 | 34015077 | G/A | 0.270 | -0.101 | 0.022 | 3.73E-06 |
ser_IgM | 7 | ARS-BFGL-NGS-12159 | 19220954 | A/C | 0.433 | -0.084 | 0.020 | 1.56E-05 |
ser_IgM | 7 | BovineHD0700005341 | 19183296 | A/G | 0.432 | -0.081 | 0.019 | 3.45E-05 |
ser_IgM | 17 | BovineHD1700021706 | 74223510 | G/A | 0.170 | -0.123 | 0.026 | 2.74E-06 |
aser_IgG1, ser_IgG2, ser_IgA and ser_IgM represented concentration of IgG1 IgG2, IgA and IgM in serum, respectively. |
bCow Chromosome number. |
cMinor allele frequency. |
dstandard error |
Candidate genes and function analysis
Appling BioMart in the Ensembl database (Ensembl Genes 92), we obtained 49, 221, 437, 252 and 408 functional genes that contained or were near to (within 1 Mb) the significant SNPs associated with total IgG, IgG1, IgG2, IgA and IgM traits, respectively. After removing the duplicates of genes, a total of 1,083 candidate genes was remained, including 706 protein-coding genes, 60 miRNA genes, 45 spliceosomal RNAs, 76 small nucleolar RNAs and 196 novel genes (Additional file 3: Table S1).
To further know about the biological functions of these candidate genes, we performed GO and KEGG analysis and observed that 151 genes were enriched in immune related biological processes and pathways such as immune response, Fc gamma R-mediated phagocytosis, negative regulation of immunoglobulin secretion, humoral immune response, Fc-epsilon receptor and NF-kappaB signaling pathways, etc (Additional file 4:Table S2). Simultaneously, we compared the physical positions of the 1,083 genes with the peak of the known QTLs that have been shown associated with immune capacity in dairy cattle (Cattle QTLdb), including IgG level, FMDV peptide-induced cell proliferation and ConA-induced cell proliferation. Consequently, 181 genes were found located within the QTL regions with distance to the peak positions of less than 1.0 cM.
Integrating the results of GO/KEGG and QTL data, 21 overlapping genes were considered as promising candidates for the concentrations of immunoglobulins in colostrum and serum (Table 4). They were ABR activator of RhoGEF and GTPase (ABR), translocase of inner mitochondrial membrane 22 (TIMM22), CRK proto-oncogene, adaptor protein (CRK), myosin IC (MYO1C), Rab interacting lysosomal protein (RILP), serpin family F member 2 (SERPINF2), AKT serine/threonine kinase 1 (AKT1), BAF chromatin remodeling complex subunit BCL11B (BCL11B), HHIP like 1 (HHIPL1), dynein cytoplasmic 1 heavy chain 1 (DYNC1H1), heat shock protein 90 alpha family class A member 1 (HSP90AA1), TNF receptor associated factor 3 (TRAF3), kinesin light chain 1 (KLC1), interleukin 6 (IL6), PYD and CARD domain containing (PYCARD), integrin subunit alpha M (ITGAM), transforming growth factor beta 1 induced transcript 1 (TGFB1I1), glucuronidase beta (GUSB), CGRP receptor component (CRCP), RAB guanine nucleotide exchange factor 1 (RABGEF1) and SBDS ribosome maturation factor (SBDS).
Table 4
The list of candidate genes contained or nearby the significant SNPs associated with total IgG, IgG1, IgG2, IgA and IgM in the colostrum and serum.
Gene ID | Gene Name | Chra | Gene Startb | Gene Endb | Traits |
ENSBTAG00000008424 | ABR | 19 | 22287405 | 22431563 | ser_IgG1 |
ENSBTAG00000008423 | TIMM22 | 19 | 22432982 | 22439070 | ser_IgG1 |
ENSBTAG00000005665 | CRK | 19 | 23139102 | 23159120 | ser_IgG1 |
ENSBTAG00000001332 | MYO1C | 19 | 23168435 | 23191280 | ser_IgG1 |
ENSBTAG00000038889 | RILP | 19 | 23320981 | 23323996 | ser_IgG1 |
ENSBTAG00000020859 | SERPINF2 | 19 | 23403657 | 23411269 | ser_IgG1 |
ENSBTAG00000017636 | AKT1 | 21 | 70878138 | 70895537 | col_IgG2, ser_IgG2 |
ENSBTAG00000018019 | BCL11B | 21 | 65841997 | 65938304 | col_IgG2, ser_IgG2 |
ENSBTAG00000026913 | HHIPL1 | 21 | 66284693 | 66314293 | col_IgG2, ser_IgG2 |
ENSBTAG00000016598 | DYNC1H1 | 21 | 68507134 | 68568024 | col_IgG2, ser_IgG2 |
ENSBTAG00000006270 | HSP90AA1 | 21 | 68595873 | 68601204 | col_IgG2, ser_IgG2 |
ENSBTAG00000013475 | TRAF3 | 21 | 69228047 | 69254153 | col_IgG2, ser_IgG2 |
ENSBTAG00000017299 | KLC1 | 21 | 69896140 | 69957173 | col_IgG2, ser_IgG2 |
ENSBTAG00000014921 | IL6 | 4 | 31578311 | 31582667 | col_IgA |
ENSBTAG00000020535 | PYCARD | 25 | 27541409 | 27542740 | ser_IgA |
ENSBTAG00000047238 | ITGAM | 25 | 27602222 | 27639821 | ser_IgA |
ENSBTAG00000002391 | TGFB1I1 | 25 | 27760811 | 27766954 | ser_IgA |
ENSBTAG00000000704 | GUSB | 25 | 28162569 | 28174955 | ser_IgA |
ENSBTAG00000037489 | CRCP | 25 | 28255764 | 28294982 | ser_IgA |
ENSBTAG00000003842 | RABGEF1 | 25 | 28509094 | 28534880 | ser_IgA |
ENSBTAG00000004051 | SBDS | 25 | 28630825 | 28636300 | ser_IgA |
aCow chromosome number. |
bThe position of gene was based on the UMD 3.1 assembly. |
col_IgG, col_IgG1, col_IgG2, col_IgA and col_IgM represented concentration of total IgG, IgG1 IgG2, IgA and IgM in colostrum; ser_IgG, ser_IgG1, ser_IgG2, ser_IgA and ser_IgM represented concentration of total IgG, IgG1 IgG2, IgA and IgM in serum.