Table 3.
Association results of the thirteen indels in eight genes on the five milk production traits (least squares mean ± SE)
| Locus | Gene | Genotype (No.) | MY | FY | FP | PY | PP |
|---|---|---|---|---|---|---|---|
| rs381714237 | FCGR2B | del/del(86) | 10,891 ± 99.80 | 385.05 ± 4.21 | 3.59 ± 0.040 | 319.32 ± 3.10ab | 2.95 ± 0.014a |
| ins/del(380) | 10,702 ± 64.80 | 383.94 ± 2.89 | 3.66 ± 0.027 | 315.86 ± 2.11Aa | 2.98 ± 0.009ab | ||
| ins/ins(282) | 10,834 ± 68.20 | 385.61 ± 3.03 | 3.64 ± 0.028 | 321.83 ± 2.20Bb | 2.99 ± 0.009b | ||
| P value | 0.0297* | 0.7926 | 0.1738 | 0.0041** | 0.0198* | ||
| ss2137349053 | CENPE | del/del(153) | 10,403 ± 55.66A | 374.36 ± 2.82Aa | 3.61 ± 0.034 | 308.40 ± 2.65A | 2.97 ± 0.024 |
| del/ins(373) | 10,661 ± 47.88B | 378.61 ± 2.43Aa | 3.57 ± 0.027 | 315.70 ± 2.14Ba | 2.97 ± 0.017 | ||
| ins/ins(209) | 10,852 ± 51.03C | 385.99 ± 2.59B | 3.58 ± 0.031 | 321.05 ± 2.37Bb | 2.97 ± 0.020 | ||
| P value | < 0.0001** | < 0.0001** | 0.3733 | < 0.0001** | 0.9882 | ||
| rs385060942 | CENPE | del/del(152) | 10,494 ± 84.00Aa | 376.49 ± 3.60Aa | 3.60 ± 0.034 | 310.45 ± 2.62B | 2.96 ± 0.012 |
| del/ins(377) | 10,717 ± 65.77Aa | 381.44 ± 2.93ab | 3.57 ± 0.027 | 318.18 ± 2.13Aa | 2.97 ± 0.009 | ||
| ins/ins(208) | 10,871 ± 74.83B | 387.82 ± 3.26Bb | 3.59 ± 0.031 | 322.24 ± 2.38Aa | 2.97 ± 0.010 | ||
| P value | < 0.0001** | 0.0045** | 0.6063 | < 0.0001** | 0.6166 | ||
| ss2137349051 | CENPE | ins/ins(206) | 10,817 ± 75.26A | 386.81 ± 3.28A | 3.60 ± 0.031 | 321.11 ± 2.39A | 2.97 ± 0.010 |
| del/ins(382) | 10,586 ± 65.52Ba | 378.41 ± 2.92Ba | 3.59 ± 0.027 | 314.42 ± 2.12Ba | 2.98 ± 0.009 | ||
| del/del(156) | 10,397 ± 83.94Bb | 374.49 ± 3.61Ba | 3.61 ± 0.034 | 308.61 ± 2.63Bb | 2.97 ± 0.012 | ||
| P value | < 0.0001** | 0.0010** | 0.7289 | < 0.0001** | 0.9571 | ||
| rs453960300 | CENPE | ins/ins(158) | 10,380 ± 83.33Aa | 375.15 ± 3.58 | 3.63 ± 0.034 | 307.63 ± 2.61Aa | 2.98 ± 0.012 |
| ins/del(381) | 10,586 ± 66.10b | 380 ± 2.95 | 3.61 ± 0.027 | 313.34 ± 2.15b | 2.98 ± 0.009 | ||
| del/del(207) | 10,764 ± 74.83Bc | 385.96 ± 3.26 | 3.61 ± 0.031 | 318.18 ± 2.38Bc | 2.97 ± 0.010 | ||
| P value | < 0.0001** | 0.0073** | 0.7589 | 0.0002** | 0.9461 | ||
| rs378415122 | CENPE | ins/ins(158) | 10,373 ± 83.79Aa | 373.03 ± 3.60Aa | 3.62 ± 0.034 | 306.81 ± 2.62Aa | 2.97 ± 0.012 |
| ins/del(386) | 10,547 ± 65.79Aa | 377.75 ± 2.93a | 3.60 ± 0.027 | 312.15 ± 2.13Aa | 2.97 ± 0.009 | ||
| del/del(207) | 10,785 ± 74.23B | 386.21 ± 3.23Bb | 3.60 ± 0.030 | 319.19 ± 2.36B | 2.97 ± 0.010 | ||
| P value | < 0.0001** | 0.0004** | 0.8913 | < 0.0001** | 0.9535 | ||
| rs134985825 | RETSAT | del/del(205) | 10,774 ± 75.77Aa | 383.94 ± 3.30ab | 3.58 ± 0.031 | 318.23 ± 2.40ab | 2.96 ± 0.010a |
| del/ins(370) | 10,563 ± 66.51B | 378.10 ± 2.95Aa | 3.60 ± 0.027 | 314.44 ± 2.15Aa | 2.98 ± 0.009ab | ||
| ins/ins(169) | 10,823 ± 79.45Aa | 388.92 ± 3.43Bb | 3.61 ± 0.032 | 323.7 ± 2.50Bb | 2.99 ± 0.011b | ||
| P value | 0.0003** | 0.0009** | 0.6500 | 0.0001** | 0.0237* | ||
| rs377943075 | ACSBG2 | del/del(62) | 10,746 ± 111.22 | 378.40 ± 4.68Aa | 3.56 ± 0.045 | 318.61 ± 3.42 | 3.00 ± 0.016ab |
| del/ins(294) | 10,776 ± 69.04 | 387.18 ± 3.03ab | 3.61 ± 0.028 | 319.22 ± 2.19 | 2.99 ± 0.009Ab | ||
| ins/ins(401) | 10,884 ± 63.81 | 391.00 ± 2.84Bb | 3.62 ± 0.026 | 319.31 ± 2.05 | 2.97 ± 0.008Ba | ||
| P value | 0.1334 | 0.0088** | 0.4393 | 0.9749 | 0.0052** | ||
| rs136639319 | TBC1D1 | ins/ins(19) | 10,752 ± 182.68 | 391.92 ± 7.47 | 3.65 ± 0.073ab | 320.14 ± 5.45 | 2.98 ± 0.026ab |
| del/ins(242) | 10,564 ± 72.44 | 383.75 ± 3.18 | 3.65 ± 0.030a | 314.38 ± 2.32 | 2.99 ± 0.010a | ||
| del/del(493) | 10,659 ± 64.49 | 380.06 ± 2.88 | 3.58 ± 0.027b | 314.42 ± 2.1 | 2.96 ± 0.009b | ||
| P value | 0.2493 | 0.1198 | 0.0224* | 0.5384 | 0.0209* | ||
| rs379188781 | NLK | ins/ins(277) | 10,676 ± 70.45 | 377.09 ± 3.11 | 3.56 ± 0.029 | 318.23 ± 2.26 | 2.99 ± 0.009Aa |
| del/ins(347) | 10,627 ± 67.41 | 381.09 ± 3.00 | 3.60 ± 0.028 | 314.48 ± 2.18 | 2.97 ± 0.009b | ||
| del/del(117) | 10,749 ± 90.28 | 384.24 ± 3.83 | 3.57 ± 0.037 | 315.92 ± 2.79 | 2.95 ± 0.013Bb | ||
| P value | 0.3389 | 0.1020 | 0.2615 | 0.1279 | 0.0047** | ||
| rs134444531 | NLK | ins/ins(197) | 10,748 ± 78.14 | 384.18 ± 3.40 | 3.58 ± 0.032 | 322.04 ± 2.47Aa | 2.99 ± 0.011a |
| del/ins(395) | 10,723 ± 65.31 | 386.23 ± 2.91 | 3.61 ± 0.027 | 317.93 ± 2.12a | 2.97 ± 0.009ab | ||
| del/del(150) | 10,563 ± 85.88 | 381.58 ± 3.68 | 3.63 ± 0.035 | 312.32 ± 2.68Bb | 2.96 ± 0.012b | ||
| P value | 0.0733 | 0.3026 | 0.4078 | 0.0012** | 0.0257* | ||
| ss2137349058 | MAP3K1 | ins/ins(152) | 10,482 ± 82.27Aa | 372.63 ± 3.54Aa | 3.58 ± 0.034 | 310.01 ± 2.58Aa | 2.97 ± 0.011 |
| del/ins(380) | 10,613 ± 66.30Aa | 376.47 ± 2.94Aa | 3.56 ± 0.027 | 314.12 ± 2.14Aa | 2.97 ± 0.009 | ||
| del/del(202) | 10,909 ± 77.27Bb | 390.47 ± 3.35Bb | 3.59 ± 0.032 | 323.13 ± 2.44Bb | 2.97 ± 0.011 | ||
| P value | < 0.0001** | < 0.0001** | 0.4863 | < 0.0001** | 0.8495 | ||
| ss2019489562 | UGDH | del/del(405) | 10,860 ± 64.35a | 387.55 ± 2.89 | 3.64 ± 0.027 | 318.31 ± 2.11 | 2.99 ± 0.009 |
| del/ins(4) | 9902 ± 384.75b | 376.58 ± 15.49 | 3.81 ± 0.153 | 299.74 ± 11.30 | 3.02 ± 0.056 | ||
| ins/ins(342) | 10,798 ± 66.31ab | 388.28 ± 2.95 | 3.64 ± 0.027 | 315.05 ± 2.13 | 2.97 ± 0.009 | ||
| P value | 0.0312* | 0.7267 | 0.5077 | 0.0532 | 0.0567 |
Note:*significant association at the significance level of 0.05; **significant association at the significance level of 0.01
The different superscripts (A,B within the same column with different superscripts indicate P < 0.01; a,b indicate P < 0.05) adjusted after correction for multiple testing indicate significant differences among the genotypes
MY milk yield, FY fat yield, FP fat percentage, PY protein yield, PP protein percentage