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Table 3 Association results of the thirteen indels in eight genes on the five milk production traits (least squares mean ± SE)

From: Determination of genetic associations between indels in 11 candidate genes and milk composition traits in Chinese Holstein population

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

  1. Note:*significant association at the significance level of 0.05; **significant association at the significance level of 0.01
  2. 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
  3. MY milk yield, FY fat yield, FP fat percentage, PY protein yield, PP protein percentage