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Table 2 Potential candidate genes related to the identified regions associated with endoparasite resistance traits

From: Genome-wide associations and functional gene analyses for endoparasite resistance in an endangered population of native German Black Pied cattle

BTA

Positiona

No. of associations (total no. of SNP markers)b

Position of maximum association (P-value)

Gene symbol

Referencec

rFEC-GIN

 4

93,956,587 – 94,148,561 §

1 (33)

94,017,547 (1.97 × 10− 6) *

AHCYL2

ENSBTAG00000001754 | 532836

 5

6,777,101 – 7,678,220 §

1 (197)

7,162,997 (3.59 × 10− 6) *

NAV3

ENSBTAG00000009852 | 528870

 18

15,929,200 – 16,156,356 §

1 (10)

16,111,659 (2.79 × 10− 6) *

PHKB

ENSBTAG00000004806 | 511783

 22

890,106 – 1,107,725 §

1 (25)

992,265 (6.41 × 10− 6) *

EGFR

ENSBTAG00000011628 | 407217

 24

61,568,972 – 61,792,092 §

2 (53)

61,565,663 (1.02 × 10− 5) *#

PHLPP1

ENSBTAG00000045832 | 615982

rFEC-FH

 1

50,331,575 – 50,562,844 §

1 (54)

50,365,140 (5.38 × 10−6) *

ALCAM

ENSBTAG00000000088 | 281614

rFLC-DV

 2

113,274,587 – 113,287,683 §

1 (2)

113,291,934 (2.10 × 10−9) **

FAM124B

ENSBTAG00000038700 | 506367

113,369,961 – 113,487,279 §

2 (23)

113,478,686 (6.59 × 10− 7) *

CUL3

ENSBTAG00000021769 | 534325

 5

1,524,095 – 1,565,010 §

3 (13)

1,562,117 (1.07 × 10−6) *#

TPH2

ENSBTAG00000020792 | 100336620

6,777,101 – 7,678,220 §

2 (197)

6,916,388 (7.69 × 10–8) **

NAV3

ENSBTAG00000009852 | 528870

65,386,934 – 65,454,111 §

1 (4)

65,424,614 (1.29 × 10−6) *

SLC5A8

ENSBTAG00000011525 | 615734

68,385,645 – 68,649,661 §

2 (72)

68,420,453 (1.42 × 10− 6) *

CHST11

ENSBTAG00000010644 | 528860

97,079,894 – 97,101,600 §

1 (13)

97,105,569 (6.46 × 10− 6) *

EMP1

ENSBTAG00000036078 | 786490

97,262,002 – 97,299,627 §

1 (9)

97,265,477 (9.46 × 10− 7) *

FAM234B

ENSBTAG00000014322 | 512120

101,572,243 – 101,708,458 §

4 (17)

101,571,894 (8.13 × 10−6) *#

RIMKLB

ENSBTAG00000003291 | 538579

 21

12,838,632 – 13,098,198 §

2 (58)

12,918,304 (1.73 × 10− 7) **

MCTP2

ENSBTAG00000013689 | 532150

32,107,362 – 32,113,036

1 (1)

32,113,699 (8.56 × 10−6) *

ISL2

ENSBTAG00000016651 | 786913

32,118,844 – 32,548,944 §

24 (26)

32,119,934 (8.56 × 10− 6) *#

SCAPER

ENSBTAG00000007382 | 100140107

32,577,840 – 32,595,999 §

2 (2)

32,580,916 (8.56 × 10−6) *#

RCN2

ENSBTAG00000015780 | 512717

 24

7,684,880 – 8,100,543 §

4 (113)

8,077,784 (2.71 × 10−9) **

DOK6

ENSBTAG00000046957 | 100336967

21,641,932 – 21,691,820 §

2 (8)

21,676,840 (5,41 × 10−6) *#

GALNT1

ENSBTAG00000011206 | 104975742

28,992,666 – 29,241,119

1 (60)

29,087,857 (9.04 × 10− 6) *

CDH2

ENSBTAG00000021190 | 281062

 26

4,520,359 – 5,584,422 §

1 (170)

4,781,510 (6.76 × 10−6) *

PCDH15

ENSBTAG00000045905 | 100140108

  1. aGene position (start-end) in NCBI annotation build on assembly UMD 3.1.1 (genes with differing start and/or end positions in NCBI 105 and ENSEMBL 90 are denoted by §)
  2. bNumber of associations that reached the suggestive chromosome-wide significance threshold (pCand, range: p = 7.47 × 10− 6 on BTA 1 to p = 2.18 × 10− 5 on BTA 28) or the Bonferroni-corrected genome-wide significance threshold (pBonf = 4.47 × 10− 7) based on the position of the identified candidate gene ±5 kb up- and downstream
  3. cEnsembl ID | Entrez ID
  4. *above pCand
  5. **above pBonf
  6. #Including several marker associations revealing the same p-value, the association bases on the SNP marker with the lowest base pair position
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BMC Genomics

ISSN: 1471-2164

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