Table 2 QTLs surpassing the significance threshold (P < 5 × 10−7) for evidence of an association with the multifocal lesions.

From: Identification of loci associated with pathological outcomes in Holstein cattle infected with Mycobacterium avium subsp. paratuberculosis using whole-genome sequence data

BTA1

QTL start (bp)

QTL end (bp)

P value most significant SNP

SNP position2

Annotation

Genes in QTL3

No of significant SNPs in QTL

3

24233907

25325344

1.50E−07

24825344

Intergenic

TBX15, U6, SPAG17, GDAP2, WDR3, ENSBTAG00000048491, ENSBTAG00000051931

12

5

24941743

26254968

1.39E−08

25667192

Intron

VEZT, METAP2, USP44, MUCL1, GLYCAM1, PPP1R1A, PDE1B, NCKAP1L, ZNF385A, GTSF1, GPR84, ITGA5, COPZ1, NFE2, HNRNPA1, CBX5, SMUG1, HOXC5, HOXC4, HOXC6, HOXC13, HOXC8, HOXC9, HOXC10, HOXC11, HOXC12, U6, ENSBTAG00000052805, ENSBTAG00000053941, ENSBTAG00000029988, ENSBTAG00000049200, ENSBTAG00000023670 ,ENSBTAG00000049405, ENSBTAG00000010711, ENSBTAG00000053336, ENSBTAG00000049915, ENSBTAG00000049837, ENSBTAG00000048717, ENSBTAG00000052958, ENSBTAG00000055223, ENSBTAG0000005385, ENSBTAG00000036381, ENSBTAG00000053232, ENSBTAG00000029788, ENSBTAG00000053186, ENSBTAG00000052715, ENSBTAG00000052501, ENSBTAG00000051607, ENSBTAG00000051555

24

5

38788039

39790008

2.04E−07

39288039

Intron

PDZRN4, CNTN1, ENSBTAG00000001079

2

5

23274617

24292059

4.92E−07

23774617

Intergenic

UBE2N, MRPL42, SOCS2, CRADD, PLXNC1, CEP83, TMCC3, ENSBTAG00000033531, ENSBTAG00000049886, ENSBTAG00000053589, ENSBTAG00000050045, ENSBTAG00000052916

5

5

27260957

28354826

1.69E−08

27777338

Intergenic

KRT77, KRT1, KRT2, KRT73, KRT72, KRT74, KRT5, KRT6A, KRT6B, KRT75, KRT82, KRT84, KRT85, KRT89, KRT83, KRT81, KRT7, KRT80, SMIM41, ATG101, NR4A1, TAMALIN, ACVR1B, ACVRL1, ANKRD33, FIGNL2, SCN8A, U6, SLC4A8, ENSBTAG00000054953, ENSBTAG00000040019, ENSBTAG00000052798, ENSBTAG00000054816, ENSBTAG00000054136, ENSBTAG00000016166, ENSBTAG00000049194, ENSBTAG00000023471

6

11

12914642

14422761

1.01E−07

13611793

Intron

DYSF, ZNF638, PAIP2B, ATP6V1B1, FIGLA, NAGK, VAX2, CLEC4F, TEX261, CD207, ANKRD53, ADD2, TGFA, FAM136A, XDH, SRD5A2, ENSBTAG00000048791, ENSBTAG00000051968, ENSBTAG00000050557, ENSBTAG00000051045

4

11

5223771

6618872

1.66E−11

5755689

Intergenic

AFF3, CHST10, NMS, PDCL3, NPAS2, TBC1D8, CNOT11, RFX8, RNF149, CREG2, MAP4K4, ENSBTAG00000050215, ENSBTAG00000043158, ENSBTAG00000054755

7

11

9416584

10698629

1.98E−07

9916584

Intergenic

TACR1, POLE4, U6, HK2, SEMA4F, M1AP, RTKN, DOK1, MRPL53, LOXL3, WBP1, DCTN1, HTRA2, WDR54, AUP1, DOX1, C11H2orf81, MGC152281, TLX2, PCGF1, LBX2, CCDC142, MOGS, INO80B, SLC4A5, MOB1A, MTHFD2, BOLA3, TET3, DGUOK, ENSBTAG00000049427 , ENSBTAG00000050345, ENSBTAG00000010072, ENSBTAG00000050408, ENSBTAG00000049783

3

22

5865513

6865513

4.85E−07

6365513

Intron

STT3B, OSBPL10, GPD1L, CMTM8, CMTM7, ENSBTAG00000050895

1

22

2638700

4937859

8.62E−10

3138700

Intergenic

CMC1, AZI2, RBMS3, bta-mir-11990, U6, ENSBTAG00000022751, ENSBTAG00000050982, ENSBTAG00000048601, ENSBTAG00000052346

15

22

1280377

2574848

1.50E−10

2008232

Intergenic

U1, SEC61G, NEK10, U6, SLC4A7, 5S_rRNA, EOMES

18

23

17326599

18326599

4.92E−07

17826599

Intergenic

VEGFA, U6, MYMX, SPATS1, TMEM63B, HSP90AB1, CDC5L, CAPN11, NFKBIE, SLC9A1, SLC35B2, TMEM151B, AARS2, SUPT3H, 5S-rRNA, ENSBTAG00000050989, ENSBTAG00000049965, ENSBTAG00000050049, ENSBTAG00000050249, ENSBTAG00000050117, ENSBTAG00000053551, ENSBTAG00000053897

1

24

37183179

38191028

2.33E−07

37683179

Intron

EMILIN2, LPIN2, MYOM1, MYL12A, MYL12B, TGIF1, DLGAP1, SNORA70, ENSBTAG00000052283

31

  1. 1QTL location, 2SNP location in the genome assembly, 3Positional candidate genes are defined as genes that are located within 50 kb on either side of the identified QTL.
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