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Table 2 Identified bovine SNPs associated with rumen microbial taxa

From: Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle

SNP

Position

Alleles

Gene

Consequence

Associated Taxon

FDR3

P

FE4

rs109763257

1:155345571

C/T

NC region1

NA2

Spirochaetes (phylum)

0.173

1.20e−05

 

Spirochaetes (class)

0.190

9.43e−06

 

rs43235157

1:156294225

A/G

TBC1D5

Intron variant

Ruminococcus (genus)

0.191

1.33e−05

DMI

rs110461771

2:92080445

C/T

RAPH1

Intron variant

Ruminococcus (genus)

0.164

3.88e−06

FCR

rs29003226

3:51976646

C/G

NC region1

NA2

YRC22 (genus)

0.107

2.53e−06

 

rs41257422

5:6266261

A/G

NC region1

NA2

YRC22 (genus)

0.155

7.33e−06

RFIf

rs41656119

7:83551608

A/G

NC region1

NA2

Ruminococcus (genus)

0.191

1.80e−05

 

rs110670001

10:10930797

C/T

NC region1

NA2

BS11 (family)

0.006

1.43e−07

 

Unclassified BS11 (genus)

0.006

1.43e−07

 

rs110071335

10:81981544

A/C

SMOC1

Intron variant

Ruminococcus (genus)

0.191

1.46e−05

 

rs109402398

12:37678844

C/T

NC region1

NA2

[Paraprevotellaceae] (family)

0.105

4.95e−06

 

rs110410597

13:28095457

C/T

OPTN

Intron variant

Spirochaetes (phylum)

0.173

2.45e−05

 

Spirochaetes (class)

0.190

2.69e−05

 

rs41604961

13:28115879

C/T

OPTN

Intron variant

Spirochaetes (phylum)

0.173

2.45e−05

 

Spirochaetes (class)

0.190

2.69e−05

 

rs109122489

13:28149879

C/T

MCM10

Intron variant

Spirochaetes (phylum)

0.173

2.45e−05

 

Spirochaetes (class)

0.190

2.69e−05

 

rs110469969

13:28183389

C/T

UCMA

Intron variant

Spirochaetes (phylum)

0.173

2.45e−05

 

Spirochaetes (class)

0.190

2.69e−05

 

rs109961459

13:24202640

A/G

NC region1

NA2

Unclassified Lachnospiraceae (genus)

0.111

2.61e−06

 

rs41627213

16:78415671

C/T

DENND1B

Intron variant

[Paraprevotellaceae] (family)

0.070

1.65e−06

 

rs41911152

19:30220186

C/T

NC region1

NA2

Lentisphaerae (phylum)

0.070

1.64e−06

DMI

Lentisphaeria (class)

0.070

1.64e−06

 

Victivallales (order)

0.034

8.05e−07

 

Victivallaceae (family)

0.038

8.92e−07

 

Unclassified Victivallaceae (genus)

0.038

8.92e−07

 

rs110728224

26:32497450

A/G

NC region1

NA2

Spirochaetes (phylum)

0.173

4.73e−06

 

Spirochaetes (class)

0.140

3.31e−06

 

rs110448978

26:37871121

C/T

KCNK18

Downstream variant

Unclassified [Mogibacteriaceae] (genus)

0.187

4.40e−06

ADG

DMI

FCR

rs42620822

27:42776720

A/G

NC region1

NA2

Spirochaetes (class)

0.196

3.24e−05

 
  1. 1NC region = non-coding region
  2. 2NA = not available
  3. 3For each microbial taxonomic feature, P value was adjusted into genome-wide false discovery rates (FDRs) using the Benjamini-Hochberg method. Associations with FDR < 0.1 were considered significant, and associations with 0.1 < FDR < 0.2 were regarded as suggestively significant
  4. 4FE = feed efficiency traits
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Microbiome

ISSN: 2049-2618

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