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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