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Table 5 Detailed information on the nearest and most significant SNPs from previous GWAS to the 31 differentially expressed genes between the mammary gland of two cows with high milk protein and fat percentage and two cows with low protein and fat percentage

From: Transcriptional profiling of mammary gland in Holstein cows with extremely different milk protein and fat percentage using RNA sequencing

Gene name Gene position (bp)1 Nearest and most significant SNPs of GWAS Traits Raw pvalue Reference
  Distance Name Position (bp)2    
SAA3 Chr29: 26668046–26671801 49.5 Kb ARS-BFGL-NGS-24998 26721324 PP 2.96E-08 Cole et al., BMC Genomics, 2011 [8]
   4.2 Mb UA-IFASA-8605 30901735 FP, PP 4.90E-13, 1.50E-16  
HEATR7B2 Chr20: 33455667–33528569 23.2 Kb ARS-BFGL-BAC-2469 33433160 PP 1.21E-08 Jiang et al., Plos One, 2010 [6]
   2.6 Mb rs41640170 36097136 PP 1E-6.88 Schopen et al., J Dairy Sci, 2011 [9]
TRIB3 Chr13: 61176217–61187210 2.1 Mb BFGL-NGS-119420 59101909 FP, PP 1.14E-21, 3.49E-18 Cole et al., BMC Genomics, 2011 [8]
   9.3 Mb rs29021058 70524323 PP 0.0018 Kolbehdari et al., J Anim Breed Genet, 2009 [5]
SESN2 Chr2: 125698159–125714128 2.0 Mb ARS-BFGL-NGS-69013 123717269 FP, PP 1.46E-11, 3.26E-09 Cole et al., BMC Genomics, 2011 [8]
   2.7 Mb BTA-31250-no-rs 128437731 FP, PP 3.75E-10, 1.26E-24  
CHAC1 Chr10: 36598393–36600764 0.16 Mb Hapmap53714-rs29017586 36758715 FP, PP 9.84E-07, 6.64E-12 Cole et al., BMC Genomics, 2011 [8]
NR4A1 Chr5: 27977006–27992869 0.99 Mb ARS-BFGL-NGS-5790 26986116 FP, PP 3.26E-14, 9.43E-28 Cole et al., BMC Genomics, 2011 [8]
SAA1 Chr29: 26693328–26696498 24.8 Kb ARS-BFGL-NGS-24998 26721324 PP 2.96E-08 Cole et al., BMC Genomics, 2011 [8]
   4.2 Mb UA-IFASA-8605 30901735 FP, PP 4.90E-13, 1.50E-16  
ATF3 Chr16: 72820025–72832974 1.9 Mb ARS-BFGL-NGS-70836 74741746 PP 3.58E-07 Cole et al., BMC Genomics, 2011 [8]
   3.3 Mb ARS-BFGL-NGS-85980 76091078 FP, PP 6.46E-07, 8.33E-09  
RPL23A Chr11: 21526905–21574655 0.5 Mb ARS-BFGL-NGS-100459 22128569 PP 1.03E-24 Cole et al., BMC Genomics, 2011 [8]
   4.0 Mb BTB-01766447 17484533 FP, PP 4.51E-18, 8.90E-11  
CDH16 Chr18: 34733117–34743031 0.75 Mb ARS-BFGL-NGS-107749 33986486 FP, PP 2.54E-13, 3.55E-18 Cole et al., BMC Genomics, 2011 [8]
VEGFA Chr23: 17255946–17269998 2.9 Mb ARS-BFGL-NGS-29490 20166517 FP, PP 4.05E-20, 2.32E-26 Cole et al., BMC Genomics, 2011 [8]
   1.8 Mb rs29016156 15422973 PP 0.00099 Kolbehdari et al., J Anim Breed Genet, 2009 [5]
   0.19 Mb rs41640789 17061460 FP 0.00012 Kolbehdari et al., J Anim Breed Genet, 2009 [5]
BoLA-DQB Chr23: 25375269–25388620 4.9 Mb ARS-BFGL-NGS-72191 30279220 FP, PP 8.46E-17, 1.09E-28 Cole et al., BMC Genomics, 2011 [8]
ARID1B Chr9: 94882343–95271883 0.37 Mb ARS-BFGL-NGS-81082 94511747 FP, PP 3.00E-11, 2.37E-08 Cole et al., BMC Genomics, 2011 [8]
PTHLH Chr5: 82246521–82258858 1.5 Mb Hapmap51303-BTA-74377 83790390 FP 1.20E-06 Jiang et al., Plos One, 2010 [6]
   0.63 Mb ARS-BFGL-NGS-29557 81612132 FP, PP 2.97E-13, 5.97E-25 Cole et al., BMC Genomics, 2011 [8]
   6.2 Mb rs41590827 76049666 PP 0.00013 Kolbehdari et al., J Anim Breed Genet, 2009 [5]
   9.9 Mb rs41569048 92162494 PP 1E-4.72 Schopen et al., J Dairy Sci, 2011 [9]
H4 Chr23: 31665561–31667068 1.4 Mb ARS-BFGL-NGS-72191 30279220 FP, PP 8.46E-17, 1.09E-28 Cole et al., BMC Genomics, 2011 [8]
FAM71A Chr16: 72811910–72814133 2.5 Mb ARS-BFGL-NGS-85980 76091078 FP, PP 6.46E-07, 8.33E-09 Cole et al., BMC Genomics, 2011 [8]
THBS4 Chr10: 10945424–10999244 0.90 Mb BTB-00411816 11899342 FP, PP 2.71E-14, 3.45E-25 Cole et al., BMC Genomics, 2011 [8]
DDIT3 Chr5: 56285007–56307931 0.46 Mb ARS-BFGL-NGS-14781 56766165 FP 5.54E-10 Cole et al., BMC Genomics, 2011 [8]
M-SAA3.2 Chr29: 26755567–26759547 34.2 Kb ARS-BFGL-NGS-24998 26721324 PP 2.96E-08 Cole et al., BMC Genomics, 2011 [8]
   4.1 Mb UA-IFASA-8605 30901735 FP, PP 7.90E-13, 1.50E-16  
HIST1H2AC Chr23: 31579046–31589230 0.95 Mb BTA-68781-no-rs 30711619 FP, PP 1.17E-17, 6.08E-27 Cole et al., BMC Genomics, 2011 [8]
P4HA2 Chr7: 23480314–23513315 1.1 Mb Hapmap49309-BTA-78604 24655689 PP 4.34E-14 Cole et al., BMC Genomics, 2011 [8]
  1. 1,2Means the position on the bovine genome sequence of UMD3.1.66.
  2. PP: protein percentage; FP: fat percentage.