Table 3 Top genes from combined analysis of gene-based association statistics and differential gene expression in udders for each QTL
Gene | Location | Gene P value | RNA-seq FDR# | Putative function | Differential expression## |
|---|---|---|---|---|---|
CYP4X1 | BTA3: 99666161~  99,714,764 | 1.42e-7 | 3.47e-4 | MP: abnormal humoral immune response | Down |
AOAH | BTA4:60940663~ 61,125,662 | 1.51e-8 | 1.66e-11 | GO: negative regulation of inflammatory response | Up |
ENSBTAG00000032429 | BTA5: 32263608~  32,264,561 | 1.02e-9 | 4.71e-2 | NA | Down |
SLC6A12 | BTA5: 107649324~  107,666,752 | 1.14e-7 | 1.03e-3 | NA | Up |
NFKB1 | BTA6:23557311~ 23,679,508 | 1.33e-9 | 4.02e-2 | GO: inflammatory response, innate immune response | Up |
CSN1S2 | BTA6: 87262457~  87,280,936 | 2.60e-17 | 7.65e-3 | KEGG: Prolactin signaling pathway | Down |
SHROOM3 | BTA6: 93340874~  93,398,475 | 1.83e-20 | 1.67e-2 | NA | Down |
FBN3 | BTA7:18006365 ~  18,076,590 | 1.13e-8 | 5.92e-10 | NA | Down |
TAGAP | BTA9: 96806294~  96,815,764 | 2.09e-6 | 2.38e-3 | NA | Up |
SLC28A2 | BTA10: 65395125~  65,427,753 | 2.93e-8 | 2.75e-3 | NA | Up |
PDIA6 | BTA11:86834898~ 86,857,648 | 3.56e-10 | 3.58e-2 | NA | Up |
HCK | BTA13: 62106257~  62,151,619 | 1.48e-12 | 3.13e-22 | GO: innate immune response | Up |
ACOT7 | BTA16: 47827124~  47,934,930 | 6.66e-14 | 2.83e-2 | NA | Up |
HPN | BTA18:45971859~ 45,991,833 | 3.50e-11 | 4.53e-2 | NA | Down |
PLEKHH3 | BTA19: 43366278~  43,374,706 | 6.46e-13 | 1.73e-3 | NA | Down |
MROH2B | BTA20: 33456349~  33,528,569 | 5.00e-15 | 8.62e-5 | MP: abnormal T cell physiology and decreased T cell proliferation | Down |
ENSBTAG00000010730 | BTA23: 10627244~  10,628,260 | 5.98e-9 | 5.36e-6 | NA | Up |
CDIP1 | BTA25: 3650394~  3,673,924 | 2.83e-9 | 1.27e-2 | NA | Down |
CRTAC1 | BTA26: 18869719~  19,013,761 | 8.49e-9 | 3.72e-2 | NA | Down |