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

Gene name	Gene position (bp) 1	Nearest and most significant SNPs of GWAS			Traits	Raw p value	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]

^1,2Means the position on the bovine genome sequence of UMD3.1.66.

PP: protein percentage; FP: fat percentage.