Table 3. SNPs for HTDMY_slope and THI_slope validated in the Jersey data set and their effects in the discovery and validation data set.

			F-value			Effect discovery
Marker Name	Chr	Position	Discovery	Holstein validation	Jersey Validation	Discovery	Holstein validation	Jersey Validation
HTDMYslope
*BFGL-NGS-14740	9	13958461	14.0	7.3		−0.42	−0.26
BTB-02047616	9	32690344	13.5	3.9	6.5	0.43	0.21	0.28
BFGL-NGS-106238	9	33261215	10.9	4.4		−0.39	−0.21
BTA-112863-no-rs	9	34602197	13.1		5.4	−0.42		−0.31
BTB-00384830	9	35241353	15.2	6.7		−0.47	−0.27
BFGL-NGS-2259	9	38045164	14.0	9.3		0.43	0.30
BFGL-NGS-170	9	45345901	14.4	5.3		0.45	0.22
BFGL-NGS-38561	9	45373250	13.7	4.6		0.42	0.21
BTB-00402956	9	84338662	11.5	4.7		0.38	0.20
BFGL-NGS-48434	9	106226558	11.1	4.6		0.38	0.22
BTB-01568010	11	51716179	13.4		6.2	−0.44		−0.32
Hapmap26998-BTA-152949	13	13253202	11.2		5.0	−0.63		−1.79
BFGL-NGS-64510	13	41797328	14.1	4.4		0.44	0.21
BTA-71452-no-rs	13	62459428	13.3	6.5		0.43	0.26
BFGL-NGS-89312	13	62648774	11.0	6.1		0.38	0.25
BFGL-NGS-20976	13	62755245	14.7	4.0		0.47	0.21
BTB-00832114	22	4971802	11.3	5.0		0.50	−0.27
UA-IFASA-6407	22	22434343	11.0		5.1	−0.49		−2.20
Hapmap33956- BES4_Contig493_3026	22	43302073	11.2	5.0		0.38	−0.22
THIslope
BFGL-NGS-139	8	18499827	11.2	8.9		0.16		0.23
BFGL-NGS-89500	10	20564990	11.9	5.4		−0.15	−0.1
BFGL-BAC-38208	25	32862254	11.4	5.6		−0.12		−0.07
BFGL-NGS-30169	29	48329079	12.1	4.7	5	−0.13	−0.09	0.06

The effects are the result of inheriting one extra copy of the second allele of the SNP (alleles in alphabetical order and called in top-bottom format). The F-value thresholds were 10.84 (P<0.001) for discovery and 3.85 (P<0.05) for validation. Blank cells indicate non-significance.

^*Note that the ARS prefix in front of BFGL in the marker names has been removed for clarity.