Bos taurus–indicus hybridization correlates with intralocus sexual-conflict effects of PRDM9 on male and female fertility in Holstein cattle

Table 4 Substitution effects on fertility traits in US Holstein cattle of BTA1 telomeric SNPs

SNP marker^a	MAF^b	β HCR^c	P_HCR	β SCR^c	P_SCR
ARS-BFGL-NGS-73542	0.4158	−0.226	0	0.015	0
ARS-BFGL-NGS-19721	0.3315	−0.280	0	0.025	0
ARS-BFGL-NGS-101788	0.3295	−0.250	0	0.023	0
BTA-105868-no-rs	0.2140	−0.126	1.4E-205	0.004	5.39E-21
BTB-01585499	0.2289	−0.315	0	0.044	0
ARS-BFGL-NGS-113905	0.0833	0.064	4.93E-26	−0.011	4.35E-56
ARS-BFGL-NGS-90894	0.1095	−0.208	0	0.034	0
ARS-BFGL-NGS-83544	0.0953	0.046	2.63E-15	−0.001	0.05
Hapmap26498-BTA-33060	0.2591	−0.259	0	0.042	0
Correlation with IL values^d	0.95	−0.78		0.60

^a Boldfaced names indicate SNP alleles with exceptional frequency and β values
^b Minor alleles were the same as in Table 2 and their frequencies were calculated based on 4,508,642 BeadChips
^c Marker effects on heifer and sire conception rates (HCR and SCR, with numbers of observations of 922,893 and 903,690, respectively) were estimated using PLINK Fisher’s exact test
^d Correlations (R) are with Table 2 β values. R was − 0.89 within the β values of Table 4

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