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

Table 3 Association analysis of BTA1 telomeric SNP haplotypes with male fertility

Haplotype^a	#	Freq^b	β^c	STAT	p	EMP1^d
GAGGAGGGGA	1	0.2760	0.0749	0.517	0.472	0.4718
AGAGGGGGAG	2	0.1190	−0.1120	0.670	0.413	0.4133
AGAAAGGGGA	3	0.0981	0.1570	0.969	0.325	0.3266
AAGGGGAGGA	4	0.0802	0.2560	2.100	0.148	0.1493
GGAAAGAGGA	5	0.0533	−0.0120	0.004	0.952	0.9518
GAGGAGGGAG	6	0.0530	−0.2140	1.050	0.306	0.3071
GGAAAGGGAA	7	0.0504	0.3230	2.070	0.151	0.1498
GAGGAGGGAA	8	0.0458	0.0161	0.005	0.945	0.9438
GAGGAAGAGA	9	0.0370	−0.5800	4.560	0.033	0.0325
GAGGGGGAGA	10	0.0257	0.1530	0.263	0.608	0.6043
GGGGAGGGAG	11	0.0184	0.5370	2.590	0.108	0.1073
AAGGAGGGAG	12	0.0154	−0.0296	0.006	0.937	0.9361
AAGGAGGGGA	13	0.0152	0.0878	0.037	0.847	0.8467
AGGGAGGGGA	14	0.0148	−0.2660	0.481	0.488	0.4859
AGGAAGGGAG	15	0.0124	−0.1210	0.090	0.764	0.7601
AGAAGGGAGA	16	0.0103	0.1830	0.131	0.717	0.7139

^a Boldfaced haplotype has a significantly low β value
^b Haplotype frequency was used to sort this table
^c Haplotype effects on male fertility were estimated using PLINK linear regression test
^d Empirical p value was the number of times the permuted haplotype-statistic exceeded p in 100,000 permutations

ISSN: 2730-6844