Homozygous haplotype deficiency reveals deleterious mutations compromising reproductive and rearing success in cattle

Table 1 Four regions with homozygous haplotype deficiency

Abbreviation	Chr	Start position	End position	Fq.	Homozygous animals			Number of matings		Difference in insemination success		Difference in stillbirth rate		Difference in juvenile mortality
					exp	obs	P	non-risk	risk	%	P	%	P	Day 10	Day 365	P
FH1	1	1,668,494	6,187,555	2.9	20	0	4.8 × 10⁻⁹	164,324	14,013	−6.64	7.1 × 10⁻²⁵	−0.4	0.64	−0.3	0.4	0.004
FH2	1	96,169,900	97,123,740	4.1	37	2	1.2 × 10⁻¹³	109,386	8,428	−1.57	0.014	0.7	0.53	1.6	6.6	2.9 × 10⁻⁴¹
FH3	10	26,929,817	35,479,280	3.3	41	3	2.1 × 10⁻¹⁴	136,286	10,936	−4.06	2.4 × 10⁻¹⁷	1.4	0.12	1.8	4.3	1.3 × 10⁻²⁶
FH4	12	10,859,759	12,805,107	3.3	33	0	1.3 × 10⁻¹⁴	86,464	4,793	−5.99	2.9 × 10⁻¹¹	0.4	0.39	0.5	0.7	0.34

Insemination success, the proportion of stillborn calves and juvenile mortality of descendants from risk matings were analyzed for four haplotypes with a significant deficit in homozygous animals. The physical position of the deleterious haplotypes was obtained based on the UMD3.1 assembly of the bovine genome.

ISSN: 1471-2164