Table 3.

Haplotypes indicating reduced homozygosity in Swiss Holstein.

Namea	chr	Pos in Mbb	Analysis	Homozygous haplotype carrier			Allele frequency %	Known and novel associated genec	Associated traits
				observed	expected	deficient			Fertility	Birth	Survival
HH18	1	10.302–104.376	pgp	7	28	75%	2.39
HH19d	1	139.874–140.643	pgp	12	47	74%	3.00		GLd
HH20	2	134.477–135.148	pgp	1	14	93%	1.66
HH21e	7	7.872–10.433	trio/pgp	0	157	100%	5.46	NOTCH3			P2b
HH22	7	93.582–94.642	pgp	2	16	88%	1.73
HH23	8	15.562–16.863	pgp	5	25	80%	2.20			MBm
HH24	8	66.699–68.006	pgp	2	59	97%	3.36		NRh	BWm, CEm, MBm
HH3f	8	90.959–92.085	trio/pgp	0	10	100%	1.38	SMC2	GLm
HH5g	9	90.928–91.824	trio/pgp	0	30	100%	2.39	TFB1M	NRh
HH25	10	86.876–87.773	trio	5	20	75%	1.96	RIOX1	DFS
HH26	11	4.531–5.362	pgp	7	34	79%	2.56		GLd
HH27	13	7.083–8.297	pgp	2	17	88%	1.82		GLm
HH28	14	24.591–24.827	pgp	3	20	85%	1.98			SBd, SBm
HH29	14	58.128–59.238	pgp	14	52	73%	3.14			SBm, CEm
HH13h	18	60.932–62.101	trio	1	17	94%	1.81	KIR2DS1		BWd	P1
		62.070–63.045	pgp	2	22	91%	2.06
HH30	21	7.844–8.671	trio	1	24	96%	2.13			BWd, CEd, CEm
HH31	22	59.811–60.704	pgp	3	17	82%	1.80		GLd, GLm
HH32	23	32.773–33.726	pgp	1	13	92%	1.57			BWd, CEm
		33.545–34.948	trio	0	13	100%	1.55		GLd, IFLc	CEm
HH33	24	44.693–45.678	pgp	14	42	67%	2.82			SBd
HH34	25	36.162–37.330	trio /pgp	0	18	100%	1.86		GLm
HH35	26	3.359–4.235	pgp	7	31	77%	2.44	PCDH15		SBm
HH36	28	28.541–29.736	pgp	2	15	87%	1.71			CEm
		29.731–30.877	trio	2	26	92%	2.25
HH37	28	40.348–41.271	pgp	6	66	91%	3.54		GLd, GLm, IFLh	CEm, SBd, MBm
HH38	29	14.243–15.317	trio	0	14	1.00	1.66			CEm

BWd weight of calve at birth in kg, direct trait, BWm weight of calve at birth in kg, maternal trait, CEd direct calving ease, scored between 1-without help to 5-dystocia, CEm maternal calving ease, scored between 1-without help to 5-dystocia, DFS interval from calving to first service in days, GLd days from successful insemination to birth, direct trait, GLm days from successful insemination to birth, maternal trait, IFLc interval between first and last insemination for cows in days, IFLh interval between first and last insemination for heifer in days, MBm percentage of multiple births, NRh heifers non-return rate after 56 days, binary, P1 survival from day 3 up to 30th day of life, P2b survival of young bulls from 31 up to 183 days, SBd percentage of calves born alive, direct trait, SBm percentage of calves born alive, maternal trait.

^aHH meaning Holstein haplotype.

^bAccording to the reference sequence ARS-UCD1.2³¹.

^cAccording to NCBI Annotation Release 106⁹¹.

^dHaplotype co-localises with previously described haplotype HHB by Shuster et al. and Cole et al.^51,85.

^eHaplotype described before as 175.5 and 07–126 by VanRaden et al. and Sahana et al.^13,18.

^fHaplotype previously described by VanRaden et al., McClure et al., Sahana et al. and Wu et al.^13,18,19,87.

^gHaplotype previously described by Schütz et al. and Fritz et al.^26,27.

^hHaplotype previously described by Fritz et al.¹⁶.