Table 2.

QTL associated with direct calving difficulty¹

Breed	BTA	Start	End	No. SNP	Strongest SNP	Strongest SNP position	+ Allele	+ Allele freq	P-value	SNP effect MCD	SNP effect PM	No. genes	Candidate gene(s)
AA	2	58317099	58398267	4	rs799051476a	58388382	G	0.012	8.76 × 10−10	++	++	0	N/A
	4	21958676	22090437	38	rs449164295b	22090437	T	0.029	2.36 × 10−8	−−	++	1	ETV1
	6	88842546	88935317	9	rs800690355a	88935317	A	0.007	1.52 × 10−8	++	++	0	GC
CH	2	1850243	1938014	44	rs110820498a	1925667	T	0.090	5.74 × 10−9	−	++	1	PLEKHB2
	2	3201163	3241531	14	rs384824032a	3241507	T	0.240	6.09 × 10−9	−	++	0	N/A
	2	3887357	3902265	20	rs210421829a	3899839	A	0.457	5.53 × 10−9	−	++	0	N/A
	2	5905672	6720629	192	rs482419628a	6630781	G	0.054	1.09 × 10−22	−−	++	9	MSTN
	2	6727404	7212998	260	rs799943285b	6808074	G	0.058	4.95 × 10−21	−−	++	1	SLC40A1 †
	2	7334284	7678545	6	rs798702162a	7609482	G	0.051	8.61 × 10−13	−−	++	1	COL3A1
	4	118379848	118960619	12	rs377892980d	118932719	C	0.990	2.80 × 10−8	−	++	4	RNF32 † , LMBR1, NOM1
	7	111633395	111639100	2	rs383826293a	111633395	T	0.008	2.49 × 10−8	−	++	0	N/A
	8	99124662	99444787	4	.a	99124662	C	0.988	3.04 × 10−8	++	+	2	KLF4
	15	80425653	80425659	2	rs42805962d	80425653	C	0.008	5.81 × 10−11	−−	−−	1	ENSBTAG00000035988 †
	20	27639892	28292172	14	.a	27888972	G	0.011	1.74 × 10−8	−	++	1	ISL1
	20	40735668	41092503	7	rs717218519b	41009804	G	0.013	6.01 × 10−9	++	++	1	NPR3 †
	22	988356	1889045	11	.a	1889045	A	0.007	3.55 × 10−9	NA	−	8	SLC4A7
	23	21839465	21839742	4	rs460572227b	21839717	T	0.007	4.87 × 10−8	−	++	1	ENSBTAG00000046237 †
	25	22436613	22497098	2	rs385805439c	22458425	T	0.005	6.56 × 10−9	NA	+	1	RBBP6 †
	28	20486363	20541765	14	rs208597252a	20506931	C	0.012	3.23 × 10−9	−−	−−	0	N/A
	28	24368554	24389785	3	rs210629062a	24368554	C	0.035	3.61 × 10−8	++	+	0	N/A
	28	45109768	45388748	24	rs476163771a	45359784	A	0.986	8.80 × 10−11	++	−−	0	TMEM72
HF	14	24847507	27124281	262	rs134489103d	24953585	T	0.968	1.51 × 10−8	+	−	17	PLAG1
	18	58141989	58407174	8	rs381577268d	58141989	T	0.025	1.63 × 10−9	+	−	4	ZNF613 †
LM	1	147046621	147071689	5	.b	147046683	G	0.009	3.21 × 10−9	−	+	1	SLC19A1 †
	2	5751482	5769372	52	rs211366913d	5751482	G	0.048	6.19 × 10−9	−	++	1	MFSD6 †
	2	6692259	6837692	94	rs137213740a	6696029	T	0.909	7.69 × 10−11	−−	++	1	SLC40A1
	5	85007482	85162856	3	rs111563671c	85162856	T	0.972	2.29 × 10−8	+	+	1	KRAS †
	7	57666736	58298162	4	rs133717945a	57666736	A	0.067	5.43 × 10−9	+	+	1	ENSBTAG00000019739
	26	2392863	2461384	5	rs111672216a	2461384	T	0.007	6.67 × 10−10	++	−	0	N/A
	28	40647337	42372750	2	rs378942567a	42372750	G	0.023	3.57 × 10−8	−	++	16	PPYR1

¹No. SNP is the number of SNP within the QTL with a P-value ≤ 5 × 10⁻⁸. P-value is the P-value of strongest SNP association. + Allele is the allele that had a positive SNP effect on direct calving difficulty. SNP effect MCD is the QTL-lead SNP’s direction effect for maternal calving difficulty; + represents SNP effects in the same direction, ++ represents the same direction and large SNP effect size for MCD, i.e., a SNP effect size in the top 20%, − represents opposing SNP effects and −− represents opposing SNP effect directions that have a large SNP effect size. N/A (Non-applicable) was if the SNP wasn’t present in that dataset due to allele frequency. SNP effect PM similar to MCD but represents the SNP effects for PM. No. of genes is the number of genes in the QTL. If no gene was present in the QTL the nearest functional candidate gene within 250 kb was chosen. ^aintergenic, ^bintronic, ^cupstream gene variant, ^ddownstream gene variant, ^†gene in which the most significant SNP within the QTL was identified in.