Table 3. Runs of Homozygosity (ROH) shared by at least 33 percent of all individuals (N = 942) across four warmblood horse breeds with candidate genes for positive selection.

Chr	position (bp)	length of ROH (bp)	SNPs in ROH	samples (%) sharing the entire ROH	annotated genes in ROH	candidate genes	QTL trait (number of QTL) 1 [47]
1	684,531–1,346,011	661,480	20	33	5
	21,937,435–22,763,212	825,777	20	33	-
2	96,475,507–97,254,688	779,181	16	33	1
	100,347,967–100,961,025	613,058	19	35	5
3	19,390,495–20,068,977	678,482	20	35	14
	22,774,232–23,723,805	949,573	24	34	19
	39,317,467–40,650,253	1,332,786	20	34	24		white2 (1), tympany3 (6)
	75,797,341–76,393,636	596,295	19	34	13	THEGL	white (1), height4 (2)
	118,524,879–119,456,949	932,070	38	37	18	MYL5
4	15,120,680–17,415,564	2,294,884	40	35	24	IGFBP1, IGFBP3
	19,079,166–20,235,933	1,156,767	19	40	10	SPATA48, ZPBP
	52,587,338–53,148,501	561,163	22	36	4
5	41,546,213–42,335,441	789,228	24	33	41
	55,293,804–56,274,553	980,749	28	34	12	WNT2B
6	29,004,794–30,308,246	1,303,452	28	34	15	WNT5B	cannon 5(1)
	34,084,026–35,230,778	1,146,752	25	35	51
	41,218,272–42,713,648	1,495,376	25	37	18
7	36,663,831–37,338,232	674,401	23	33	6
	39,405,488–41,489,510	2,084,022	47	34	7
8	22,113,249–23,719,695	1,606,446	32	34	43		height (1)
	36,329,323–37,420,192	1,090,869	20	34	12		height (4)
9	43,718,150–44,540,142	821,992	20	38	13
11	21,692,258–22,655,280	963,022	19	33	35	KRT complex, IGFBP4, ZPBP2	hair 6(3), coat7 (1),
	24,038,863–24,990,015	951,152	16	38	27	IGF2BP1 HOXB complex	hair (1)
	26,909,643–27,819,093	909,450	33	37	4
	32,322,500–33,580,784	1,258,284	29	35	39	TEX14	insect8 (2)
15	44,286,531–45,105,390	818,859	16	38	16
	67,528,191–68,378,301	850,110	18	37	7
17	20,690,428–22,444,884	1,754,456	28	33	22		racing 9 (1)
18	48,042,468–49,758,616	1,716,148	39	36	23	NOSTRIN, MYO3B	racing (1)
	58,962,761–59,847,420	884,659	22	34	8		weight10 (1)
22	4,359,148–4,944,734	585,586	15	35	5	RALGAPA2 CFAP61
	15,520,818–16,561,219	1,040,401	18	36	6	BMP2
	26,103,882–26,914,845	810,963	18	34	20	GDF5, SPAG4,
25	26,318,531–26,942,120	623,589	18	43	33	*
28	14,158,917–15,080,406	921,489	19	34	7	KITLG
	45,594,055–46,121,975	527,920	17	34	29

* suspected copy number variation

¹ selection signature overlaps with QTL position, data downloaded from AnimalGenome.ORG animal QTL database (accessed 4 February 2019)

² white markings

³ guttural pouch tympany

⁴ height of withers

⁵ cannon bone circumference

⁶ hair density

⁷ coat texture

⁸ insect bite hypersensitivity

⁹ racing ability

¹⁰ body weight