Table 3.

Top 0.1% ROH islands overlapped with reported QTLs for 5 populations

Population	Chromosome	Start (bp)	End (bp)	Number of SNPs	Associated QTL trait
SH	1	190,913,541	191,008,990	46	Feed intake
	2	144,110,859	144,201,790	45	Wattles weight
	3	37,006,451	37,110,698	54	Comb weight
	3	85,264,887	85,339,273	23	Comb weight
	3	85,362,178	85,530,321	89	Comb weight
	7	7,051,986	7,293,162	59	Ovary weight
	7	7,917,536	8,273,027	131	Ovary weight
	8	31,868	702,746	267	Ileum weight
	8	742,239	797,216	54	Ileum weight
	8	11,310,511	11,656,850	81	Ovary percentage
	11	2,781,379	3,782,297	125	Feed intake
NM	1	127,562,685	127,670,930	62	Bursa of Fabricius weight
	1	148,097,189	148,502,945	271	Fear-tonic immobility duration
	2	93,414,138	93,804,523	192	Feather-crested head
	3	37,019,870	37,444,374	202	Comb weight
	3	85,136,461	85,311,108	79	Comb weight
	3	85,335,481	85,477,712	77	Comb weight
	5	2,234,882	2,605,876	141	Body weight (28 days)
	7	8,089,149	8,139,910	12	Ovary weight
	7	7,239,376	8,061,927	104	Ovary weight
	8	198,456	643,706	177	Ileum weight
	11	3,367,829	3,766,928	130	Feed intake
	14	31,804	780,922	364	Wattles length
DZ	1	41,890,128	42,183,082	103	Yolk weight
	2	82,252,562	82,590,119	120	Feather-crested head
	2	82,995,651	83,236,647	99	Feather-crested head
	2	143,417,810	143,575,154	88	Wattles weight
	3	36,964,612	37,202,503	113	Comb weight
	3	37,203,796	37,293,935	33	Comb weight
	8	37,270	401,505	108	Ileum weight
	8	9,055,060	9,347,374	117	Ovary percentage
	8	9,712,707	10,369,442	222	Ovary percentage
	8	10,503,250	11,473,553	108	Ovary percentage
	8	11,475,230	11,998,950	129	Ovary percentage
	28	4,669,120	4,969,625	72	Abdominal fat weight
LZ	2	134,425,921	134,528,295	29	Wattles weight
	4	41,794,287	41,979,935	33	Ileum weight
	7	8,252,320	8,252,320	1	Ovary weight
	7	9,960,252	10,065,745	42	Ovary weight
	7	8,284,975	8,814,836	65	Ovary weight
	7	8,252,320	8,252,320	1	Comb weight
	7	9,960,252	10,065,745	42	Comb weight
	7	8,284,975	8,814,836	65	Comb weight, Receiving feather pecking
	7	9,960,252	10,065,745	42	Pectoralis minor weight
	8	781,122	1,127,960	67	Ileum weight, Body weight (36 days), Body weight (46 days), Spleen weight
	8	1,443,038	1,580,622	40	Ileum weight, Body weight (36 days), Body weight (46 days)
LW	1	127,516,561	127,828,483	102	Bursa of Fabricius weight
	1	150,304,925	150,605,645	120	Fear-tonic immobility duration
	1	160,765,702	160,956,991	87	Fear-tonic immobility duration
	2	73,319,835	73,368,670	11	Feather-crested head
	2	82,462,750	83,287,108	429	Feather-crested head
	3	60,530,655	60,739,692	107	Comb weight
	4	71,334,142	71,797,285	181	Gizzard weight
	8	357,766	657,445	112	Ileum weight
	12	19,551,518	19,936,175	171	Breast muscle pH

Note: SH, NM, DZ, LZ and LW denote Shigatse, Nyemo, Dagze, Ningychi and Lhasa white chicken population, respectively. ROHs highlighted in bold denote the shared QTL on chromosome 8 in 5 chicken populations