Table 4 Overlapping region among the ROH islands across commercials (layers, broilers) and Red Junglefowl

Chicken group	CHR	Start position (bp)	Stop position (bp)	Number of SNPs	Size (bp)	Associated QTL	Associated Gene	Overlapping region with Qanbari et al. 2019^{^a}
Layers	2	27826712	29293102	63	1466.4
Broilers	1	96797489	97225788	1806	428.5	QTL:24387 “Antibody response to Newcastle virus”	ROBO2
	2	24570640	25113952	2198	217.3	QTL:24925 “Eggshell color”	GLCCI1, ICA1, UMAD1
	2	25685016	26072852	1515	387.8	QTL:24961 “Eggshell color”	GLCCI1, ICA1, UMAD1
	2	133839172	134258895	994	419.7
	2	143422482	143691103	1602	268.6			RJFs/Coms, RJFs/LRs
	3	84024798	84360723	1401	335.9
	5	30060267	31863497	7508	1803.2	QTL:153752 “Body weight 56 days”; QTL:14402 “Antibody titer to SRBC antigen”; QTL:15656 “Feather pecking”	Meis2a.1, uc_338	RJFs/Coms, RJFs/BRs, BRs/LRs
Red Junglefowl	1	56231495	56890000	11264	658.5
	1	57324733	59237097	29851	1912.4	QTL:57888 “Eggshell strength”; QTL:24832 “Visceral peritoneum pigmentation”	ENSGALG00000034601, DNM1L, ENSGALG00000032288, ENSGALG00000032522, PTN, ENSGALG00000029704, CREB3L2, ENSGALG00000030026, DENND5B, ENSGALG00000037580, ENSGALG00000033096, IPO8, ENSGALG00000040988, CCDC77, WEE2, ENSGALG00000037563, C7orf73, SLC13A4, IQSEC3, ENSGALG00000039636, SSBP1, TMTC1, ENSGALG00000027056, FGD4, ENSGALG00000012947, gga-mir-1593, SLC6A12 KDM5A, gga-mir-490, ENSGALG00000019291, WASH1, ENSGALG00000035394, KIAA1147, FAM180A BICD1, gga-mir-6700, PKP2, ENSGALG00000012958, DGKI, AGK, ENSGALG00000035141, SYT10, AMN1 SLC6A13, MTPN, B4GALNT3, CHRM2, ENSGALG00000012969, NINJ2, ENSGALG00000034403, ENSGALG00000034718, ENSGALG00000012919, FAM60A
	1	59262386	60460076	24311	1197.7	QTL:57881,”Eggshell strength”; QTL:57882,”Eggshell strength”; QTL:57886,”Eggshell strength”; QTL:57887,”Eggshell strength”; QTL:57888,”Eggshell strength”; QTL:57892 “Eggshell thickness”; QTL:57893,”Eggshell thickness”; QTL:57894 “Eggshell thickness”; QTL:57895 “Eggshell thickness”; QTL:57896 “Eggshell thickness”
	1	116333453	116675094	3428	341.6
	1	191191672	191740607	5886	548.9	QTL:64552 “Feed intake”
	2	52312949	52315876	55	2.9
	2	52841836	52869770	24	27.9
	2	94716992	94969646	2337	252.7
	2	95070084	95126392	676	56.3
	3	11705822	11714324	23	8.5
	3	12219370	12232316	120	12.9
	3	86109072	86406883	3322	297.8
	3	89916285	90709757	7549	793.5
	4	18397372	18778149	923	380.8	QTL:24914 “Average daily gain”
	5	41644677	42139793	3630	495.1
	5	42277347	42279153	7	1.8
	5	42432216	42799441	4007	367.2
	7	274155	653362	3321	379.2	QTL:24982 “Age at sexual maturity”

↵a Overlapping ROH islands with the putative selective sweeps identified in Qanbari et al. 2019. RJFs/Coms: Red Junglefowls vs. Commercials; RJFs/LRs: Red Junglefowls vs. Layers; RJFs/BRs: Red Junglefowls vs. Broilers; BRs/LRs: Broilers vs. Layers.