A medium density genetic map and QTL for behavioral and production traits in Japanese quail

Recoquillay, Julien; Pitel, Frédérique; Arnould, Cécile; Leroux, Sophie; Dehais, Patrice; Moréno, Carole; Calandreau, Ludovic; Bertin, Aline; Gourichon, David; Bouchez, Olivier; Vignal, Alain; Fariello, Maria Ines; Minvielle, Francis; Beaumont, Catherine; Leterrier, Christine; Le Bihan-Duval, Elisabeth

doi:10.1186/s12864-014-1210-9

BMC Genomics

Table 3 QTL for social, emotional and production traits in the F2 population

From: A medium density genetic map and QTL for behavioral and production traits in Japanese quail

Chromosome	Traits	Position (cM)	Nearest markers	Confidence interval (cM)	Flanking markers	Model	Level of significance ⁽¹⁾	QTL effect ⁽²⁾	Sires ⁽³⁾	Dams
CJA1	HeadNO	132	snp_soc_3409-snp_soc_3085	131-133	snp_soc_3409-snp_soc_3085	S + D	P < 0.01^†	0.49[0.15; 1.71]	2	5
	WEgg	193	snp_soc_3301-snp_soc_3547	179-203	snp_soc_3733-snp_soc_4023	S	P < 0.01	0.28[0.20; 0.49]	5	-
	AgrP	236	snp_soc_3475-snp_soc_2139	224-245	snp_soc_4684-snp_soc_2782	S	P = 0.025	0.40[0.28; 0.69]	3	-
	DistSR	281	snp_soc_4666-snp_soc_2881	278-285	snp_soc_4127-snp_soc_4345	S + D	P = 0.037	0.31[0.18; 0.48]	3	9
	W65	317	snp_soc_3213-snp_soc_4360	316-319	snp_soc_3481-snp_soc_3247	S + D	P < 0.01^†	0.51[0.17; 1.512]	3	9
	W17	319	snp_soc_4529-snp_soc_3247	316-328	snp_soc_3481-snp_FSIEL0M01BAIJK_30	S	P < 0.01^†	0.21[0.10; 0.46]	5	-
	W17	325	snp_F3SDQUK02BW99J_142-snp_soc_4532	323-325	snp_soc_1488-snp_FJXLD7H02JJLTX-0_66	S + D	P < 0.01^†	0.39[0.15; 0.79]	5	9
CJA2	AgrP	141	snp_soc_0368-snp_soc_0890	131-153	snp_FSIEL0M02D0BGS_129-snp_soc_2344	S	P = 0.039	0.28[0.16; 0.39]	5	-
	DistSR	149	snp_soc_1978-snp_soc_3824	146-155	snp_soc_4483-snp_soc_4405	S + D	P = 0.043	0.36[0.16; 0.65]	3	6
	DistSR	155	snp_soc_4405-snp_soc_3819	152-159	snp_soc_1978-snp_soc_2372	S	P = 0.024	0.22[0.10; 0.36]	4	-
	DistIso	319	snp_soc_3054-snp_soc_0012	302-337	snp_soc_4310-snp_soc_2553	S	P = 0.038	0.21[0.18; 0.26]	4	-
CJA3	WEgg	156	snp_soc_4141-snp_soc_3447	154-158	snp_soc_4141-snp_soc_3447	S + D	P < 0.01^†	0.53[0.18; 1.49]	5	3
	W65	156	snp_soc_4141-snp_soc_3447	148-161	snp_soc_0755-snp_soc_0929	S	P < 0.01^†	0.21[0.12; 0.32]	6	-
	NEgg	225	snp_soc_4257-snp_soc_2884	215-229	snp_soc_4257-snp_soc_3740	S	P = 0.025	0.31[0.15; 0.52]	5	-
	AFEgg	302	snp_soc_3800-snp_soc_4350	294-313	snp_soc_4338-snp_soc_3680	S	P = 0.026	0.39[0.27; 0.48]	4	-
CJA4	DistIso	105	snp_soc_2929-snp_soc_3811	100-118	snp_soc_0843-snp_soc_3328	S + D	P < 0.01^†	0.26[0.16; 0.70]	4	8
CJA5	W17	54	snp_soc_0024-snp_FSIEL0M02D2UBC_47	45-75	snp_soc_1561-snp_soc_2224	S	P < 0.01^†	0.24[0.10; 0.43]	4	-
	TI	59	snp_soc_3635-snp_soc_2699	38-68	snp_soc_2028-snp_soc_0641	S	P = 0.050	0.25[0.16; 0.34]	3	-
	W65	88	snp_soc_3485-snp_FSIEL0M02DEXEG_146	83-99	snp_soc_0380-snp_soc_3299	S + D	P < 0.01^†	0.30[0.12; 0.60]	4	9
	W17	90	snp_FSIEL0M02DEXEG_146-snp_ble_0738	87-101	snp_soc_3485-snp_ble_0738	S + D	P < 0.01^†	0.38[0.11; 0.80]	4	11
	W65	97	snp_soc_3485-snp_FSIEL0M02DEXEG_146	56-115	snp_FSIEL0M02D2UBC_47-snp_FSIEL0M02D7AG8_195	S	P < 0.01^†	0.26[0.17; 0.38]	4	-
CJA7	DistIso	96	snp_soc_2405-snp_soc_1537	92-99	snp_soc_2405-snp_soc_1826	S + D	P < 0.01	0.29[0.11; 0.56]	4	12
CJA8	W17	41	snp_soc_2116-snp_soc_2490	37-44	snp_soc_0876-snp_soc_1323	S + D	P = 0.021	0.30[0.15; 0.74]	3	10
	W17	56	snp_soc_2933-snp_soc_2335	53-60	snp_soc_2074-snp_soc_1161	S	P = 0.026	0.23[0.19; 0.26]	4	-
	HeadNO	65	snp_soc_1161-snp_FSIEL0M02DE4EL_249	53-69	snp_soc_2074-snp_soc_1987	S	P = 0.024	0.19[0.13; 0.29]	5	-
CJA9	DistSR	42	snp_soc_1270-snp_soc_0268	39-53	snp_soc_0028-snp_soc_0558	S + D	P < 0.01	0.43[0.19; 1.33]	3	7
CJA9	DistSR	55	snp_soc_2491-snp_soc_0558	37-60	snp_soc_0028-snp_soc_2117	S	P = 0.016	0.28[0.11; 0.49]	2	-
CJA10	DistIso	11	snp_soc_2706-snp_soc_0126	8-13	snp_FSIEL0M02C42PC_418-snp_FSIEL0M03HDV3S_67	S + D	P = 0.035	0.36[0.10; 0.81]	2	9
	W65	21	snp_soc_0359-snp_soc_2673	17-22	snp_soc_2915-snp_soc_1219	S + D	P = 0.034	0.42[0.13; 1.25]	3	8
	W17	30	snp_soc_0939-snp_FQU5R7M02IBV7P-0	27-31	snp_soc_0968-snp_FQU5R7M02IBV7P-0_110	S + D	P < 0.01	0.37[0.18; 0.65]	1	9
CJA11	TI	1	snp_soc_0708-snp_soc_1139	0-6	snp_soc_0157-snp_soc_2036	S + D	P < 0.01	0.35[0.18; 0.58]	4	11
	TI	5	snp_soc_0003-snp_soc_1569	0-26	snp_soc_0157-snp_soc_1166	S	P = 0.018	0.21[0.15; 0.38]	5	-
	DistSR	47	snp_soc_1642-snp_soc_1220	34-49	snp_soc_1436-snp_FSIEL0M01BMPFH_253	S	P = 0.023	0.21[0.13; 0.34]	4	-
CJA13	DistSR	4	snp_soc_0855-snp_FSIEL0M02D43ZD_185	0-15	snp_soc_1438-snp_soc_1000	S	P = 0.031	0.21[0.14; 0.28]	4	-
CJA15	DistIso	63	snp_soc_1598-snp_ble_0416	60-65	snp_soc_2236-snp_ble_0416	S	P = 0.033	0.31[0.18; 0.52]	3	-
CJA18	NEgg	3	snp_soc_0250-snp_soc_0714	0-22	snp_soc_2064-snp_soc_0279	S + D	P = 0.025	0.45[0.19; 1.41]	4	-
	W65	18	snp_soc_2042-snp_soc_1172	13-26	snp_soc_2085-snp_soc_1907	S + D	P < 0.01	0.33[0.19; 0.50]	3	9
	W65	42	snp_soc_0424-snp_soc_0163	20-50	snp_soc_1172-snp_soc_0772	S	P < 0.01	0.23[0.12; 0.38]	4	-
	WEgg	61	snp_soc_0010-snp_soc_0395	57-75	snp_soc_1648-snp_soc_1792	S	P < 0.01	0.29[0.15; 0.51]	5	-
	WEgg	62	snp_soc_0395-snp_soc_0042	58-73	snp_soc_0010-snp_FZVM8I102DNHYX_129	S + D	P < 0.01	0.34[0.13; 0.79]	5	3
CJA19	AFEgg	4	snp_soc_0193-snp_soc_0715	0-10	snp_soc_1697-snp_soc_0483	S + D	P = 0.029	0.36[0.24; 0.51]	5	4
	DistIso	8	snp_soc_0715-snp_soc_0483	6-16	snp_soc_0193-snp_soc_1227	S + D	P = 0.020	0.29[0.14; 0.50]	4	9
	DistIso	14	snp_soc_0396-snp_soc_1227	0-20	snp_soc_1697-snp_soc_1227	S	P = 0.039	0.23[0.10; 0.29]	4	-
CJA23	HeadNO	57	snp_soc_1394-snp_ble_033	45-63	snp_soc_1286-snp_FSIEL0M02EPU6F_133	S	P < 0.01	0.20[0.14; 0.30]	5	-
CJA26	DistSR	21	snp_FQU5R7M02I6ZE8-0_225-snp_soc_1180	19-27	snp_soc_1867-snp_soc_0288	S	P = 0.025	0.30[0.15; 0.46]	3	-

⁽¹⁾Level of significance of the QTL at the chromosome level; ^†indicates that the QTL is genome-wide significant; ⁽²⁾The effect of the QTL was estimated as the average of the significant parent’s effects (P < 0.05) and expressed in phenotypic standard deviation. The minimum and the maximum effects are given between square brackets; ⁽³⁾Number of significant parents.

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