Construction of a high-density genetic map and mapping of QTLs for soybean (Glycine max) agronomic and seed quality traits by specific length amplified fragment sequencing

Zhang, Yanwei; Li, Wei; Lin, Yanhui; Zhang, Lifeng; Wang, Caijie; Xu, Ran

doi:10.1186/s12864-018-5035-9

Table 3 QTLs identified by ICIM

From: Construction of a high-density genetic map and mapping of QTLs for soybean (Glycine max) agronomic and seed quality traits by specific length amplified fragment sequencing

QTL	Chr^a	Left marker	Right marker	Genetic position (cM)			Physical position (bp)			LOD^b	PVE(%)^c	ADD^d	QTLs reported^e
QTL	Chr^a	Left marker	Right marker	Start	End	Distance	Start	End	Distance	LOD^b	PVE(%)^c	ADD^d	QTLs reported^e
qPH1–1	1	Marker4368622	Marker4217409	20.62	21.09	0.47	2,481,199	2,518,043	36,844	8.81	4.66	2.65	qPH-1-1 [14]
qPH5–1	5	Marker1701487	Marker1739184	0.81	1.29	0.48	3,041,062	3,116,230	75,168	6.65	9.30	5.05	qPH05–1 [26]
qPH6–1	6	Marker131534	Marker172599	76.69	77.50	0.81	17,471,671	18,171,743	700,072	12.68	7.62	5.02	plant height 17–6 [25]
qPH7–1	7	Marker5882404	Marker5762234	52.83	54.57	1.74	42,930,499	42,952,373	21,874	7.86	4.09	−3.21
qPH8–1	8	Marker2999607	Marker2981023	63.87	65.77	1.90	13,832,458	14,205,949	373,491	19.61	37.61	8.58
qPH8–2	8	Marker2962002	Marker2806136	174.90	175.24	0.34	45,424,861	45,433,165	8304	7.09	3.94	3.65
qPH16–1	16	Marker3112758	Marker3182372	81.56	84.52	2.96	6,932,336	7,381,056	448,720	4.19	2.66	−3.20
qPH17–1	17	Marker403730	Marker599785	41.57	44.66	3.08	15,333,360	15,937,896	604,536	8.28	11.88	5.78	qPH17–1 [26]
qPH19–1	19	Marker2154660	Marker1993462	33.77	35.14	1.36	38,782,154	38,837,787	55,633	17.29	11.56	6.43	plant height 6–4 [19]
qSW5–1	5	Marker1790368	Marker1713283	21.62	22.63	1.01	5,022,424	5,076,531	54,107	7.63	7.44	0.53	seed weight 25–1 [37]; seedweight 50–17 [67]
qSW5–2	5	Marker1954345	Marker1983847	100.58	101.74	1.16	37,080,533	37,099,610	19,077	3.56	3.48	−0.15
qSW9–1	9	Marker4666534	Marker4706727	96.89	101.89	5.00	13,567,369	13,932,346	364,977	8.78	9.53	0.53	seed weight 15–6 [28]
qSW11–1	11	Marker1480158	Marker1628838	2.55	5.27	2.72	1,243,413	1,813,344	569,931	6.20	5.17	0.38
qSW11–2	11	Marker1573686	Marker1603890	59.13	65.87	6.74	10,726,154	25,136,002	14,409,848	6.41	5.43	−0.37	seed weight 32–1 [68]
qSW12–1	12	Marker5558494	Marker5592791	18.47	23.12	4.65	3,998,395	4,965,904	967,509	17.83	22.77	−0.77
qSW13–1	13	Marker3613921	Marker3643913	103.37	104.05	0.68	29,371,757	29,486,787	115,030	15.12	18.55	−0.70	seed weight 6–6 [27]; seed weight 15–3 [28]; seed weight 49–14 [30]; seed weight 44–2 [29]
qSW15–1	15	Marker2580154	Marker2712589	22.49	26.30	3.81	13,761,334	13,880,441	119,107	12.51	12.21	−0.46	seed weight 2–3 [31]; seed weight 34–12 [32]
qSW20–1	20	Marker809331	Marker998443	87.30	89.41	2.11	35,452,608	35,720,703	268,095	5.97	5.26	0.39	seed weight 36–5 [32]
qSW20–2	20	Marker846233	Marker994705	165.31	169.83	4.52	45,972,286	46,673,050	700,764	3.96	3.97	0.35	seed weight 50–16 [67]
qOil1–1	1	Marker4303320	Marker4156660	61.50	66.40	4.90	35,010,738	37,973,804	2,963,066	22.89	30.25	0.42
qOil1–2	1	Marker4417270	Marker4449632	77.85	80.37	2.51	35,669,867	36,135,498	465,631	12.29	14.19	−0.24
qOil6–1	6	Marker172599	Marker293115	77.50	78.32	0.82	18,171,372	18,533,013	361,641	7.98	5.59	−0.22	seed oil 23–1 [28]
qOil10–1	10	Marker1115605	Marker1053573	9.00	9.81	0.82	5,243,953	5,694,905	450,952	11.41	8.12	−0.23
qOil10–2	10	Marker1281634	Marker1235885	180.85	183.08	2.23	41,520,254	41,545,664	25,410	23.61	20.17	0.37
qOil13–1	13	Marker3440932	Marker3635368	42.22	44.89	2.67	14,747,494	16,600,118	1,852,624	6.62	4.31	−0.09	seed oil 24–4 [33]
qOil19–1	19	Marker2188637	Marker2054649	8.92	10.22	1.31	34,198,684	34,698,502	499,818	12.69	8.92	−0.24	mqseed oil-022 [34]
qOil19–2	19	Marker2061159	Marker2270561	18.20	19.09	0.88	36,014,695	36,059,931	45,236	4.58	2.91	0.11	seed oil 2–7 [35]
qProtein1–1	1	Marker4337527	Marker4303320	58.32	61.50	3.18	14,274,646	37,973,804	23,699,158	11.05	17.68	−0.37
qProtein3–1	3	Marker6774045	Marker6819354	146.11	151.72	5.61	37,481,860	38,933,728	1,451,868	2.61	3.57	−0.14	seed protein 21–9 [25]
qProtein4–1	4	Marker6548332	Marker6730760	31.65	32.83	1.18	5,276,137	5,604,533	328,396	3.86	9.85	0.23	seed protein 19–1 [69]
qProtein5–1	5	Marker1695301	Marker1847746	74.43	77.65	3.23	32,108,882	32,889,638	780,756	2.90	4.05	−0.17
qProtein8–1	8	Marker2934032	Marker2871125	186.80	189.12	2.32	43,600,623	43,628,816	28,193	3.19	4.56	0.18	seed protein 21–1 [25]
qProtein10–1	10	Marker1235885	Marker1249450	183.08	184.24	1.16	41,545,293	42,037,748	492,455	6.94	16.83	−0.36	seed protein 27–5 [37]; qPro10a [38]
qProtein15–1	15	Marker2482668	Marker2379482	56.98	57.12	0.13	15,668,567	15,751,338	82,771	5.51	14.36	−0.25	seed protein 4–13 [36]
qProtein16–1	16	Marker3134296	Marker3275652	122.68	125.74	3.06	31,042,213	31,372,812	330,599	4.18	6.24	0.23

^achr, chromosome; ^b LOD, logarithm of odds; ^c PVE, phenotypic variance explained; ^d ADD, additive effect; ^e QTL names based on soybase.org and previous reports

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ISSN: 1471-2164

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