Multi-omics analysis reveals novel loci and a candidate regulatory gene of unsaturated fatty acids in soybean (Glycine max (L.) Merr)

Zhao, Xunchao; Zhan, Yuhang; Li, Kaiming; Zhang, Yan; Zhou, Changjun; Yuan, Ming; Liu, Miao; Li, Yongguang; Zuo, Peng; Han, Yingpeng; Zhao, Xue

doi:10.1186/s13068-024-02489-2

Biotechnology for Biofuels and Bioproducts

Table 2 QTNs identified for unsaturated fatty acid content using the QTN detection model in 3VmrMLM

From: Multi-omics analysis reveals novel loci and a candidate regulatory gene of unsaturated fatty acids in soybean (Glycine max (L.) Merr)

Trait	Year	SNP	Chr	Position (bp)	LOD	Additive effect	Dominant effect	Variance	r² (%)	p-value	Known QTL	References
Oleic	2013	rs25094202	2	25094202	25.92	− 1.53	− 0.54	0.35	3.88	1.2E−26
		rs6124789	4	6124789	19.04	− 1.22	− 0.43	0.31	3.45	9E−20
		rs40652518	4	40652518	19.99	− 1.23		0.76	8.48	8.5E−22
		rs14903097	6	14903097	6.23	− 0.39	− 1.78	0.14	1.59	5.9E−07
		rs29444284	6	29444284	11.36	0.68	− 2.62	0.58	6.50	4.4E−12
		rs32503987	6	32503987	17.07	− 1.11		0.57	6.41	7.6E−19
		rs545702	7	545702	28.94	1.61	1.24	0.84	9.37	1.2E−29
		rs29716728	7	29716728	3.32	0.44	− 0.06	0.17	1.96	0.00048
		rs19742379	8	19742379	11.13	0.01	7.58	0.72	8.10	7.5E−12
		rs2762447	9	2762447	13.18	− 0.17	− 3.02	0.70	7.87	6.6E−14
		rs18612544	9	18612544	4.55	0.04	3.75	0.26	2.95	2.8E−05
		rs15583833	11	15583833	6.67	0.64		0.28	3.12	3E−08
	2014	rs25962449	3	25962449	13.08	− 0.98	− 0.06	0.21	3.10	8.3E−14
		rs9480030	4	9480030	23.29	1.37		0.74	10.93	3.9E−25
		rs24966112	4	24966112	10.53	− 0.91	0.26	0.22	3.23	2.9E−11
		rs37372282	7	37372282	6.50	− 0.65		0.27	3.95	4.5E−08
		rs13246407	8	13246407	12.51	− 0.79	4.87	0.45	6.75	3.1E−13
		rs4633292	9	4633292	6.26	0.63	0.60	0.36	5.41	5.5E−07
		rs7608184	11	7608184	7.75	− 0.69	2.38	0.33	4.96	1.8E−08
		rs86980	14	86980	6.96	0.67		0.36	5.27	1.5E−08
		rs21488603	16	21488603	7.07	− 0.57	1.80	0.35	5.25	8.6E−08
		rs42357728	19	42357728	9.79	0.78	2.22	0.23	3.48	1.6E−10
	2015	rs14131618	2	14131618	9.20	0.62	5.83	0.37	5.75	6.3E−10
		rs648720	3	648720	7.62	− 0.21	7.18	0.59	9.19	2.4E−08
		rs1225280	12	1225280	4.41	− 0.58	− 0.73	0.32	4.92	3.9E−05
		rs16802809	13	16802809	8.65	− 0.83		0.30	4.73	2.8E−10
		rs19292381	13	19292381	9.58	− 0.47	5.11	0.70	10.91	2.7E−10
		rs30304375	13	30304375	3.38	0.07	3.91	0.25	3.81	0.00042
		rs23631249	17	23631249	6.54	0.72		0.45	6.94	4.1E−08	Seed oleic 6–9	[22]
		rs37263037	17	37263037	7.38	0.74	− 1.42	0.28	4.36	4.2E−08	Seed oleic 6–9	[22]
Linoleic	2013	rs39587481	2	39587481	16.48	− 0.83	− 0.77	0.15	1.93	3.3E−17
		rs28569907	3	28569907	24.14	− 1.09	− 0.06	0.26	3.36	7.3E−25
		rs41402037	4	41402037	12.32	0.70	0.45	0.37	4.68	4.8E−13
		rs48166843	4	48166843	11.78	− 0.68	0.44	0.17	2.22	1.7E−12
		rs4602961	9	4602961	12.39	0.69	− 1.08	0.45	5.71	4.1E−13
		rs11516441	9	11516441	15.27	− 0.80		0.37	4.75	5E−17
		rs38142875	9	38142875	12.93	0.54	− 4.23	0.31	3.99	1.2E−13
		rs9167160	10	9167160	8.83	0.58		0.32	4.05	1.8E−10
		rs46493899	10	46493899	7.06	0.47	− 1.85	0.25	3.26	8.8E−08	Seed oleic 6–10	[22]
		rs34135970	12	34135970	11.07	− 0.36	2.82	0.42	5.43	8.6E−12
		rs1501986	14	1501986	6.23	0.47		0.20	2.59	8.6E−08
		rs48109369	14	48109369	5.18	− 0.07	2.65	0.18	2.35	6.7E−06
		rs6755025	15	6755025	5.60	− 0.44	− 0.98	0.17	2.16	2.5E−06
		rs32005810	16	32005810	4.43	0.39	− 0.66	0.14	1.80	3.7E−05
		rs30412910	17	30412910	11.47	0.64	− 2.71	0.40	5.17	3.4E−12
		rs9070866	18	9070866	6.15	0.28	− 3.37	0.18	2.30	7.1E−07
		rs4876597	19	4876597	7.75	0.22	1.86	0.18	2.28	1.8E−08
	2014	rs4953186	2	4953186	20.77	− 1.01	0.66	0.24	6.07	1.7E−21	rs4953186	[2]
		rs14587513	2	14587513	5.80	0.47		0.22	5.71	2.4E−07
		rs6481810	3	6481810	17.03	0.86	2.05	0.36	9.28	9.4E−18	rs6481810	[2]
		rs24966112	4	24966112	18.84	1.00	− 0.08	0.20	5.21	1.5E−19
		rs17451809	6	17451809	3.43	− 0.36		0.12	3.16	7.1E−05
		rs14264702	7	14264702	14.81	− 0.80		0.20	5.28	1.5E−16
		rs13246407	8	13246407	4.89	0.28	− 3.14	0.14	3.59	1.3E−05
		rs37217687	12	37217687	3.61	− 0.22	− 2.31	0.12	2.99	0.00025
		rs9446804	15	9446804	6.72	− 0.12	− 2.23	0.22	5.54	1.9E−07	Seed oleic 4–1	[36]
		rs39216169	17	39216169	5.23	− 0.45		0.12	3.11	9.2E−07
	2015	rs25887810	1	25887810	17.08	1.04		0.26	6.29	7.3E−19
		rs46294440	6	46294440	4.98	− 0.51	− 0.85	0.27	6.39	1E−05
		rs36974795	12	36974795	7.52	0.46	− 2.09	0.33	7.85	3E−08
		rs16802809	13	16802809	7.43	0.64		0.18	4.33	4.9E−09
		rs25691662	13	25691662	8.76	− 0.27	− 6.21	0.39	9.48	1.7E−09
		rs21353920	15	21353920	17.96	1.07	0.40	0.28	6.83	1.1E−18
		rs14234658	18	14234658	6.51	− 0.18	− 3.45	0.29	6.96	3.1E−07
Linolenic	2013	rs7344385	2	7344385	9.69	0.44		0.13	6.80	2.4E−11
		rs5009451	3	5009451	7.39	− 0.38		0.09	4.47	5.4E−09
		rs15602593	4	15602593	18.65	0.64	− 0.80	0.14	6.99	2.2E−19
		rs35874955	4	35874955	4.18	− 0.13	1.36	0.07	3.69	6.6E−05
		rs45800101	14	45800101	6.16	− 0.34	0.01	0.08	4.13	6.9E−07
		rs30575841	15	30575841	7.74	0.13	1.86	0.12	5.96	1.8E−08
		rs4718078	17	4718078	22.54	− 0.74		0.15	7.90	2.3E−24
		rs41437124	17	41437124	4.82	0.06	2.10	0.08	4.14	1.5E−05
		rs47611415	18	47611415	7.11	0.29	− 1.06	0.10	5.10	7.7E−08
		rs18173239	20	18173239	7.13	0.37	− 0.68	0.05	2.39	7.5E−08
	2014	rs42280985	4	42280985	7.76	0.03	1.43	0.08	6.95	1.8E−08
		rs42904836	4	42904836	9.14	0.33	0.27	0.03	2.59	7.3E−10
		rs4633296	9	4633296	10.72	− 0.36	0.83	0.12	10.00	1.9E−11
		rs21698230	14	21698230	5.68	− 0.25		0.04	3.36	3.2E−07	Seed oleic 7–3	[25]
		rs5443771	16	5443771	5.07	− 0.24	0.31	0.06	4.72	8.5E−06
		rs39098643	17	39098643	6.31	− 0.28	− 0.15	0.06	5.16	4.9E−07
		rs41268049	17	41268049	5.73	0.10	− 1.02	0.06	5.41	1.8E−06
		rs52833743	18	52833743	10.50	− 0.36		0.06	5.04	3.5E−12	rs52833743; Seed oleic 3–3; Seed oleic 5–2	[2, 24]
	2015	rs6099191	2	6099191	8.39	0.14	2.49	0.06	5.41	4.1E−09
		rs5660143	3	5660143	9.24	0.12	2.23	0.08	6.82	5.8E− 10
		rs32069131	6	32069131	20.28	0.51	− 0.14	0.06	4.86	5.3E−21
		rs38597109	8	38597109	18.99	− 0.47		0.07	5.93	8.6E−21
		rs18435729	10	18435729	6.46	− 0.01	2.43	0.06	5.37	3.5E−07
		rs39609078	12	39609078	6.66	− 0.26		0.05	4.29	3.1E−08
		rs2599191	14	2599191	10.61	0.33	− 0.06	0.09	7.78	2.5E−11
		rs9834940	14	9834940	9.71	0.32	− 0.21	0.04	3.58	2E−10
		rs26951252	14	26951252	10.54	0.30	− 0.66	0.08	6.90	2.9E−11	Seed oleic 6–10; Seed oleic 7–3	[22, 25]
		rs21822969	15	21822969	7.38	0.05	2.56	0.07	5.98	4.2E−08
		rs30575841	15	30575841	15.05	− 0.40	0.58	0.07	5.56	9E−16
		rs35024325	17	35024325	12.77	0.37	− 0.18	0.03	2.78	1.7E−13	rs35024325; Seed oleic 6–9	[2, 22]

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