Table 4. SNPs significantly associated with branch angle.

QTLs	SNPs	Chr	Position	MAFa	Allele	−log10(p) (MLM)	Environment (MLM)b	R2 (MLM)	−log10(p) (GLM)	Environment (GLM)b	R2 (GLM)	−log10(p) (A-D test)	Environment (A-D test)b
1	Bn-A01-p7430311	A01	6794653	0.32	[A/G]				5.1–5.7	BLUP,CS14	3.9–5	6.1–6.4	BLUP,CS14
2	Bn-A01-p7974551	A01	7156865	0.42	[T/C]				4.3–4.4	CS14,WH14	3.1–3.7	6.0–7.1	BLUP,NJ13,WH14
3	Bn-A02-p27245861	A02	24567443	0.30	[A/G]							5.7–7	BLUP,NJ13,WH14
4	Bn-A03-p4342338	A03	3874153	0.32	[T/C]	5.5	BLUP	4.9	5.0–6.2	BLUP,NJ13	3.7–5.1
5	Bn-A03-p5814447	A03	5245728	0.41	[A/G]				4.3	BLUP	3.3
6	Bn-A03-p6228570	A03	5594660	0.27	[T/C]	4.7–6.3	BLUP,CS13	3.6–3.9	4.4–5.5	BLUP,CS13,NJ13	2.9–3.3	5.6–5.7	BLUP,NJ13
7	Bn-A03-p7178650	A03	6451720	0.16	[T/C]				4.7–5.2	BLUP,NJ13	3.4–4.0
8	Bn-A03-p7572128	A03	6882418	0.10	[T/G]	4.3	BLUP	3.2	5.5–6.3	BLUP,NJ13,WH14	3.5–4.0
9	Bn-A03-p8033095	A03	7321907	0.27	[T/C]				5.0–5.1	BLUP,NJ13	3.7–3.9	6.2–6.8	BLUP,NJ13,WH14
10	Bn-A03-p8554739	A03	7848675	0.33	[T/C]				4.5–6.0	BLUP,CS13,WH14	3.6–4.6	6.5–7.1	BLUP,WH14
11	Bn-A03-p15347967	A03	14385059	0.30	[A/G]							6.2	BLUP
12	Bn-A03-p25868537	A03	24234777	0.27	[A/G]				4.5–5.7	BLUP,WH14	3.4–4.3
13	Bn-A03-p28982546	A03	27392934	0.24	[T/C]				5.4–5.7	BLUP,CS13,NJ13	4.0–4.5
14	Bn-A04-p3631563	A04	3299951	0.13	[A/G]	4.8–6.7	BLUP,NJ13,CS13	4.1–6.0	4.5–8.6	BLUP,CS13,NJ13,CS14	3.5–6.6
15	Bn-A04-p4410144	A04	4532791	0.27	[T/C]	4.7–5.5	BLUP,NJ13	4.2–4.9	6.0–6.4	BLUP,NJ13	4.6–5.2	5.9	NJ13
16	Bn-A04-p2411039	A04	5850169	0.14	[A/G]	4.6–4.8	BLUP,NJ13,CS13	3.8–4.3	5.5–6.3	BLUP,CS13,NJ13	4.3–4.9
17	Bn-A04-p6296526	A04	7519507	0.23	[A/C]	4.9	BLUP	3.7	4.8–4.8	CS13,NJ13	3.2–3.2
18	Bn-A04-p6929056	A04	8211241	0.35	[T/C]				4.4	BLUP	3.5
19	Bn-A05-p6415983	A05	5963980	0.07	[A/G]				4.6	BLUP	3.0
20	Bn-A05-p21065087	A05	19223021	0.43	[A/G]				4.6	BLUP	3.7
21	Bn-A06-p5114770	A06	4927748	0.27	[T/C]				4.4	BLUP	3.4
22	Bn-A10-p11839950	A07	2293313	0.27	[T/C]				4.5–4.5	BLUP,WH14	3.5–3.6
23	Bn-A07-p4191541	A07	6111458	0.47	[T/C]				5.7–7.6	BLUP,NJ13,WH14	4.7–6.4	6.7–7.7	BLUP,NJ13,WH14
24	Bn-A07-p5412930	A07	7273126	0.47	[A/G]				4.6–5.1	BLUP,CS13,WH14	3.4–4.1	5.8–6.6	BLUP,CS13,WH14
25	Bn-A07-p9921856	A07	11205489	0.24	[T/G]				4.4–5.6	BLUP,NJ13	2.7–3.8
26	Bn-A07-p10869578	A07	12103546	0.27	[T/C]				4.5–4.7	BLUP,WH14	3.3–3.6
27	Bn-A07-p13172047	A07	15255974	0.22	[A/G]	5.1	CS13	4.5	4.9–5.7	BLUP,CS13,WH14	3.6–4.5	6.1	CS13
28	Bn-A07-p13662635	A07	15655194	0.17	[T/C]				5.4–5.5	BLUP,WH14	3.9–3.9
29	Bn-A07-p15007983	A07	16890653	0.32	[T/G]							5.6	BLUP
30	Bn-A07-p15505090	A07	17408302	0.46	[T/G]				4.3	BLUP	2.6
31	Bn-A07-p18021746	A07	19874380	0.33	[T/C]				4.7–5.1	BLUP,CS14	3.7–4.5
32	Bn-A08-p13638847	A08	11390087	0.29	[T/G]				4.3–6.7	BLUP,CS14	2.6–4.7	5.5	BLUP
33	Bn-A09-p2208929	A09	1382771	0.20	[A/G]				4.4–5.2	BLUP,CS14	2.9–3.9
34	Bn-A09-p36803825	A09	33753723	0.09	[T/C]	4.9–5.4	BLUP,CS14,CS13	3.9–4.3	4.5–7.7	BLUP,CS13,NJ13, CS14,WH14	3.2–5.1
35	Bn-A10-p7394578	A10	9067281	0.48	[A/G]				4.3–5.2	BLUP,WH14	3.3–4.1
36	Bn-A10-p10671726	A10	12042143	0.15	[T/C]				4.4–6.6	BLUP,CS13	3.2–5.3
37	Bn-A10-p13818569	A10	13855272	0.40	[T/C]				4.6–4.6	BLUP,CS13	4.0	5.6–6.3	BLUP,CS13
38	Bn-A10-p17414621	A10	17217158	0.08	[T/C]	4.4	NJ13	3.6	4.8–6.3	BLUP,NJ13	3.3–4.6
39	Bn-scaff_20461_1-p322463	C02	9345306	0.11	[A/C]				5.6	BLUP	3.5
40	Bn-scaff_16614_1-p1480092	C03	660277	0.08	[T/G]				4.5–5.1	BLUP,WH14	2.7–3.2
41	Bn-scaff_18936_1-p472353	C03	3058478	0.32	[A/G]				4.6	BLUP	3.3	6.2–8.7	BLUP,NJ13,WH14
42	Bn-scaff_18322_1-p2487448	C03	6744282	0.40	[A/C]							6.2–6.6	BLUP,WH14
43	Bn-scaff_15794_3-p533873	C03	55055879	0.34	[T/C]				4.4	BLUP	3.2
44	Bn-scaff_16876_1-p1162532	C04	33772508	0.29	[A/C]	4.4–5.8	BLUP,CS13	3.3–4.5	6.3	CS13	4.2
45	Bn-scaff_15798_1-p281492	C04	36910519	0.15	[T/C]	5.0–5.0	BLUP,CS14	4.3–4.3	5.7–7.5	BLUP,CS14,WH14	4.4–5.3
46	Bn-scaff_16062_1-p345501	C05	15699504	0.40	[A/G]	4.9	CS13	4.5	4.4–7.4	BLUP,CS13,CS14,WH14	3.2–6.2	6.1–7.3	BLUP,CS13
47	Bn-scaff_18206_1-p453711	C06	18723815	0.45	[T/C]							6.0–6.3	BLUP,WH14
48	Bn-scaff_19106_1-p76331	C07	18982139	0.26	[A/G]							6.3–9.9	BLUP,NJ13
49	Bn-scaff_18501_1-p114150	C07	21145676	0.35	[A/G]	4.6–5.7	BLUP,NJ13	3.9–5.0	4.6–5.3	BLUP,NJ13	3.4–4.2
50	Bn-scaff_16468_1-p450133	C08	13342433	0.09	[T/G]							5.6	BLUP
51	Bn-scaff_16200_1-p208618	C08	27277109	0.19	[T/C]				4.3–5.2	BLUP,CS13,NJ13,CS14	3.4–4.2	5.6	NJ13
52	Bn-scaff_16197_1-p2492352	C08	31718611	0.47	[T/C]	4.5	BLUP	3.9	4.3–5.8	BLUP,CS13,CS14	3.2–4.7
53	Bn-scaff_16197_1-p1333425	C08	32784282	0.28	[A/T]				4.6–5.3	BLUP,NJ13,WH14	3.4–3.9	6.1	WH14
54	Bn-scaff_16389_1-p436578	C08	37667324	0.08	[A/G]							5.9–6.1	BLUP,WH14
55	Bn-scaff_17526_1-p1470085	C09	1151339	0.35	[T/G]	5.0	WH14	3.8	5.7–8.0	BLUP,CS14,WH14	3.9–5.2
56	Bn-scaff_16362_1-p621813	C09	43501182	0.20	[A/G]				5.4	WH14	3.8	5.6–6.0	BLUP,WH14

^aMAF: minor allele frequency.

^bNJ13: 2012/2013 Nanjing, CS13: 2012/2013 Changsha, CS14: 2013/2014 Changsha, WH14: 2013/2014 Wuhan. SNPs indicated in bold were consistently detected in at least two environments in the present study.