TABLE 2.

SNP loci that significantly associated with pod dehiscence based on GWAS in the association panel.

Chr	MSS	MSS Position	Mss P-value	Significant region		No. of SNPs	Env	Related QTL or gene identified in previous studies
				Start	End
1	AX-93963018	5388850	2.58 × 10–06	5258850	5518850	1	Env2	–
4	AX-93708700	25726440	2.17 × 10–05	25596440	25856440	1	Env2	–
6	AX-93727683	11784406	1.13 × 10–5	10563310	41546032	3	Env2 (2), Env1 (1)	–
8	AX-93930129	42050788	7.83 × 10–07	41864756	42186397	11	Env1	Pod dehiscence 4-1 (Yamada et al., 2009)
9	AX-93762848	5145974	2.58 × 10–07	4940686	5275974	3	Env3 Env5 (2), Env3 (1)	–
11	AX-94082716	577915	1.19 × 10–06	447915	707915	1	Env2
16	AX-93853895	29601807	2.06 × 10–15	29365082	29736722	1	Env1 Env2 Env3 Env4 Env5 BLUP
16	AX-93853825	29421300	5.78 × 10–10	29194421	29850274	51	Env1 Env2 Env4 Env5 BLUP	Pod dehiscence 1-7 (Bailey et al., 1997) Pod dehiscence 2-1 (Funatsuki et al., 2006) Pod dehiscence 3-4 (Kang et al., 2009) Pod dehiscence 4-2 (Yamada et al., 2009) Pod wall width 1-9 (Guang-yu et al., 2011) pdh1 (Funatsuki et al., 2014)
16	AX-93853894	29600010	1.29 × 10–10	29136226	29870913	18	Env1 Env2 Env5 BLUP (14) Env1 Env4 Env5 BLUP (4)
16	AX-93853796	29340570	2.84 × 10–08	29210570	29879081	19	Env1 Env2 BLUP (16) Env2 Env5 BLUP (3)
16	AX-93946746	29215338	1.15 × 10–07	29005922	29968491	11	Env1 BLUP
16	AX-93853865	29545423	5.30 × 10–07	29018509	29990917	36	Env1 (12), Env2 (4), BLUP (20)
17	AX-94289430	11868679	1.98 × 10–5	11738679	12008912	3	Env1	–
18	AX-94165965	2292799	8.60 × 10–06	2162799	54328119	3	Env1	–
20	AX-93901310	8202869	2.03 × 10–05	8072869	8332869	1	Env1	–

Chr, chromosome; MSS, most significant SNP; Significant region, significant region was defined as the LD decay distance flanking the significant SNPs; No. of SNPs, number of significant SNPs; Env, environment. The number in brackets indicates the number of significant SNPs detected in different environments.