Identification of novel loci associated with maturity and yield traits in early maturity soybean plant introduction lines

Table 2 Significant loci associated with important agronomic traits identified using genome-wide association analyses (Bonferroni correction P < 0.01)

Trait	Chr.^a	MSS^b P value	Total SNPs^c	Region		Average diff.^d	Data set^e	Novel loci^f	Known genes/QTL^g	Ref.^h
Trait	Chr.^a	MSS^b P value	Total SNPs^c	Start	End
Days to maturity	3	1.82E-07	1	38,602,824	38,602,824	2.9	M,G	*
	5	4.14E-09	12	1,927,907	3,263,938	7.2	M,G	*
	6	1.08E-08	20	11,386,388	20,263,848	6.0	M,G		E1	[10]
	10	1.37E-07	4	40,769,008	46,434,446	3.1	M		E2	[9]
	13	2.90E-07	4	15,226,603	15,278,116	1.6	M,G	*
	13	8.90E-09	14	29,022,554	31,262,263	3.8	M	*
	13	2.67E-10	16	31,354,945	32,109,291	4.4	M,S		20-1	SoyBase
	16	3.08E-07	1	34,285,082	34,285,082	3.1	M	*
	17	1.99E-07	2	40,939,386	40,970,920	5.6	M	*
Days to flowering	5	5.11E-08	1	3,131,408	3,131,408	2.4	M,G,S	*
	5	1.82E-07	1	33,211,040	33,211,040	4.2	M	*
	6	6.35E-10	21	19,919,551	20,263,848	3.5	M,G		E1	[10]
	9	2.42E-07	1	3,031,973	3,031,973	6.0	M		24-2	SoyBase
	10	1.35E-09	8	46,241,807	46,580,047	2.9	M		24-4	SoyBase
	15	1.59E-08	9	48,460,246	51,379,618	4.1	M,G	*
Days to pod filling	3	1.48E-07	1	38,579,331	38,579,331	2.9	M,G	*
	10	3.62E-08	3	40,769,008	40,793,025	1.0	M,S	*
	13	2.33E-07	1	29,387,862	29,387,862	8.3	M,G,S		7-2	SoyBase
	14	2.83E-07	1	31,326,567	31,326,567	1.0	M,S	*
100 seed weight	4	1.12E-07	4	635,354	8,191,897	1.6	M		2-1; 6-2; 6-7; 13-4; 38-2; 47-3	SoyBase
	4	1.08E-07	1	37,659,105	37,659,105	1.6	M		36-15	SoyBase
	6	3.51E-09	2	18,315,510	18,446,052	2.1	M		15-1; 16-1; 16-2; 19-1; 34-16	SoyBase
	9	1.26E-07	1	17,708,693	17,708,693	1.7	M		30-5	SoyBase
	19	2.65E-10	33	40,130,037	43,116,996	1.8	M		5-1; 15-7; 17-1; 34-7; 35-7; 36-7	SoyBase
Yield	11	1.90E-08	1	2,584,048	2,584,048	574	M		2-1	SoyBase
Yield	16	3.40E-08	2	7,914,714	7,985,838	67	M		23-13; 29-2; 31-9; 32-4	SoyBase

^aChr., chromosome number
^bMSS, most significant SNP
^cTotal SNPs and regions including SNPs in 100% linkage disequilibrium with significant SNPs at Bonferroni correction P < 0.01
^dAverage difference in number of days to maturity, flowering, pod filling, 100 seed weight (mg) or yield (kg ha⁻¹) between the different haplotypes of the most significant SNP (MSS) within the locus
^eData set(s) in which the significant locus was detected. M, merged data set; G, genotyping-by-sequencing data set; M, SoySNP50K microarray data set
^fLoci not reported in SoyBase.org or recent literature for pod maturity (R8 full maturity), first flower, reproductive stage length (days to pod filling), seed weight or seed yield. Loci lacking stars represent known or previously reported loci, some of which genes are known and identified in the “Known Genes” column. Not all known loci have had associated genes identified
^gLoci with known and identified genes or QTL previously reported as associated with the trait of interest
^hReferences referring to genes or QTL previously identified. SoyBase refers to QTLs reported in the SoyBase database (www.soybase.org)

ISSN: 1471-2164