Table 3.

SNPs significantly associated with white mould resistance and a subset of candidate genes identified by RNA‐Seq from the field trials

Panel	Loci	SNP	Chr.	Positiona	P	Allele	R 2(%)	QTLb	Subset of candidate genesc based on RNA‐seq
									Name	Annotation	Log2 (fold change)	TP d (hpi)
Improved lines	1	ss715583735	2	6447172	3.1 × 10−5	T/C	5.3		Glyma.02G073700	Aquaporin transporter	2.5	12
	2	ss715587841	4	3732457	3.4 × 10−5	C/T	5.3		Glyma.04G046600	Hypothetical protein	−2.1	12
		ss715587850	4	3752035	5.3 × 10−5	T/G	5.1
		ss715587866	4	3797774	3.9 × 10−5	G/A	5.1
	3	ss715587925	4	42372944	2.6 × 10−5	T/C	5.6		Glyma.04G184400	F‐BOX	1.5	12
		ss715588278	4	46104694	3.2 × 10−5	T/C	5.5
	4	ss715590176	5	3924139	1.6 × 10−6	G/A	6.9		Glyma.05G044000*	Pectate lyase	1.6	12
	5	ss715601283	8	2789107	4.5 × 10−5	T/G	5.1		Glyma.08 g035900	Glycosyl hydrolase	1.6	12
	6	ss715605011	9	49559911	3.6 × 10−5	G/A	5.3	2‐18	Glyma.09G281900	O‐methyltransferase	2.2	48
		ss715605026	9	49749681	4.7 × 10−7	C/T	8.2
	7	ss715624465	16	31915854	7.7 × 10−6	T/G	6.1		Glyma.16G158100	Glucuronosyltransferases	2.0	48
	8	ss715630705	18	43030373	1.2 × 10−5	T/C	6.0		Glyma.18G177400	Laccase	2.0	12
PIs	9	ss715590828	5	33208876	5.9 × 10−5	T/C	5.2	2‐1	Glyma.05G138800	Cytochrome b	1.8	12
	10	ss715596286	7	10514582	4.6 × 10−5	T/G	5.3	1‐2	–	–	–	–
	11	ss715607488	10	45331299	2.3 × 10−5	C/T	5.8		Glyma.10G221700	Solute carrier	1.5	12
	12	ss715618590	14	3852549	6.6 × 10−5	C/T	6.8		Glyma.14G049400	Protein binding	1.7	12
		ss715618599	14	3878273	3.7 × 10−5	A/G	5.9
		ss715618604	14	3885274	1.5 × 10−5	T/C	6.0	8‐2
	13	ss715620418	15	12264951	4.0 × 10−5	T/C	5.4	G.S	Glyma.15G147100	5′‐3′ exoribonuclease 3	4.2	12
		ss715620421	15	12278417	7.1 × 10−5	T/C	5.2
	14	ss715624027	16	29081835	5.5 × 10−5	C/T	5.2		Glyma.16 g134000, Glyma.16G134400	SAM dependent carboxyl methyltransferase	1.8; 1.6	12
		ss715624030	16	29090022	2.3 × 10−5	T/G	6.0
		ss715624031	16	29095909	5.3 × 10−6	G/A	7.7
	7	ss715624900	16	31667215	6.1 × 10−5	C/T	5.2		Glyma.16G158100	Glucuronosyltransferases	2.0	12
	15	ss715636086	19	579512	6.1 × 10−5	G/A	5.2		Glyma.19G005800	Polyribonucleotide nucleotidyltransferase	1.6	12
	16	ss715634194	19	3498043	6.4 × 10−5	G/A	5.1		Glyma.19G026900	Plastocyanin‐like domain	1.9	12

^aPosition in base pairs for the peak SNP according to soya bean reference sequence (a2.v1) of Williams 82.

^bthe position of significant SNP is located in one of the QTL or GWAS (G.S) intervals (defined as physical position of associated markers) as reported previously (http://www.soybase.org/search/index.php?qtl=white mould).

^cCandidate genes selected by RNA‐seq results as having the significant changes ((FDR<0.05) in abundance between partially resistant and susceptible genotypes by comparisons of fold change (log2‐transformed) of reads per kilobase per million (FPKM) around peak SNP.

^dTP stands for time point (hours postinoculation).