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Table 3
SNPs causing non-synonymous changes in Conrad (C) genes compared to Sloan (S) and Williams82 (W)
GlymaID/Affy ID^a	PFAM^b	GO function^c	PANTHER^d	KOG^e	BLASTP function	E-value	BLAST hit species	SNP position^f	Amino acid		IR^g
									C	SW	C	S
Glyma19g40800/	WD domain, G-beta repeat	-	WD repeat protein	WD-repeat protein WDR6, WD repeat superfamily	Transducin/WD40 domain-containing protein	0E+00	Arabidopsis thaliana	47113947	V	M
								47116418	L	V
								47116517	T	A
								47116586	I	V
								47116637	G	R
								47118102	G	D
								47118156	N	S
								47118234	S	L
								47118485	Y	H
								47119034	V	I
Glyma19g41230/ -	POT family	Oligopeptide transport; membrane; transporter activity	Oligopeptide transporter-related	H+/oligopeptide symporter	Nitrate transporter, putative	0E+00	Ricinus communi	47535046	Q	K
Glyma19g41630/ GmaAffx.82770.1.S1_at	Nicotianamine synthase protein	Nicotianamine synthase activity	-	-	Nicotianamine synthase	2E-177	Lotus japonicus	47867334	R	K	−3,-5	−3,-5
Glyma19g41740/-	Calmodulin binding protein-like	Calmodulin binding	-	-	Calmodulin-binding protein, putative	2E-50	Oryza sativa	47939823	S	A
								47940855	L	M
Glyma19g41800/GmaAffx.67321.1.S1_at	Kinesin motor domain	ATPase activity microtubule binding microtubule motor activity	Kinesin heavy chain	Kinesin (KAR3 subfamily)	Kinesin heavy chain, putative	0E+00	Ricinus communis	47974179	M	K	-	-
								47974243	N	K
								47974369	STOP	Y
Glyma19g41900/-	F-box domain	-	-	-	Phloem-specific lectin PP2-like protein	2E-82	Arabidopsis thaliana	48050493	P	S
Glyma19g42210/ GmaAffx.69813.1.A1_at	RAD9	DNA repair	DNA repair protein RAD9	Checkpoint 9-1-1 complex, RAD9 component	Rad9	0E+00	Medicago truncatula	48232086	A	V	-	-
Glyma19g42220/ GmaAffx.33386.1.A1_at	Respiratory burst NADPH oxidase\|EF hand\|Ferric reductase like transmembrane component\|FAD-binding domain\|Ferric reductase NAD binding domain	Calcium ion binding iron ion binding oxidoreductase activity FAD binding	NADPH oxidase	Ferric reductase, NADH/NADPH oxidase and related proteins	Respiratory burst oxidase 2	0E+00	Medicago truncatula	48239628	G	A	2	2
								48240340	F	S

^a GlymaID/Affymetrix probe IDs that match with the predicted genes underlying QTL (http://soybase.org/AffyChip/ webcite), where “-” means there was no Affymetrix IDs available for the specific gene;

^b PFAM description provided by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php webcite, updated on July 2011);

^c Gene Ontology Descriptions obtained from the (http://soybase.org webcite, updated on July 2011);

^d PANTHER description provided by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php webcite, updated on July 2011);

^e KOG Description assigned by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php webcite, updated on July 2011);

^f SNP position shown as their coordinate on Chr. 19 reference sequence (http://www.phytozome.net/soybean.php webcite, Glyma1);

^g IR: Infection response—significant differences in transcript abundance of inoculated samples compared to mock-inoculated samples in Conrad (C) or Sloan (S) (microarray data, TST-FDR, P < 0.05) at specified time points (dai); where “-” means there was no significant response observed at any time point after inoculation, a positive value indicates that the gene was up-regulated at the specified time point, and a negative value indicates the gene was down-regulated at the specified time point [10,21].

Wang et al. BMC Genomics 2012 13:428 doi:10.1186/1471-2164-13-428

Table 3