Table 2.

Eleven genes in which Conrad had unique SNPs vs. Sloan & Williams82

GlymaID/Affy IDa	PFAMb	GO functionc	PANTHERd	KOGe	BLASTP	E-value	BLAST hit species	# of SNPs	SNP locations	IRf_C	IR_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	47	exon, intron, downstream
Glyma19g40840/-	Pectinesterase/Plant invertase/pectin methylesterase inhibitor	Pectinesterase activity; cell wall; cell wall modification	-	-	Pectinesterase; Pectinesterase inhibitor	0E+00	Medicago truncatula	1	downstream
Glyma19g40940/-	Glycosyl hydrolases family 28	Carbohydrate metabolism; polygalacturonase activity	-	-	Glycoside hydrolase family 28 protein	0E+00	Arabidopsis thaliana	2	upstream, intron
Glyma19g41590/ Gma.14131.1.S1_atGmaAffx.26456.1.S1_at GmaAffx.76884.1.S1_at	Haloacid dehalogenase-like hydrolase|Redoxin|NHL repeat	Hydrolase activity	2-deoxyglucose-6-phosphate phosphatase 2	Predicted haloacid-halidohydrolase and related hydrolases	2-deoxyglucose-6-phosphate phosphatase, putative	0E+00	Ricinus communis	1	intron	-	-
Glyma19g41900/-	F-box domain	-	-	-	Phloem-specific lectin PP2-like protein	2E-82	Arabidopsis thaliana	8	upstream, 5' UTR, exon, downstream
Glyma19g42120/ Gma.14232.1.S1_at	-	-	-	Uncharacterized conserved protein	heparan-alpha-glucosaminide N-acetyltransferase	0+00	Arabidopsis thaliana	1	intron	−2,-3	−2,-3,-5
Glyma19g42200/ Gma.9498.1.S1_a_at	Rapid ALkalinization Factor (RALF)	Signal transducer activity	-	-	Rapid ALkalinization Factor	9e-47	Medicago truncatula	11	upstream, intron	2	-
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	12	upstream, exon, intron	-	-
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	29	upstream, exon, intron	2	2
Glyma19g42240/ Gma.13144.1.S1_at	Core histone H2A/H2B/H3/H4;Histone-like transcription factor (CBF/NF-Y) and archaeal histone	DNA binding	Histone H2A	Histone 2A	Histone H2A 7	2e-73	Arabidopsis thaliana	2	upstream, 5' UTR	−2,5	3,5
Glyma19g42390/-	Cyclin, N-terminal domain	-	Family not named	Cyclin	Cyclin-dependent protein kinase, putative	6e-59	Ricinus communis	8	upstream, intron, downstream

^a GlymaID/Affymetrix probe IDs that match with the predicted genes underlying QTL (http://soybase.org/AffyChip/), 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, updated on July 2011);

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

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

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

^f 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].