Table 4.

Genes with significant expression differences in Conrad vs. Sloan in qRT-PCR

GlymaID	PFAMa	GO functionb	PANTHERc	KOGd	BLASTP	E-value	BLAST hit species	Contrasts	Sampling points (hai)
									12	24	48	72_Ih	72_Ui
Glyma19g35340	Zinc-binding dehydrogenase	Zinc ion binding	Alcohol dehydrogenase related	Alcohol dehydrogenase, class III	Alcohol dehydrogenase, putative	0E + 00	Ricinus communis	CCe				−1.8
								RCf				2.0
								ICg			−1.5
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	CC				−2.4
								RC				2.4
								IC					−1.9
Glyma19g40940	Glycosyl hydrolases family 28	Carbohydrate metabolism; polygalacturonase activity	-	-	Glycoside hydrolase family 28 protein	0E + 00	Arabidopsis thaliana	CC					1.7
								RC			−1.9	−1.6
								IC			−2.2
Glyma19g40950	WRKY DNA -binding domain	Transcription factor activity; sequence-specific DNA binding	-	-	Putative WRKY transcription factor 42	9E-91	Arabidopsis thaliana	CC				−1.7
								RC				2.0
								IC
Glyma19g40970	AUX/IAA family	Transcription factor activity	-	-	Auxin-responsive protein IAA20, putative	1E-48	Ricinus communis	CC
								RC					−2.1
								IC					−2.4
Glyma19g41580	-	-	-	-	Transcription factor bHLH149	1E-30	Arabidopsis thaliana	CC			−2.7	−7.3	−3.2
								RC			1.5	7.3	2.5
								IC			−1.9
Glyma19g41800	Kinesin motor domain	ATPase activity microtubule binding microtubule motor activity	Kinesin heavy chain	Kinesin (KAR3 subfamily)	Kinesin heavy chain, putative	0E + 00	Ricinus communis	CC	−7.0	−6.6	−9.1	−6.4	−3.4
								RC				2.0
								IC	−5.4	−4.8	−8.6	−3.2	−4.7
Glyma19g41900	F-box domain	-	-	-	Phloem-specific lectin PP2-like protein	2E-82	Arabidopsis thaliana	CC				−1.9	−1.9
								RC			2.0		1.5
								IC	1.8
Glyma19g41930	Leucine Rich Repeat	Protein binding	F-box/leucine rich repeat protein	Leucine rich repeat proteins, some proteins contain F-box	Ubiquitin-protein ligase, putative	0E + 00	Ricinus communis	CC
								RC				3.3
								IC
Glyma19g42050	Calcineurin-like phosphoesterase	Protein serine/threonine phosphatase activity	Serine/threonine protein phosphatase	Serine/threonine specific protein phosphatase PP1, catalytic subunit	Serine/threonine-protein phosphatase PP1 isozyme 8	0E + 00	Arabidopsis thaliana	CC
								RC			1.7
								IC
Glyma19g42120	-	-	-	Uncharacterized conserved protein	heparan-alpha-glucosaminide N-acetyltransferase	0 + 00	Arabidopsis thaliana	CC				−2.1
								RC				3.6	2.4
								IC
Glyma19g42200	Rapid ALkalinization Factor (RALF)	Signal transducer activity	-	-	Rapid ALkalinization Factor	9e-47	Medicago truncatula	CC
								RC			1.8		−3.9
								IC	1.5				−3.4
Glyma19g42220	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	CC
								RC
								IC	1.8
Glyma19g42240	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	CC
								RC					−1.9
								IC
Glyma19g42340	Protein tyrosine kinase	Protein-tyrosine kinase activity; protein amino acid phosphorylation; ATP binding	Mapkk-related serine/threonine protein kinases	MEKK and related serine/threonine protein kinases	NPK1-related protein kinase 1 L	0E + 00	Arabidopsis thaliana	CC
								RC			2.4	2.9
								IC				2.5
Glyma19g42460	Core histone H2A/H2B/H3/H4|Histone-like transcription factor (CBF/NF-Y) and archaeal histone	DNA binding transcription factor activity	Histone-like transcription factor ccaat-related	CCAAT-binding factor, subunit C (HAP5)	ccaat-binding transcription factor, putative	1e-114	Ricinus communis	CC
								RC				1.5
								IC

P < 0.05, Fold difference > 1.5. Empty cell indicates that there was no significant difference, and a negative value indicates the fold that Sloan’s expression ratio was greater than Conrad’s.

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

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

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

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

^e CC: Constitutive contrast—significant fold difference in transcript abundance between Conrad and Sloan (C : S) in mock-inoculated samples at specified time points (HAI);

^f RC: Response contrast—significant fold differences in infection response ratios (inoculated / mock-inoculated) in Conrad compared to Sloan (C : S) at specified time points (HAI);

^g IC: Infection contrast—significant fold difference in transcript abundance between Conrad and Sloan (C : S) in infected samples at specified time points (HAI);

^h Samples were collected from the inoculation site at 72 HAI;

ⁱ Samples were collected from the front of lesion margin at 72 HAI.