Table 5.

Genes with significant expression differences in the R group vs. S group in qRT-PCR.P  < 0.05, Fold difference > 1.5

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
								RCf				1.5
								ICg
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
								RC				1.8
								IC
Glyma19g40940	Glycosyl hydrolases family 28	Carbohydrate metabolism; polygalacturonase activity	-	-	Glycoside hydrolase family 28 protein	0E + 00	Arabidopsis thaliana	CC
								RC			−1.9
								IC			−1.6
Glyma19g40950	WRKY DNA -binding domain	Transcription factor activity; sequence-specific DNA binding	-	-	Putative WRKY transcription factor 42	9E-91	Arabidopsis thaliana	CC
								RC
								IC			−1.5
Glyma19g40970	AUX/IAA family	Transcription factor activity	-	-	Auxin-responsive protein IAA20, putative	1E-48	Ricinus communis	CC	−1.5
								RC					−1.9
								IC		−2.2			−1.8
Glyma19g41580	-	-	-	-	Transcription factor bHLH149	1E-30	Arabidopsis thaliana	CC			−1.6	−2.8
								RC			1.5	2.3
								IC
Glyma19g41780	GATA zinc finger	Transcription factor activity; regulation of transcription, DNA-dependent; zinc ion binding; sequence-specific DNA binding	Transcription factor gata (gata binding factor)	-	GATA transcription factor 16	1E-23	Arabidopsis thaliana	CC
								RC			−1.5
								IC
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	−5.1	−5.6	−6.7	−2.9	−3.3
								RC				2.0
								IC	−5.4	−6.2	−7.1	−6.2	−2.7
Glyma19g41870	Protein phosphatase 2C	Protein serine/threonine phosphatase activity	Protein phosphatase 2c	Serine/threonine protein phosphatase	Protein phosphatase 2c, putative	0E + 00	Ricinus communis	CC
								RC			1.6
								IC
Glyma19g41900	F-box domain	-	-	-	Phloem-specific lectin PP2-like protein	2E-82	Arabidopsis thaliana	CC
								RC			1.9
								IC
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				2.1
								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			1.8
								IC
Glyma19g42120	-	-	-	Uncharacterized conserved protein	heparan-alpha-glucosaminide N-acetyltransferase	0 + 00	Arabidopsis thaliana	CC
								RC				2.0
								IC
Glyma19g42200	Rapid ALkalinization Factor (RALF)	Signal transducer activity	-	-	Rapid ALkalinization Factor	9e-47	Medicago truncatula	CC
								RC			1.6
								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	Mitogen activated protein kinase kinase kinase 3, mapkkk3, mekk3, putative	0E + 00	Ricinus communis	CC
								RC				2.8
								IC				2.1	2.0

R group: lines with the Conrad haplotype (Conrad, the RILs 2022, and 1960); S group: lines with the Sloan haplotype (Sloan, the RILs 1974, and 2022). Empty cell indicates that there was no significant difference, and a negative value indicates the fold of greater expression ratio in the group with the Sloan haplotype.

^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 the group with Conrad haplotype and the group with Sloan haplotype in mock-inoculated samples at specified time points (hai);

^f RC: Response contrast—significant fold differences in infection response ratios (inoculated / mock-inoculated) in the group with Conrad haplotype compared to the group with Sloan haplotype at specified time points (hai);

^g IC: Infection contrast—significant fold difference in transcript abundance between the group with Conrad haplotype and the group with Sloan haplotype 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.