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 webcite, updated on July 2011);

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

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

d KOG Description assigned by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php webcite, 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.

Wang et al.

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

Open Data