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Table 4 Genes with significant expression differences in Conrad vs. Sloan in qRT-PCR

From: Dissection of two soybean QTL conferring partial resistance to Phytophthora sojae through sequence and gene expression analysis

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

     
  1. 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.
  2. a PFAM description provided by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php, updated on July 2011);
  3. b Gene Ontology Descriptions obtained from the (http://soybase.org, updated on July 2011);
  4. c PANTHER description provided by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php, updated on July 2011);
  5. d KOG Description assigned by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php, updated on July 2011);
  6. 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);
  7. 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);
  8. g IC: Infection contrast—significant fold difference in transcript abundance between Conrad and Sloan (C : S) in infected samples at specified time points (HAI);
  9. h Samples were collected from the inoculation site at 72 HAI;
  10. i Samples were collected from the front of lesion margin at 72 HAI.