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Table 2 Eleven genes in which Conrad had unique SNPs vs. Sloan & Williams82

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

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

  
  1. 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;
  2. b PFAM description provided by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php, updated on July 2011);
  3. c Gene Ontology Descriptions obtained from the (http://soybase.org, updated on July 2011);
  4. d PANTHER description provided by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php, updated on July 2011);
  5. e KOG Description assigned by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php, updated on July 2011);
  6. 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].