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Table 3 SNPs causing non-synonymous changes in Conrad (C) genes compared to Sloan (S) and Williams82 (W)

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 function

E-value

BLAST hit species

SNP positionf

Amino acid

IRg

         

C

SW

C

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

47113947

V

M

  
        

47116418

L

V

  
        

47116517

T

A

  
        

47116586

I

V

  
        

47116637

G

R

  
        

47118102

G

D

  
        

47118156

N

S

  
        

47118234

S

L

  
        

47118485

Y

H

  
        

47119034

V

I

  

Glyma19g41230/

-

POT family

Oligopeptide transport; membrane; transporter activity

Oligopeptide transporter-related

H+/oligopeptide symporter

Nitrate transporter, putative

0E+00

Ricinus communi

47535046

Q

K

  

Glyma19g41630/

GmaAffx.82770.1.S1_at

Nicotianamine synthase protein

Nicotianamine synthase activity

-

-

Nicotianamine synthase

2E-177

Lotus japonicus

47867334

R

K

−3,-5

−3,-5

Glyma19g41740/-

Calmodulin binding protein-like

Calmodulin binding

-

-

Calmodulin-binding protein, putative

2E-50

Oryza sativa

47939823

S

A

  
        

47940855

L

M

  

Glyma19g41800/GmaAffx.67321.1.S1_at

Kinesin motor domain

ATPase activity microtubule binding microtubule motor activity

Kinesin heavy chain

Kinesin (KAR3 subfamily)

Kinesin heavy chain, putative

0E+00

Ricinus communis

47974179

M

K

-

-

        

47974243

N

K

  
        

47974369

STOP

Y

  

Glyma19g41900/-

F-box domain

-

-

-

Phloem-specific lectin PP2-like protein

2E-82

Arabidopsis thaliana

48050493

P

S

  

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

48232086

A

V

-

-

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

48239628

G

A

2

2

        

48240340

F

S

  
  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 SNP position shown as their coordinate on Chr. 19 reference sequence (http://www.phytozome.net/soybean.php, Glyma1);
  7. g 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].
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BMC Genomics

ISSN: 1471-2164

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