Table 3.
SNPs causing non-synonymous changes in Conrad (C) genes compared to Sloan (S) and Williams82 (W)
|
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 | ||||||||||
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;
b PFAM description provided by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php, updated on July 2011);
c Gene Ontology Descriptions obtained from the (http://soybase.org, updated on July 2011);
d PANTHER description provided by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php, updated on July 2011);
e KOG Description assigned by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php, updated on July 2011);
f SNP position shown as their coordinate on Chr. 19 reference sequence (http://www.phytozome.net/soybean.php, Glyma1);
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].