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/ webcite), 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 webcite, updated on July 2011);

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

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

e KOG Description assigned by the Soybean Genome Project, DoE Joint Genome Institute (http://www.phytozome.net/soybean.php webcite, updated on July 2011);

f SNP position shown as their coordinate on Chr. 19 reference sequence (http://www.phytozome.net/soybean.php webcite, 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].

Wang et al.

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

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