Table 2

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

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 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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