Table 5.
Candidate master regulators of key hotspots.
| eQTL hotspota | Candidate master regulatorsb | Descriptionc | TF/SM/cis-eQTLd |
|---|---|---|---|
| GM_1 e,f (23,919) | Glyma.01G017000 | 3-Phosphoinositide-dependent protein kinase-1, putative | SM/cis-eQTL |
| Glyma.01G021000 | Auxin response factor 19 | SM/cis-eQTL | |
| Glyma.01G022000 | Methyl-CPG-binding domain protein 02; IPR011124 (zinc finger, CW-type) | TF/cis-eQTL | |
| Glyma.01G002400 | Phospholipase A2 family protein | SM/cis-eQTL | |
| GM_1_B f, i (2,136) | Glyma.01G156200 | Membrane transport protein, auxin efflux carrier | SM/cis-eQTL |
| Glyma.01G156600 | Thioredoxin reductase, pyridine nucleotide disulfide oxidoreductase | SM/cis-eQTL | |
| Glyma.01G156700 | Hydroxymethylglutaryl-CoA reductase, mevalonate pathway 1 | SM/cis-eQTL | |
| GM_2_B e,f ,j (16,909) | Glyma.02G306300 | WRKY DNA-binding domain, zinc-dependent activator protein | TF/cis-eQTL |
| Glyma.02G307300 | Aldo/keto reductase family, flavonoid biosynthesis- | SM/cis-eQTL | |
| Glyma.02G307900 k | FIMBRIN/PLASTIN, Ca2+-binding actin-bundling protein, EF-Hand protein superfamily | TF/cis-eQTL | |
| Glyma.02G308800 | 5′-AMP-activated protein kinase beta subunit, interaction domain, involved assembly of snf1 protein complex | SM/cis-eQTL | |
| Glyma.02G309100 | Zinc finger, C3HC4 type (RING finger), E3 Ubiquitin protein ligase | TF/cis-eQTL | |
| Glyma.02G310400 | Leucine-rich repeat receptor-like protein kinase, BR-signaling kinase 1 | SM/cis-eQTL | |
| GM_5h (423) | Glyma.05G021300 | Zinc-finger double-stranded RNA-binding, DNAJ homolog | TF/cis-eQTL |
| Glyma.05G021800 | Cytochrome P450, CYP2 subfamily, leucopelargonidin and leucocyanidin biosynthesis | SM/cis-eQTL | |
| Glyma.05G021900 | Cytochrome P450, CYP2 subfamily, leucopelargonidin and leucocyanidin biosynthesis | SM/cis-eQTL | |
| GM_11 e,f,g (14,801) | Glyma.11G051500 | Mn2+ and Fe2+ transporters of the NRAMP family, natural resistance-associated macrophage protein | SM/cis-eQTL |
| Glyma.11G052100 | Myb-like DNA-binding domain, TF, MYB superfamily | TF/cis-eQTL | |
| Glyma.11G053100 | WRKY DNA-binding protein, transcription factor | TF/cis-eQTL | |
| GM_13 e,f ,j (6,889) | Glyma.13G062400 | Reticulon | SM/cis-eQTL |
| Glyma.13G062700 k | Glycosyl transferases group 1, glycogen biosynthesis (ADP-d-glucose) | SM/cis-eQTL | |
| GM_13_Ah (20) | Glyma.13G049000 | GDSL/SGNH-like acyl-esterase family found in Pmr5 and Cas1p | SM/cis-eQTL |
| GM_15 e,f (25,727) | Glyma.15G053600 | IPT/TIG domain, calmodulin binding transcription activator | TF/cis-eQTL |
| Glyma.15G053700 | Protein phosphatase 2C, serine/threonine protein phosphatase | SM/cis-eQTL | |
| Glyma.15G054100 | Caspase domain, metacaspase is involved in the regulation of apoptosis | SM/cis-eQTL | |
| Glyma.15G054500 | UDP-glucoronosyl and UDP-glucosyl transferase | SM/cis-eQTL | |
| Glyma.15G054600 | Phosphate-induced protein 1 conserved region | SM/cis-eQTL | |
| Glyma.15G054800 | RNA recognition motif (a.k.a. RRM, RBD, or RNP domain), splicing factor RNPS1, SR protein superfamily | SM/cis-eQTL | |
| Glyma.15G055100 | EF-hand domain pair, calcium-binding protein | TF/cis-eQTL | |
| Glyma.15G055200 | F-box domain | TF/cis-eQTL | |
| Glyma.15G055500 | Amidohydrolase family, thymine degradation | SM/cis-eQTL | |
| Glyma.15G056000 | Ring finger domain, anaphase-promoting complex | TF/cis-eQTL | |
| GM_17 e (6,966) | Glyma.17G155500 | Kinesin motor domain | SM/cis-eQTL |
| GM_17_Dh (303) | Glyma.17G200200 | C2H2 type zinc-finger | TF |
| Glyma.17G200500 | Transcription factor PCC | TF | |
| GM_17_F e (120) | Glyma.17G204300 | PHD finger proteins | TF |
| Glyma.17G204600 | Leucine-rich repeat receptor-like protein kinase, cytoplasmic | SM | |
| GM_18 e (91) | Glyma.18G206400 | Leucine-rich repeat receptor-like protein kinase (serine/threonine) | SM |
| Glyma.18G207700 | Dirigent-like protein, disease resistance responsive | SM | |
| Glym.18G208100 | Protein phosphatase 2C, serine/threonine protein phosphatase | SM | |
| Glyma.18G208800 | WRKY DNA-binding domain | TF | |
| Glyma.18G209400 | SWIM zinc finger | SM | |
| GM_18_A e (88) | Glyma.18G209400 | SWIM zinc finger | TF |
| Glyma.18G209500 | Wound-induced protein WI12 | TF | |
| GM_19i (30) | Glyma.19G217800 | WRKY DNA-binding | TF |
| Glyma.19G218800 | MYB-LIKE DNA-binding | TF | |
| Glyma.19G219000 | MYB-LIKE DNA-binding | TF | |
| Glyma.19G220000 | Zinc finger protein | SM | |
| Glyma.19G220300 | Leucine-rich repeat receptor kinase (serine/threonine) | SM | |
| GM_19_Ai (34) | Glyma.19G221700 | WRKY DNA-binding domain (overlap with GM_19) | TF |
| GM_19_Bi (67) | Glyma.19G222200 | MYB-LIKE DNA-binding (overlap with GM_19 and 19_A) | TF |
| Glyma.19G244200 | Two-component sensor histidine kinase—SNP in the gene (overlap with GM_19_A) | SM | |
| Glyma.19G224600 | MYB-LIKE DNA binding (overlap with GM_19_A) | TF | |
| Glyma.19G224700 | Basic helix-loop-helix/leucine zipper transcription factor (overlap with GM_19_A) | TF | |
| Glyma.19G226000 | Interleukin-1 receptor-associated kinase (serine/threonine) | SM | |
| Glyma.19G226900 | Zinc finger five domain-containing protein | SM |
aParenthetical number is the number of eQTL associated with each key hotspot. Key eQTL hotspots were those enriched QDR pathways based on the iBMQ analysis or overlap a phQTL of the Conrad × Sloan recombinant inbred population following inoculation with Phytophthora sojae.
bCandidate master regulators were identified as genes within a 242-kb (average linkage disequilibrium (LD) block size) upstream or downstream of the hotspot SNP, and genes with cis-eQTL mapping were identified as initial candidate master regulators. Genes were then selected as candidate master regulators if their putative function included transcription factors, signaling molecules, or known associations involved in the enriched quantitative disease resistance (QDR) pathways. Gene ID based on the Wms82.a2.v1 sequence (soybase.org).
cDescription, PFAM, Panther, and pathway were retrieved from https://phytozome.jgi.doe.gov (accessed July 2023).
dResults from mapping genes to the KEGG Pathway database (accessed August 2023; http://www.genome.jp/kegg/pathway.html). Classification of the putative master regulator: putative signaling molecule (SM), putative transcription factor (TF), and cis-eQTL for this gene (cis-eQTL).
eGenes controlled by this SNP have significant gene ontology (GO) enrichment at a false discovery rate (FDR) of 5%.
fSignificant pathway enrichment of the plant interaction pathway (adjusted p-value ≤ 0.05; Fisher’s exact test with Benjamini–Hochberg correction). Gene lists derived from the KEGG pathway database (accessed, February 2018; http://www.genome.jp/kegg/pathway.html).
gSignificant pathway enrichment of the isoflavonoid pathway (p-value ≤ 0.05; Fisher’s exact test with Benjamini–Hochberg correction). Gene lists derived from the KEGG pathway database (accessed, February 2018; http://www.genome.jp/kegg/pathway.html).
hSignificantly correlated with co-expression modules at a p-value <0.05 (Fisher’s exact test).
iCo-localizes with phenotypic quantitative trait loci (phQTL).
jIntragenic hotspot SNP.
kThe hotspot SNP is located within this putative master regulator.