Table 3.
List of candidate genes identified for disease resistance/stress tolerance traits using GWAS from individual studies and meta-GWAS
| Chromosome | Likely gene | Meta-GWAS | Individual studies GWAS | Trait(s) | Studies source |
|---|---|---|---|---|---|
| 1 | RLK3 | * | Bacterial pustule | bp488001 | |
| 3 | Glyma.03g127100 | * | Pythium root rot | PYU.11002 | |
| Glyma.03g130600 | * | * | Iron deficiency chlorosis | lssleepyeye04, meta | |
| Glyma.03g262500 | * | SCN races: 14 | Meta | ||
| Rps1 | * | * | Phytophthora root rot races: 1, 2, 3, 4, 5, 7, 10, 17 | meta, PRR1, PRR1.10001, PRR1.10002, PRR1.10004, PRR1.11002, PRR1.11003, PRR1.461592, PRR1.488001, PRR1.492577, PRR1.492990, PRR10, PRR17, PRR17.491404, PRR17.492448, PRR17.492990, PRR2, PRR3, PRR3.492577, PRR3.492990, PRR4, PRR4.492990, PRR5, PRR5.492990, PRR7, PRR7.491404, PRR7.492448, PRR7.492990, prrdl96_1, prrdl96_3, prrfs04_17, prrfs04_7, prrrs01_1 | |
| Rps7 | * | * | Phytophthora root rot races: 1, 2, 3, 4, 5, 7, 10, 17 | meta, PRR1, PRR1.10002, PRR1.10003, PRR1.10004, PRR1.11003, PRR1.488001, PRR1.492577, PRR1.492990, PRR10, PRR17, PRR17.491404, PRR17.492448, PRR17.492990, PRR2, PRR3, PRR3.492990, PRR5, PRR5.492990, PRR7, PRR7.491404, PRR7.492448, PRR7.492990, prrfs04_17, prrfs04_7 | |
| 4 | Glyma.04g190400 | * | * | SCN races: 3, 4, 14 | meta, SCN14, soyscnyoung94_3 |
| Glyma.04g227900 | * | Brown stem rot | bsrcodeall | ||
| 5 | Glyma.05g137500/Glyma.05g137800 | * | Brown stem rot | bsr97, bsrcode492477 | |
| 6 | Glyma.06g199600/Glyma.06g197800 | * | * | Frogeye leaf spot, race 2 | 2ky91, Fe2, meta |
| 7 | Glyma.07g192200 | * | * | SCN races: 1, 3, 5, 14 | meta, SCN14, SCN14.491576, SCN14code.491576, soyscnanand_3, soyscnanand_5, soyscnyoung94_3, soyscnyoung94_5 |
| 8 | Glyma.08g231100 | * | * | SCN races: 3, 5, 14 | meta, SCN14, soyscnyoung94_5, soyscnyoung94_14 |
| Rhg4 | * | * | SCN races: 1, 3, 5, 14 | meta, SCN1, SCN14, soyscnyoung94_3 | |
| 10 | Glyma.10g273300/276600 | * | * | SCN races: 14 | meta, SCN14, SCN14.491576, SCN14code.491576, soyscnyoung94_14 |
| 11 | Glyma.11g233500 | * | Phytophthora root rot races: 17 | PRR17.492990 | |
| Glyma.11g234500 (SNAP11) | * | * | SCN races 1, 3, 4, 14 | meta, SCN14, sojascnarelli00, soyscnanand_5, soyscnyoung88_5, soyscnyoung94_5, soyscnyoung94_14 | |
| 12 | Glyma12g22660 | * | SCN races: 1 | SCN1 | |
| 13 | Glyma.13g222300 | * | * | SCN races: 1, 3, 14 | meta, SCN14, sojascnarelli00, soyscnyoung94_14 |
| Rag2/Rag5 | * | Soybean aphid | aphidcm02 | ||
| Rps3 | * | * | Phytophthora root rot races: 1, 4, 12, 20, 25 | PRR1, PRR1.10004, PRR1.11003, PRR1.492990, PRR12, PRR20, PRR25, PRR25.491404, PRR25.492990, PRR4, PRR4.492990, meta | |
| Rsv1 | * | Peanut mottle virus | pmv | ||
| 14 | Glyma.14g098900 | * | Brown stem rot | bsr97, bsrcode492477 | |
| NSC14 | * | Northern stem canker | NSC, NSC.491493 | ||
| 15 | Glyma.15g052000 | * | Phytophthora root rot races: 2 | PRR2 | |
| 16 | Glyma.16g096900 | * | Phytophthora root rot races: 2 | PRR2 | |
| Rag3 | * | Soybean aphid | aphidcm02 | ||
| Rbs1/ Rbs2/ Rbs3 | * | Brown stem rot | bsr97, bsr491584, bsrall, bsrcodeall | ||
| Rcs3 | * | * | Frogeye leaf spot, race 2 | 2il81.1, Fe2, meta | |
| Rps2 | * | * | Phytophthora root rot races: 2, 25 | PRR2, meta | |
| 17 | Glyma.17g090200 | * | Bean pod mottle virus | bpmvall | |
| 18 | Glyma.18g138700 | * | Phytophthora root rot races: 5 | PRR5, PRR5.492990 | |
| Rhg1 | * | * | SCN races: 3, 4, 5, 14 | meta, SCN14, soyscnanand_3, soyscnyoung88_5, soyscnyoung94_3, soyscnyoung94_14 | |
| Rps4 | * | * | Phytophthora root rot races: 1, 3, 4, 25 | meta, PRR1, PRR1.10001, PRR1.10002, PRR1.10004, PRR1.488001, PRR25, PRR25.491404, PRR4 |
* Bonferroni corrected P-value threshold [p-value 0.05 / number of markers].