Table 2.
List of 24 single-nucleotide polymorphism (SNP) markers associated and flanked (genomic window of 1 kb) to 22 genes related with the heat stress (HS) response such as activation of heat shock proteins (22.73%), abiotic stress signaling (18.18%), germination and seedling development (18.18%), flowering time (9.09%), protein domain thermostability (9.09%), molecular chaperones (9.09%), and stability of the cell wall (4.55%) using PhytoMine B and reference genome of common bean v2.1.
| Gene Name | GEA Model | Associated SNPs | Gen |
|---|---|---|---|
| Activation of heat shock proteins—five genes (22.73%) | |||
| Phvul.003G021100 | HITSUPER(CMLM)-PC-EMMA | S1_103273611 | MED23 |
| Phvul.003G028300 | HITSUPER(CMLM)-PC-EMMA | S1_104075622 | MED25 |
| Phvul.003G038600 | HITSUPER(CMLM)-PC-EMMA, HSISUPER(CMLM)-PC-EMMA, HITBLINK-PC-EMMA | S1_105404421 | Hsp40 —Pv03 |
| Phvul.002G136100 | HSIFARMCPU-PC-EMMA, HITFARMCPU-PC-EMMA, HSIBLINK-PC-EMMA, HIT BLINK-PC-EMMA | S1_80309359 | Hsp40—Pv02 |
| Phvul.006G182100 | HITFARMCPU-TESS3-EMMA, HITBLINK-TESS3-EMMA | S1_268677251 | Hsp40—Pv06 |
| Phvul.002G019100 | HSIFARMCPU-TESS3-EMMA | S1_54254560 | HSFB1 (HSF4) |
| Phvul.008G227900 | PCA1FARMCPU-TESS3-EMMA, PCA1BLINK-TESS3-EMMA | S1_381855152 | HSP20 |
| Abiotic stress signaling—four genes (18.18%) | |||
| Phvul.008G204500 | PCA1SUPER(CMLM)-PC-EMMA | S1_379270378 | NFY |
| Phvul.002G142500 | PCA1FARMCPU-PC-EMMA, PCA1BLINK-PC-EMMA | S1_81263655 | AUX_IAA |
| Phvul.006G014100 | HSIFARMCPU-TESS3-EMMA | S1_246823134 | Phospholipase CPLC |
| Phvul.001G202000 | HSIFARMCPU-PC-EMMA, PCA1FARMCPU-PC-EMMA, HSIBLINK-PC-EMMA, PCA1BLINK-PC-EMMA, HITBLINK-TESS3-EMMA | S1_46052073 | Auxin response factor |
| Germination and seedling development–four genes (18.18%) | |||
| Phvul.005G175800 | HSISUPER(CMLM)-PC-EMMA, HITSUPER(CMLM)-PC-EMMA | S1_239620265 | Glycoside hydrolases family 28 |
| Phvul.002G016700 | HSIFARMCPU-TESS3-EMMA | S1_53999562 | Family AP2/ERF |
| Phvul.001G171600 | HSISUPER(CMLM)-PC-EMMA, PCA1SUPER(CMLM)-PC-EMMA | S1_42870591 | Ankyrin-B (Ankyrin-2) |
| Phvul.011G054400 | PCA1FARMCPU-PC-EMMA, PCA1BLINK-PC-EMMA | S1_469234219 | Pkinase_Tyr |
| Flowering time—two genes (9.09%) | |||
| Phvul.006G119900 | PCA1SUPER(CMLM)-PC-EMMA | S1_263134744 | Poly(A) polymerase PAP |
| Phvul.004G017600 | HITSUPER(CMLM)-PC-EMMA, PCA1FARMCPU-TESS3-EMMA, HSIFARMCPU-TESS3-EMMA, PCA1BLINK-TESS3-EMMA | S1_155643598 | MBD9 |
| Protein domain thermostability—two genes (9.09%) | |||
| Phvul.011G058100 | PCA1FARMCPU-PC-EMMA, PCA1BLINK-PC-EMMA | S1_469639214 | Zinc finger A20 and AN1 |
| Phvul.002G287600 | PCA1FARMCPU-PC-EMMA, HSIFARMCPU-PC-EMMA, HSIBLINK-PC-EMMA, PCA1BLINK-PC-EMMA | S1_97861798 | S1 |
| Molecular chaperones—two genes (9. 09%) | |||
| Phvul.009G032500 | HSIFARMCPU-TESS3-EMMA | S1_391075082 | 14-3-3 proteins family |
| Phvul.010G024400 | PCA1FARMCPU-PC-EMMA, PCA1BLINK-PC-EMMA | S1_424636676 | FKBP |
| DNA transcription—two genes (9. 09%) | |||
| Phvul.008G022950 | PCA1FARMCPU-PC-EMMA, PCA1BLINK-PC-EMMA | S1_325947871 | BRIX |
| Phvul.006G130200 | HSIFARMCPU-PC-EMMA, HITFARMCPU-PC-EMMA, PCA1FARMCPU-PC-EMMA, HSIBLINK-PC-EMMA, HITBLINK-PC-EMMA, HITFARMCPU-TESS3-EMMA, HITBLINK-TESS3-EMMA | S1_264118438 | YTH protein domain |
| Stability of the cell wall—one gene (4.55%) | |||
| Phvul.001G267000 | PCA1FARMCPU-PC-EMMA, PCA1BLINK-PC-EMMA | S1_51236796 | GAE6 |