Table 3.
Significant SNP markers associated with stress susceptibility indexes (SSI) for measured traits.
| Trait | SSI-DW | SSI-PH | SSI-LCC | SSI-SC | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Marker | Variant | Chr. | F | P-value | R2 | F | P-value | R2 | F | P-value | R2 | F | P-value | R2 | Candidate |
| S1_203399656 | T/A | 6 | 46.32 | 1.96E-16 | 0.38 | 9.98 | 8.46E-05 | 0.12 | NS | NS | NS | NS | NS | NS | core-2/I-branching enzyme |
| S1_177465179 | G/A | 5 | 37.02 | 4.50E-14 | 0.33 | NS | NS | NS | NS | NS | NS | NS | NS | NS | FPGS |
| S1_92290094 | T/C | 3 | 35.07 | 2.41E-13 | 0.31 | NS | NS | NS | NS | NS | NS | NS | NS | NS | GRF |
| S1_77343899 | A/G | 3 | 30.56 | 5.75E-12 | 0.28 | NS | NS | NS | NS | NS | NS | NS | NS | NS | – |
| S1_213944479 | G/T | 7 | 26.62 | 1.36E-10 | 0.27 | NS | NS | NS | 22.13 | 3.97E-09 | 0.23 | 10.09 | 7.84E-05 | 0.12 | – |
| S1_6017132 | A/G | 1 | 24.85 | 4.59E-10 | 0.25 | NS | NS | NS | 18.48 | 6.52E-08 | 0.25 | 9.09 | 1.86E-04 | 0.11 | B3-DBP |
| S1_192366282 | A/G | 6 | 18.98 | 4.61E-08 | 0.20 | NS | NS | NS | NS | NS | NS | – | |||
| S1_165051149 | T/C | 5 | 30.06 | 1.48E-07 | 0.15 | NS | NS | NS | 20.3 | 1.22E-05 | 0.11 | NS | NS | NS | – |
| S1_5487588 | T/G | 1 | 23.17 | 3.12E-06 | 0.11 | 16.8 | 6.26E-05 | 0.08 | 38.91 | 3.06E-09 | 0.18 | NS | NS | NS | cold regulated protein |
| S1_5487587 | T/G | 1 | 16.26 | 8.15E-05 | 0.08 | 18.24 | 3.16E-05 | 0.09 | 41.49 | 1.05E-09 | 0.19 | NS | NS | NS | cold regulated protein |
| S1_144642771 | C/T | 4 | 13.21 | 4.36E-06 | 0.13 | NS | NS | NS | NS | NS | NS | NS | NS | NS | xylose isomerase |
| S1_96848431 | A/T | 3 | 22.04 | 5.49E-06 | 0.12 | NS | NS | NS | NS | NS | NS | NS | NS | NS | – |
| S1_185177431 | G/A | 5 | 12.75 | 7.61E-06 | 0.14 | NS | NS | NS | NS | NS | NS | NS | NS | NS | – |
| S1_245279638 | T/A | 8 | 12.62 | 7.96E-06 | 0.13 | NS | NS | NS | NS | NS | NS | NS | NS | NS | – |
| S1_238398605 | A/T | 7 | 12.42 | 8.72E-06 | 0.12 | NS | NS | NS | 11.05 | 2.94E-05 | 0.11 | NS | NS | NS | TPPPK |
| S1_238398606 | T/C | 7 | 12.42 | 8.72E-06 | 0.12 | NS | NS | NS | 11.05 | 2.94E-05 | 0.11 | NS | NS | NS | TPPPK |
| S1_238398607 | C/A | 7 | 12.42 | 8.72E-06 | 0.12 | NS | NS | NS | 11.05 | 2.94E-05 | 0.11 | NS | NS | NS | TPPPK |
| S1_90053345 | T/C | 3 | 20.92 | 9.14E-06 | 0.11 | 18.48 | 2.87E-05 | 0.12 | NS | NS | NS | NS | NS | NS | – |
| S1_191745080 | T/G | 6 | 11.98 | 1.44E-05 | 0.13 | NS | NS | NS | NS | NS | NS | NS | NS | NS | O-glycosyl hydrolase family 17 protein |
| S1_385914996 | A/G | 1* | 11.7 | 1.78E-05 | 0.12 | NS | NS | NS | NS | NS | NS | NS | NS | NS | cytochrome P450 |
| S1_299186321 | T/C | 1* | 10.7 | 4.05E-05 | 0.11 | NS | NS | NS | NS | NS | NS | NS | NS | NS | 3'-5' exonuclease |
| S1_288752900 | T/A | 1* | 10.54 | 4.70E-05 | 0.10 | NS | NS | NS | 12.26 | 1.02E-05 | 0.12 | NS | NS | NS | IQ-CAM |
| S1_290085723 | T/C | U | 17.34 | 4.87E-05 | 0.09 | NS | NS | NS | NS | NS | NS | NS | NS | NS | – |
| S1_153571394 | T/C | 5 | 10.32 | 5.63E-05 | 0.10 | NS | NS | NS | NS | NS | NS | NS | NS | NS | polyol/monosaccharide transporter 1 |
| S1_305729693 | T/A | 7* | 10.39 | 5.63E-05 | 0.11 | NS | NS | NS | NS | NS | NS | NS | NS | NS | PCD protein |
| S1_113265269 | T/C | 4 | 16.92 | 5.86E-05 | 0.08 | NS | NS | NS | NS | NS | NS | NS | NS | NS | – |
| S1_20159066 | T/C | 1 | 10.18 | 6.91E-05 | 0.11 | NS | NS | NS | NS | NS | NS | NS | NS | NS | syntaxin of plants protein |
| S1_303117164 | C/T | U | 10.21 | 6.97E-05 | 0.12 | NS | NS | NS | NS | NS | NS | NS | NS | NS | E3 ubiquitin-protein ligase ARI7, putative |
| S1_149685785 | C/T | 5 | 16.35 | 7.72E-05 | 0.08 | NS | NS | NS | NS | NS | NS | NS | NS | NS | – |
| S1_330116900 | C/T | U | 9.76 | 9.52E-05 | 0.10 | 10.22 | 6.32E-05 | 0.13 | NS | NS | NS | NS | NS | NS | – |
| S1_259280034 | G/A | 8 | 9.69 | 1.01E-04 | 0.13 | NS | NS | NS | NS | NS | NS | NS | NS | NS | – |
| S1_305729831 | C/T | 7* | 9.53 | 1.18E-04 | 0.14 | NS | NS | NS | NS | NS | NS | NS | NS | NS | PCD protein |
| S1_356690471 | A/T | 4* | 15.25 | 1.33E-04 | 0.08 | NS | NS | NS | 15.15 | 1.39E-04 | 0.08 | NS | NS | NS | peptide/nitrate transporter |
| S1_102344252 | A/C | 3 | NS | NS | NS | NS | NS | NS | 18.21 | 3.17E-05 | 0.09 | NS | NS | NS | RING/U-box protein |
| S1_102344288 | T/A | 3 | NS | NS | NS | NS | NS | NS | 18.21 | 3.17E-05 | 0.09 | NS | NS | NS | RING/U-box protein |
| S1_267271170 | A/G | 8 | NS | NS | NS | NS | NS | NS | 17.21 | 5.51E-05 | 0.10 | NS | NS | NS | – |
| S1_290477928 | A/G | 7* | NS | NS | NS | NS | NS | NS | 16.82 | 6.15E-05 | 0.08 | NS | NS | NS | exportin-T-like protein |
| S1_330575424 | T/C | U | NS | NS | NS | NS | NS | NS | NS | NS | NS | 13.69 | 3.19E-06 | 0.14 | – |
| S1_168377260 | G/T | 5 | NS | NS | NS | NS | NS | NS | NS | NS | NS | 21.39 | 7.08E-06 | 0.12 | – |
| S1_103491012 | T/A | 4 | NS | NS | NS | NS | NS | NS | NS | NS | NS | 17.08 | 5.63E-05 | 0.09 | – |
| S1_81295531 | T/C | 3 | NS | NS | NS | NS | NS | NS | NS | NS | NS | 16.36 | 7.70E-05 | 0.08 | – |
| S1_75996285 | C/G | 3 | NS | NS | NS | NS | NS | NS | NS | NS | NS | 9.86 | 9.31E-05 | 0.11 | – |
Same markers identified in different traits were highlighted by same color. Underlined markers with the same first 6 digitals are located at the same locus. Candidate, putative candidate genes linked to the significant markers. FPGS, folylpolyglutamate synthase; GRF, growth-regulating factor; B3-DBP, B3 DNA-binding protein; TPPK, Thiaminepyrophosphokinase; IQ-CAM, IQ calmodulin-binding motif protein; PCD, programmed cell death protein.
“*″
Unknowns were reassigned to corresponding chromosomes based on the BLAST of the flanking sequence tags against the updated version of M. truncatula genome (Mt4.0 v1).