Table 4. Association mapping for alkaline and salt tolerance traits using epistasis association mapping and an enriched compressed mixed linear model (E-cMLM).
| Trait | Epistatic association mapping | Similar result | |||||||
| Marker | Linkage group | Position (cM) | LOD | Var | r 2(%) | E-cMLM | Jointly E-cMLM | Previous study | |
| LR | satt289 | C2 | 112.34 | 24.49 | 0.03 | 0.18 | sat_252☆(09CK§,09AL) | staga001(M×Y) | Cho et al(2002) |
| sat_252 | C2 | 127 | 4.69 | 0.10 | 0.73 | √(09CK, 09AL) | √(M×Y) | Cho et al(2002) | |
| satt580 | D1a | 62.36 | 6.55 | 0.02 | 0.18 | satt077(M×Y) | |||
| satt296 | D1b | 52.61 | 4.70 | 0.03 | 0.19 | √(09CK) | satt282(M×Y) | Chen et al (2008) | |
| satt459 | D1b | 118.62 | 5.37 | 0.08 | 0.56 | satt274(10AL) | √(M×Y) | ||
| satt672 | D2 | 114.97 | 4.32 | 0.03 | 0.21 | satt413(10CK,10SA) | satt413(M×Y) | ||
| satt263 | E | 45.4 | 3.33 | 0.06 | 0.45 | satt452(09AL), sat_381(10AL) | √(M×Y) | ||
| satt149 | F | 18.12 | 4.31 | 0.03 | 0.25 | √(10CK), satt659(09CK), BE806387(10AL) | AW186493(M×Y) | ||
| satt222 | H | 68.08 | 3.76 | 0.07 | 0.48 | satt142(09SA) | √(M×Y) | ||
| sat_224 | J | 75.12 | 3.15 | 0.13 | 0.98 | √(09CK), satt431(09AL) | |||
| satt244 | J | 65.04 | 3.79 | 0.32 | 2.38 | sat_224(09CK), satt431(09AL) | sat_165(M×Y) | Chen et al (2008) | |
| sct_190 | K | 77.37 | 7.81 | 0.04 | 0.30 | √(M×Y) | |||
| satt166 | L | 66.51 | 27.34 | 0.04 | 0.28 | ||||
| satt683 | N | 34.52 | 7.86 | 0.11 | 0.81 | sat_266(10AL) | satt631(M×Y) | ||
| satt234 | N | 84.59 | 3.47 | 0.01 | 0.07 | satt237(10SA) | satt255(M×Y) | Li et al (2004);Chen et al (2008) | |
| satt022 | N | 102.05 | 3.86 | 0.31 | 2.31 | √(M×Y) | Li et al (2004);Chen et al (2008) | ||
| satt331 | O | 93.37 | 6.07 | 0.04 | 0.29 | satt592(09SA) | √(M×Y) | ||
| FWR | sat_267 | A1 | 78.44 | 3.40 | 0.00 | 0.86 | satt200(09CK,10CK) | √(M) | |
| satt390 | A2 | 9.14 | 3.14 | 0.00 | 0.25 | √(M,M×T) | |||
| satt509 | B1 | 32.5 | 6.39 | 0.00 | 0.37 | Chen et al (2008) | |||
| satt289 | C2 | 112.34 | 18.14 | 0.00 | 0.27 | satt277(09SA,09AL,10SA) | √(M) | Cho et al (2002) | |
| sat_252 | C2 | 127 | 4.17 | 0.00 | 0.99 | satt277(09SA, 09AL,10SA) | √(M) | Cho et al (2002) | |
| satt672 | D2 | 114.97 | 8.78 | 0.00 | 0.23 | satt256(09CK,09SA,10CK) | √(M) | ||
| sat_381 | E | 64.18 | 6.12 | 0.00 | 0.78 | √(M) | |||
| satt269 | F | 11.37 | 6.21 | 0.00 | 0.21 | BE806387(09CK,09AL),satt149(10SA) | satt149(M) | ||
| sat_390 | F | 1.79 | 3.40 | 0.00 | 1.06 | BE806387(09CK,09AL),satt149(10SA) | √(M) | ||
| satt215 | J | 44.08 | 3.81 | 0.00 | 0.35 | √(09SA),satt132(10AL) | satt244(M) | Chen et al (2008) | |
| sct_190 | K | 77.37 | 40.07 | 0.00 | 0.19 | satt260(10SA) | √(M) | ||
| satt238 | L | 19.93 | 3.86 | 0.00 | 0.30 | satt652(M) | |||
| satt463 | M | 50.09 | 5.31 | 0.00 | 0.87 | √(09AL),satt626(09CK),satt245(09SA) | √(M,M×Y) | Chen et al (2008) | |
| satt234 | N | 84.59 | 87.87 | 0.00 | 0.06 | satt022(09CK),satt237(09SA) | satt237(M) | Li et al (2004);Chen et al (2008) | |
| DWR | satt453 | B1 | 123.95 | 3.83 | 0.00 | 4.38 | √(10SA) | ||
| satt669 | D2 | 67.7 | 3.11 | 0.00 | 0.13 | ||||
| satt302 | H | 81.04 | 3.33 | 0.00 | 0.32 | ||||
| sct_190 | K | 77.37 | 10.32 | 0.00 | 0.08 | ||||
| LH | satt453 | B1 | 123.95 | 5.65 | 0.05 | 0.75 | √(09SA) | √(M) | |
| sat_355 | B2 | 66.23 | 3.78 | 0.01 | 0.22 | satt534(10SA) | √(M) | Chen et al (2008) | |
| satt289 | C2 | 112.34 | 24.06 | 0.02 | 0.25 | sat_252(09CK),staga001(09SA,10SA,10AL),satt202(10CK) | satt277(M) | Cho et al (2002) | |
| satt254 | D1a | 56.43 | 3.49 | 0.03 | 0.42 | satt580(09SA) | AW781285(M) | ||
| satt580 | D1a | 62.36 | 11.47 | 0.00 | 0.01 | satt580(09-NaCl) | AW781285(M) | ||
| satt296 | D1b | 52.61 | 10.20 | 0.03 | 0.48 | √(09AL,10SA,10AL),sat_254(09CK) | √(M) | Chen et al (2008) | |
| sat_254 | D1b | 46.91 | 4.36 | 0.06 | 1.00 | √(09CK),satt296(09AL,10SA,10AL) | satt296(M) | Chen et al (2008) | |
| satt669 | D2 | 67.7 | 3.55 | 0.02 | 0.33 | satt226(10CK) | satt226(M) | Tuyen et al (2010) | |
| sat_354 | D2 | 93.7 | 4.75 | 0.12 | 2.00 | √(09SA),satt514(10CK) | √(M,M×Y) | Tuyen et al (2010) | |
| sat_381 | E | 64.18 | 7.56 | 0.03 | 0.46 | √(09AL),satt045(09SA),satt263(10AL) | √(M) | ||
| satt149 | F | 18.12 | 16.35 | 0.00 | 0.07 | BE806387(09CK,09AL,10CK,10AL),AW186493(09SA),satt659(10SA) | BE806387(M) | ||
| satt160 | F | 33.18 | 3.74 | 0.11 | 1.82 | BE806387(09CK,09AL,10CK),AW186493(09SA),satt659(10SA,10AL) | √(M) | ||
| satt309 | G | 4.53 | 4.25 | 0.10 | 1.55 | satt688(10CK) | √(M,M×Y) | Cho et al(2002) | |
| satt222 | H | 68.08 | 4.03 | 0.02 | 0.36 | √(M,M×Y) | |||
| satt354 | I | 46.22 | 3.73 | 0.06 | 0.98 | √(10CK,10AL),satt270(09CK,09AL) | √(M,M×Y) | ||
| sat_228 | J | 23.91 | 4.41 | 0.02 | 0.39 | sat_165(09AL,10SA,10AL) | sat_165(M) | Chen et al (2008) | |
| satt441 | K | 46.2 | 4.61 | 0.03 | 0.42 | √(M) | Chen et al (2008) | ||
| satt166 | L | 66.51 | 5.46 | 0.01 | 0.17 | satt527(10SA) | |||
| satt683 | N | 34.52 | 18.58 | 0.03 | 0.43 | √(M) | |||
| satt234 | N | 84.59 | 85.46 | 0.00 | 0.07 | satt237(M,M×Y) | Li et al (2004);Chen et al (2008) | ||
| sat_266 | N | 47.27 | 5.49 | 0.06 | 0.97 | √(M) | |||
| BS | satt390 | A2 | 9.14 | 5.67 | 0.00 | 0.22 | √(09SA,09AL) | √(M) | |
| satt233 | A2 | 100.08 | 6.10 | 0.00 | 0.55 | √(09CK,10SA,10AL) | √(M,M×Y) | ||
| satt453 | B1 | 123.95 | 4.13 | 0.00 | 0.46 | √(M) | |||
| satt565 | C1 | 0 | 5.65 | 0.00 | 0.53 | ||||
| sat_252 | C2 | 127 | 3.84 | 0.00 | 0.74 | satt277(09SA,09AL) | √(M) | Cho et al (2002) | |
| satt580 | D1a | 62.36 | 3.41 | 0.00 | 0.21 | AW781285(10CK) | √(M×Y) | ||
| satt274 | D1b | 116.34 | 9.04 | 0.00 | 0.58 | √(09CK,09AL,10AL) | √(M) | ||
| satt256 | D2 | 124.3 | 3.28 | 0.00 | 0.51 | √(09CK,09SA,09AL) | satt672(M) | ||
| satt413-satt672 | D2 | 113.61–114.97 | 5.91–13.60 | 0.00 | 0.27–0.41 | satt256(09CK,09SA,09AL) | √(M) | ||
| sat_381 | E | 64.18 | 5.37 | 0.00 | 0.74 | √(M) | |||
| satt269 | F | 11.37 | 6.44 | 0.00 | 0.27 | BE806387(09CK,09AL) | √(M) | ||
| satt656 | F | 135.11 | 4.82 | 0.00 | 0.95 | √(M) | Chen et al (2008) | ||
| satt659×sat_354 | F×D2 | 26.7×93.7 | 3.04 | 0.01 | 3.29 | BE806387(09CK,09AL),sat_354(09SA) | satt659(M),sat_362(M) | Tuyen et al (2010) | |
| sat_390×sat_254 | F×D1b | 1.79×46.91 | 3.23 | 0.01 | 9.00 | BE806387(09CK,09AL),sat_254(09CK) | sat_390(M),satt296(M) | ||
| satt222 | H | 68.08 | 7.70 | 0.00 | 0.29 | √(09SA,09AL) | √(M) | ||
| satt132 | J | 39.18 | 4.79 | 0.00 | 0.46 | satt215(09AL) | √(M) | Chen et al (2008) | |
| satt244 | J | 65.04 | 4.18 | 0.00 | 1.60 | satt215(09AL) | √(M) | Chen et al (2008) | |
| satt244×sat_160 | J×D1a | 65.04×104.27 | 3.15 | 0.02 | 11.41 | satt215(09AL) | satt244(M),sat_160(M) | ||
| sct_190 | K | 77.37 | 42.52 | 0.00 | 0.11 | √(09CK,09AL),satt260(10CK,10SA) | √(M) | ||
| satt238 | L | 19.93 | 4.23 | 0.00 | 0.18 | satt652(M) | |||
| sat_391 | M | 1.02 | 5.57 | 0.00 | 1.36 | √(10CK) | √(M) | ||
| satt234 | N | 84.59 | 20.49 | 0.00 | 0.08 | satt022(09CK,09AL) | √(M) | Li et al (2004);Chen et al (2008) | |
| satt022 | N | 102.05 | 3.97 | 0.00 | 1.42 | √(09CK,09AL) | √(M) | Li et al (2004);Chen et al (2008) | |
| satt331 | O | 93.37 | 5.54 | 0.00 | 0.18 | sat_274(09AL) | √(M) | ||
: the same association marker detected by different approach;
: year, i.e., 2009, and 2010; SA: salt; AL: alkaline.
: marker in similar result column is linked to the associated marker in this study; M: main-effect QTL; Y: year; T: treatment. LR: Length of main root; FWR: Fresh weight of root; DWR: Dried weight of root; LH; Length of hypocotyl; BS: Biomass.