Table 2. Association of 18 rice starch-related genes with rice starch physico-chemical traits in a population of 233 Australian rice breeding lines.
| Gene | Trait | Locus/SNP | F-test | p-adjusted value | R2_Marker | |
|---|---|---|---|---|---|---|
| AGPS2b | Section 1 | No functional polymorphism found in this gene | - | - | - | |
| SPHOL | Section 2 | No functional polymorphism found in this gene | - | - | - | |
| GBSSI | Section 3 | Peak1 | WAXYEXIN1 | 34.346 | 9.99E-04 | 0.23 |
| Trough1 | WAXYEX10 | 36.9498 | 9.99E-04 | 0.1384 | ||
| Breakdown | WAXYEXIN1 | 35.1893 | 9.99E-04 | 0.2343 | ||
| Breakdown | WAXYEX10 | 18.9223 | 9.99E-04 | 0.076 | ||
| Final Viscosity | WAXYEXIN1 | 15.0534 | 9.99E-04 | 0.1157 | ||
| Final Viscosity | WAXYEX10 | 106.068 | 9.99E-04 | 0.3156 | ||
| Setback | WAXYEXIN1 | 76.2739 | 9.99E-04 | 0.3988 | ||
| Setback | WAXYEX10 | 59.8068 | 9.99E-04 | 0.2064 | ||
| Martin_N | WAXYEXIN1 | 223.294 | 9.99E-04 | 0.6601 | ||
| Martin_N | WAXYEX10 | 147.783 | 9.99E-04 | 0.3912 | ||
| Martin_N | WAXYEX6 | 16.8014 | 9.99E-04 | 0.0681 | ||
| AC_percent | WAXYEXIN1 | 121.53 | 9.99E-04 | 0.5138 | ||
| AC_percent | WAXYEX10 | 44.0661 | 9.99E-04 | 0.1608 | ||
| AC_percent | WAXYEX6 | 16.2252 | 9.99E-04 | 0.0659 | ||
| predicted_N | WAXYEXIN1 | 121.543 | 9.99E-04 | 0.5138 | ||
| predicted_N | WAXYEX10 | 43.967 | 9.99E-04 | 0.1605 | ||
| predicted_N | WAXYEX6 | 16.3841 | 9.99E-04 | 0.0665 | ||
| GBSSII | Section 4 | Past_temp | GBSSII_GA_Ref1638 | 27.8519 | 9.99E-04 | 0.2028 |
| GT | GBSSII_GA_Ref1638 | 9.7254 | 9.99E-04 | 0.0938 | ||
| SSI | Section 5 | Trough1 | SSI_TBGU272768_5153 | 14.2713 | 9.99E-04 | 0.0592 |
| FinalVisc | SSI_TBGU272768_5153 | 43.6138 | 9.99E-04 | 0.1612 | ||
| Setback | SSI_TBGU272768_5153 | 28.8805 | 9.99E-04 | 0.1129 | ||
| Martin_N | SSI_TBGU272768_5153 | 45.7145 | 9.99E-04 | 0.1676 | ||
| AC_percent | SSI_TBGU272768_5153 | 20.5891 | 9.99E-04 | 0.0832 | ||
| predicted_N | SSI_TBGU272768_5153 | 20.4244 | 9.99E-04 | 0.0825 | ||
| SSIIa | Section 6 | Breakdown | ALKSSIIA4 | 22.4536 | 9.99E-04 | 0.1682 |
| PeakTime | ALKSSIIA4 | 53.0867 | 9.99E-04 | 0.3235 | ||
| Past_temp | ALKSSIIA4 | 199.652 | 9.99E-04 | 0.6427 | ||
| GT | ALKSSIIA4 | 32.806 | 9.99E-04 | 0.2547 | ||
| Chalk% | ALKSSIIA4 | 8.9273 | 9.99E-04 | 0.0744 | ||
| SSIIb | Section 7 | No functional polymorphism found in this gene | - | - | - | |
| SSIIIa | Section 8 | FinalVisc | SSIIIa_GA_Ref1379 | 9.0413 | 9.99E-04 | 0.0753 |
| FinalVisc | SSIIIa_GA_Ref1722ER | 8.8028 | 9.99E-04 | 0.0723 | ||
| FinalVisc | SSIIIa_GA_Ref5466 | 8.9423 | 9.99E-04 | 0.0736 | ||
| Setback | SSIIIa_GA_Ref1680 | 7.8821 | 9.99E-04 | 0.0655 | ||
| Setback | SSIIIa_GA_Ref1379 | 11.6269 | 9.99E-04 | 0.0948 | ||
| Setback | SSIIIa_GA_Ref1722ER | 10.1037 | 9.99E-04 | 0.0821 | ||
| Setback | SSIIIa_GA_Ref5466 | 9.0543 | 9.99E-04 | 0.0745 | ||
| Past_temp | SSIIIa_GA_Ref1058 | 8.7158 | 9.99E-04 | 0.0722 | ||
| Past_temp | SSIIIa_GA_Ref1680 | 7.4574 | 9.99E-04 | 0.0622 | ||
| Past_temp | SSIIIa_GA_Ref1379 | 7.9273 | 9.99E-04 | 0.0667 | ||
| Past_temp | SSIIIa_GA_Ref1722ER | 9.3315 | 9.99E-04 | 0.0763 | ||
| Past_temp | SSIIIa_GA_Ref10761 | 7.2026 | 9.99E-04 | 0.062 | ||
| Past_temp | SSIIIa_GA_Ref5466 | 8.756 | 9.99E-04 | 0.0722 | ||
| Martin_N | SSIIIa_GA_Ref1058 | 13.2478 | 9.99E-04 | 0.1058 | ||
| Martin_N | SSIIIa_GA_Ref1680 | 20.8545 | 9.99E-04 | 0.1564 | ||
| Martin_N | SSIIIa_GA_Ref1379 | 27.7893 | 9.99E-04 | 0.2002 | ||
| Martin_N | SSIIIa_GA_Ref1708 | 16.5211 | 9.99E-04 | 0.1301 | ||
| Martin_N | SSIIIa_GA_Ref1722ER | 20.6652 | 9.99E-04 | 0.1546 | ||
| Martin_N | SSIIIa_GA_Ref1357 | 7.6136 | 9.99E-04 | 0.0639 | ||
| Martin_N | SSIIIa_GA_Ref5466 | 20.4182 | 9.99E-04 | 0.1536 | ||
| AC_percent | SSIIIa_GA_Ref1680 | 10.3167 | 9.99E-04 | 0.084 | ||
| AC_percent | SSIIIa_GA_Ref1379 | 14.2201 | 9.99E-04 | 0.1136 | ||
| AC_percent | SSIIIa_GA_Ref1708 | 9.3351 | 9.99E-04 | 0.0779 | ||
| AC_percent | SSIIIa_GA_Ref1722ER | 10.6866 | 9.99E-04 | 0.0864 | ||
| AC_percent | SSIIIa_GA_Ref5466 | 11.1556 | 9.99E-04 | 0.0902 | ||
| predicted_N | SSIIIa_GA_Ref1680 | 10.2716 | 9.99E-04 | 0.0837 | ||
| predicted_N | SSIIIa_GA_Ref1379 | 14.2099 | 9.99E-04 | 0.1135 | ||
| predicted_N | SSIIIa_GA_Ref1708 | 9.3091 | 9.99E-04 | 0.0777 | ||
| predicted_N | SSIIIa_GA_Ref1722ER | 10.6615 | 9.99E-04 | 0.0862 | ||
| predicted_N | SSIIIa_GA_Ref5466 | 11.1281 | 9.99E-04 | 0.09 | ||
| GT | SSIIIa_GA_Ref1680 | 10.0271 | 9.99E-04 | 0.0946 | ||
| GT | SSIIIa_GA_Ref1708 | 30.2791 | 9.99E-04 | 0.2436 | ||
| GT | SSIIIa_GA_Ref1722ER | 15.2535 | 9.99E-04 | 0.1365 | ||
| Chalk% | SSIIIa_GA_Ref3559 | 8.9878 | 9.99E-04 | 0.0821 | ||
| SSIIIb | Section 9 | Peak Viscosity | SSIIIb_GA_Ref7255ER | 7.7442 | 9.99E-04 | 0.0666 |
| Past_temp | SSIIIb_GA_Ref4543 | 21.3553 | 9.99E-04 | 0.2251 | ||
| Past_temp | SSIIIb_GA_Ref5451 | 23.0673 | 9.99E-04 | 0.176 | ||
| Past_temp | SSIIIb_GA_Ref1315 | 25.0653 | 9.99E-04 | 0.1849 | ||
| Past_temp | SSIIIb_GA_Ref7232 | 41.4018 | 9.99E-04 | 0.3151 | ||
| Past_temp | SSIIIb_GA_Ref7255ER | 29.1937 | 9.99E-04 | 0.212 | ||
| Past_temp | SSIIIb_GA_Ref7437 | 21.0809 | 9.99E-04 | 0.1572 | ||
| SSIVa | Section 10 | PeakTime | SSIva_GA_Ref7160 | 10.7899 | 9.99E-04 | 0.0875 |
| Past_temp | SSIva_GA_Ref4048 | 27.6864 | 9.99E-04 | 0.1989 | ||
| Past_temp | SSIva_GA_Ref7160 | 39.5053 | 9.99E-04 | 0.2599 | ||
| Past_temp | SSIva_GA_Ref7823 | 30.2856 | 9.99E-04 | 0.2159 | ||
| Past_temp | SSIva_GA_Ref8383 | 30.8007 | 9.99E-04 | 0.2227 | ||
| Past_temp | SSIva_GA_Ref7506 | 29.3874 | 9.99E-04 | 0.205 | ||
| AC_percent | SSIva_GA_Ref7160 | 9.1222 | 9.99E-04 | 0.075 | ||
| predicted_N | SSIva_GA_Ref7160 | 9.077 | 9.99E-04 | 0.0747 | ||
| GT | SSIva_GA_Ref4048 | 8.5371 | 9.99E-04 | 0.0825 | ||
| GT | SSIva_GA_Ref7160 | 19.7873 | 9.99E-04 | 0.1709 | ||
| GT | SSIva_GA_Ref7823 | 10.209 | 9.99E-04 | 0.098 | ||
| GT | SSIva_GA_Ref8383 | 10.4426 | 9.99E-04 | 0.1014 | ||
| GT | SSIva_GA_Ref7506 | 10.6137 | 9.99E-04 | 0.0982 | ||
| SSIVb | Section 11 | No polymorphism detected in this gene | ||||
| BEI | Section 12 | Peak Viscosity | BEI_GA_Ref1558 | 9.5546 | 9.99E-04 | 0.0796 |
| Breakdown | BEI_GA_Ref1558 | 11.2003 | 9.99E-04 | 0.092 | ||
| FinalViscosity | BEI_GA_Ref1558 | 13.0129 | 9.99E-04 | 0.1054 | ||
| Setback Viscosity | BEI_GA_Ref1558 | 32.1812 | 9.99E-04 | 0.2255 | ||
| Past_temp | BEI_GA_Ref1558 | 8.4131 | 9.99E-04 | 0.0708 | ||
| Martin_N | BEI_GA_Ref1558 | 34.5608 | 9.99E-04 | 0.2383 | ||
| AC_percent | BEI_GA_Ref1558 | 38.8652 | 9.99E-04 | 0.2602 | ||
| predicted_N | BEI_GA_Ref1558 | 39.1031 | 9.99E-04 | 0.2614 | ||
| BEIIa | Section 13 | No significant association was observed with starch traits | - | - | - | |
| BEIIb | Section 14 | No significant association was observed with starch traits | - | - | - | |
| Iso1 | Section 15 | No polymorphism detected in this gene | - | - | - | |
| Iso2 | Section 16 | Breakdown | Iso2_GA_Ref1712 | 8.2378 | 9.99E-04 | 0.0768 |
| Breakdown | Iso2_GA_Ref960 | 9.0028 | 9.99E-04 | 0.076 | ||
| Past_temp | Iso2_GA_Ref1712 | 7.8355 | 9.99E-04 | 0.0733 | ||
| Past_temp | Iso2_GA_Ref960 | 7.8341 | 9.99E-04 | 0.0668 | ||
| Chalk% | Iso2_GA_Ref1712 | 7.2855 | 9.99E-04 | 0.0685 | ||
| Chalk% | Is02_GA_Ref960 | 8.2391 | 9.99E-04 | 0.07 | ||
| Pullulanase | Section 17 | Past_temp | Pullu_TBGU185983_1938 | 23.5989 | 9.99E-04 | 0.1747 |
| GT | Pullu_TBGU185983_1938 | 19.1496 | 9.99E-04 | 0.167 | ||
| Chalk% | Pullu_TBGU185989_2380 | 7.5266 | 9.99E-04 | 0.0666 | ||
| GPT1 | Section 18 | Peak Viscosity | GPT1_GA_Ref_1188 | 21.1979 | 9.99E-04 | 0.092 |
| Break down | GPT1_GA_Ref_1188 | 37.1798 | 9.99E-04 | 0.148 | ||
| Final viscosity | GPT1_GA_Ref_1188 | 31.1074 | 9.99E-04 | 0.126 | ||
| Set back viscosity | GPT1_GA_Ref_1188 | 83.2826 | 9.99E-04 | 0.282 | ||
| Martin_N | GPT1_GA_Ref_1188 | 292.143 | 9.99E-04 | 0.577 | ||
| AC_percent | GPT1_GA_Ref_1188 | 123.047 | 9.99E-04 | 0.365 | ||
| Predicted N | GPT1_GA_Ref_1188 | 122.543 | 9.99E-04 | 0.364 | ||