Table 1. Name and characteristics of SNPs genotyped in 18 rice starch-related genes in a population of 233 Australian rice breeding lines.
| No | Gene | SNP ID* | Coordinates on gDNA | Expected SNP | SNP Assayed† | Association with Physiochemical traits | Status |
|---|---|---|---|---|---|---|---|
| 1 | AGPS2b | TBGU388647 | 233 | G/T | G/G | N/A | No polymorphism |
| 2 | AGPS2b | TBGI050742 | 1507 | T/C | T/T | N/A | No polymorphism |
| 3 | SPHOL | TBGU168031 | 2501 | G/T | G/G | N/A | No polymorphism |
| 4 | SPHOL | TBGU168032 | 2920 | C/T | C/C | N/A | No polymorphism |
| 5 | SPHOL | TBGU168027 | 1001 | C/A | C/C | N/A | No polymorphism |
| 6 | SPHOL | TBGU168024 | 176 | G/T | G/G | N/A | No polymorphism |
| 7 | SPHOL | TBGU168039 | 5514 | G/T | G/G | N/A | No polymorphism |
| 8 | GBSSI | WAXYEXIN1 | 246 | T/G | T/G | P1,BD,FV,SB,MT,AC,PN | Highly associated |
| 9 | GBSSI | WAXYEX6 | 2494 | A/C | A/C | SB,BD,MT,AC | Highly associated |
| 10 | GBSSI | WAXYEX10 | 3486 | C/T | C/T | T1,FV,SB,MT,AC,PN | Highly associated |
| 11 | GBSSII | GBSSII_GA_1638 | 1638 | G/A | G/A | PT, GT | Low-Medium association |
| 12 | SSI | TBGU272768 | 5153 | T/C | T/C | FV,SB,MT | Low-Medium association |
| 13 | SSIIa | SSIIa_GA_Ref631 | 631 | G/T | G/T | N/A | No association |
| 14 | SSIIa | ALKSSIIA4 | 4827–4828 | GC/TT | GC/TT | BDV,SB,PKT,PT,GT,CHK | Highly associated |
| 15 | SSIIb | TBGU116115 | 3416 | A/G | A/A | N/A | No polymorphism |
| 16 | SSIIb | TBGU116120 | 3948 | G/C | G/G | N/A | No polymorphism |
| 17 | SSIIb | TBGU116121 | 3979 | T/C | T/T | N/A | No polymorphism |
| 18 | SSIIb | TBGU116109 | 330 | G/A | A/A | N/A | No polymorphism |
| 19 | SSIIb | TBGU116119 | 3946 | C/T | C/C | N/A | No polymorphism |
| 20 | SSIIb | TBGU116116 | 3487 | T/G | T/T | N/A | No polymorphism |
| 21 | SSIIIa | GA_Ref1058 | 1058 | T/A | T/A | PT,MT, | Low-Medium association |
| 22 | SSIIIa | GA_Ref1680 | 1680 | G/A | G/A | SB,PT,MT,AC,PN,GT | Low associated |
| 23 | SSIIIa | GA_Ref3136 | 3136 | G/A | G/A | N/A | No association |
| 24 | SSIIIa | GA_Ref3391 | 3391 | T/A | T/A | N/A | No association |
| 25 | SSIIIa | GA_Ref3559 | 3559 | T/A | T/A | CHK | Low association |
| 26 | SSIIIa | GA_Ref4384 | 4384 | G/A | G/A | N/A | No association |
| 27 | SSIIIa | GA_Ref1379 | 1379 | A/C | A/C | FV,SB,PT,MT,AC,PN | Low-Medium association |
| 28 | SSIIIa | GA_Ref1708 | 1708 | G/A | G/A | MT,AC,PN,GT | Low-Medium association |
| 29 | SSIIIa | GA_Ref3274 | 3274 | G/A | G/A | N/A | No association |
| 30 | SSIIIa | GA_Ref6242 | 6242 | T/C | T/C | N/A | No association |
| 31 | SSIIIa | GA_Ref1457 | 1457 | A/C | A/C | N/A | No association |
| 32 | SSIIIa | GA_Ref1615 | 1615 | C/T | C/T | N/A | No association |
| 33 | SSIIIa | GA_Ref1834 | 1834 | C/T | C/T | N/A | No association |
| 34 | SSIIIa | GA_Ref2758 | 2758 | G/A | G/A | N/A | No association |
| 35 | SSIIIa | GA_Ref1722ER | 1722 | G/A | G/A | FV,SB,PT,MT,AC,PN,GT | Low-Medium association |
| 36 | SSIIIa | GA_Ref2488 | 2488 | C/T | C/T | N/A | No association |
| 37 | SSIIIa | GA_Ref3073 | 3073 | G/A | G/A | N/A | No association |
| 38 | SSIIIa | GA_Ref1357 | 1357 | G/A | G/A | MT | No association |
| 39 | SSIIIa | GA_Ref2080 | 2080 | C/T | C/T | N/A | No association |
| 40 | SSIIIa | GA_Ref3481 | 3481 | G/A | G/A | N/A | No association |
| 41 | SSIIIa | GA_Ref5466 | 5466 | G/A | G/A | FV,SB,PT,MT,AC,PN, | Low-Medium association |
| 42 | SSIIIa | GA_Ref10761 | 10761 | C/T | C/T | PT | Low association |
| 43 | SSIIIb | GA_Ref1315 | 1315 | T/C | T/C | PT | Medium association |
| 44 | SSIIIb | GA_Ref4543 | 4543 | C/A | C/A | PT | Medium association |
| 45 | SSIIIb | GA_Ref5451 | 5451 | T/C | T/C | PT | Medium association |
| 46 | SSIIIb | GA_Ref7232 | 3232 | T/G | T/G | PT | Medium-High association |
| 47 | SSIIIb | GA_Ref7255ER | 7255 | C/A | C/A | PKV | Medium association |
| 48 | SSIIIb | GA_Ref7437 | 7437 | A/C | A/C | PT | Low-Medium association |
| 49 | SSIVa | GA_Ref4048 | 4048 | C/T | C/T | PT,GT | Low-Medium association |
| 50 | SSIVa | GA_Ref7160 | 7160 | A/G | A/G | PKT,PT,AC,PN,GT | Low-Medium association |
| 51 | SSIVa | GA_Ref7506 | 7506 | A/T | A/T | PT,GT | Low-Medium association |
| 52 | SSIVa | GA_Ref7823 | 7823 | T/C | T/C | PT,GT | Low-Medium association |
| 53 | SSIVa | GA_Ref8383 | 8383 | C/A | C/A | PT,GT | Medium association |
| 54 | SSIVb | TBGU260749 | 5090 | G/C | G/G | N/A | No polymorphism |
| 55 | SSIVb | TBGU260765 | 9525 | G/A | G/G | N/A | No polymorphism |
| 56 | BEI | GA_Ref1558 | 1558 | C/T | C/T | PV,BDV,FV,SB,PT,MT,AC,PN | Low-Medium association |
| 57 | BEIIa | GA_Ref3266 | 3266 | T/G | T/G | N/A | No association |
| 58 | BEIIb | GA_Ref9035 | 9035 | C/T | C/T | N/A | No association |
| 59 | BEIIb | GA_Ref10068 | 10068 | C/A | C/A | N/A | No association |
| 60 | ISA1 | TBGU362347 | 1748 | G/A | G/G | N/A | No polymorphism |
| 61 | ISA1 | TBGU362346 | 1746 | C/G | C/C | N/A | No polymorphism |
| 62 | ISA2 | Iso2_GA_Ref960 | 960 | T/C | T/C | BDV, PT, CHK | Low association |
| 63 | ISA2 | Iso2_GA_Ref1712 | 1712 | C/A | C/A | BDV, PT, CHK | Low association |
| 64 | Pullulanase | TBGU185983 | 1938 | G/A | G/A | PT, GT | Low association |
| 65 | Pullulanase | TBGU185989 | 2380 | T/C | T/C | CHK | Low association |
| 66 | GPT1 | GPT1_GA_Ref_1188 | 1188 | T/C | T/C | AC, MT,BD,FV,SB | Highly associated |
*SNP identification can be found from Kharabian-Masouleh et al., 2011 (starting with GA code) or OryzaSNP MSU database (http://oryzasnp.plantbiology.msu.edu/) starting with TBG or TBU codes.
†Homozygosity of SNP calls mean no polymorphism in the corresponding allele.
MT = Martin test (retrogradation), PN = Predicted Nitrogen, CHK = Chalkiness (%).